Comprehensive analysis of antimicrobial resistance in the Southwest Indian Ocean: focus on WHO critical and high priority pathogens

The spread of antimicrobial resistance (AMR) is a major global concern, and the islands of the Southwest Indian Ocean (SWIO) are not exempt from this phenomenon. As strategic crossroads between Southern Africa and the Indian subcontinent, these islands are constantly threatened by the importation of multidrug-resistant bacteria from these regions. In this systematic review, our aim was to assess the epidemiological situation of AMR in humans in the SWIO islands, focusing on bacterial species listed as priority by the World Health Organization. Specifically, we examined Enterobacterales, Acinetobacter spp., Pseudomonas spp. resistant to carbapenems, and Enterococcus spp. resistant to vancomycin. Our main objectives were to map the distribution of these resistant bacteria in the SWIO islands and identify the genes involved in their resistance mechanisms. We conducted literature review focusing on Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar. Our findings revealed a growing interest in the investigation of these pathogens and provided evidence of their active circulation in many of the territories investigated. However, we also identified disparities in terms of data availability between the targeted bacteria and among the different territories, emphasizing the need to strengthen collaborative efforts to establish an efficient regional surveillance network.


Introduction
The spread of antimicrobial resistance (AMR) is recognized as an increasing global threat.It was estimated that in 2019, there were 4.95 million deaths worldwide associated with AMR, among which 1.27 million were directly attributable to AMR (1).This alarming situation originates from the emergence of multidrug-resistant strains and the lack of new effective therapeutic approaches.In 2017, the World Health Organization (WHO) established its firstever priority list of antibiotic resistant pathogens (2).For instance, Gram-negative bacteria including Enterobacterales, Acinetobacter spp., and Pseudomonas spp.resistant to carbapenems, were classified as critical priority pathogens (2).Similarly, Grampositive bacteria, such as Enterococcus spp.(specifically Enterococcus faecium), resistant to vancomycin (known as vancomycin resistant Enterococci or VRE), were classified as high priority pathogen (2).
The Southwest Indian Ocean (SWIO) is made up of multitude islands.Despite their relative isolation, these territories face significant pressure from the importation of antibiotic-resistant pathogens from Southern Africa and the Indian subcontinent, and they are highly concerned about AMR.In 2015, the Indian Ocean Commission (IOC), which includes Comoros, Madagascar, Mauritius, Reunion Island, and Seychelles, declared AMR a priority health issue (3).Gay et al. (4) conducted a systematic review of the literature in 2016 to assess the prevalence of AMR for bacterial species prone to develop multidrug resistance, and fecal-oral foodborne bacteria in humans and animals within the IOC and Mayotte.They pointed out that many resistant strains were circulating in both humans and animals (4).The main concerns were extended-spectrum β-lactamase-producing Enterobacterales and carbapenemase-producing Enterobacterales (CPE) (4).
In the present review, our aim is to portray the current AMR epidemiological situation in the SWIO, six years after the initial review.We will focus specifically on bacterial species that are registered on the WHO priority list, including Enterobacterales, Acinetobacter spp., and Pseudomonas spp.resistant to carbapenems, as well as Enterococcus spp.resistant to vancomycin.The objectives of our study were to (i) map the distribution of these resistant bacteria in the SWIO, and (ii) identify the specific resistance genes that may be involved.

Method
Our study was conducted between August and November 2023.We chose to include the following territories in the screening: Comoros, Madagascar, Maldives, Mauritius, Mayotte, Reunion Island, Seychelles, Sri Lanka, and Zanzibar.Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines (5), we used published data by searching in the Google Scholar (RRID:SCR_008878), PubMed (RRID:SCR_004846), and Web of Science (RRID:SCR_022706) databases for articles, posters, and conference abstracts, in French or English from 1990 until November 2023.We collected relevant information on carbapenemresistant Enterobacterales (previously named Enterobacteriaceae), Pseudomonas spp.and Acinetobacter spp. in each territory by combining bacteria names and locations with the keywords "carbapenem resistance" or "carbapenemase resistance." Similarly, we collected information on vancomycin-resistant Enterococcus spp.by using the keywords "vancomycin resistance Enterococcus" or "vancomycin resistance Enterococci." Only studies reporting the detection of at least one resistant isolate were included.References and data were discarded when original sources were not identified.

Results
A total of 102 studies were identified.Out of these, 58 were excluded for not meeting the inclusion criteria.The final analysis included 44 studies (Supplementary Table S1).None of these studies were published before 2010, and the number of studies has been increasing over time (Figure 1).The number of published studies varied according to territories (Figure 2), with Sri Lanka and Reunion Island accounting for 31 out of 44 studies (70.5%).Among the selected studies, 29 (65.9%)investigated the presence of antimicrobial resistance genes in addition to antimicrobial susceptibility studies (Supplementary Table S2).However, studies investigating the localization of these genes were scarce, representing only 27.2% (12/44) of the total studies (Supplementary Table S2).Carbapenemresistant Gram-negative bacteria were reported in 42 out of 44 studies (95.5%), while VRE were reported in 13.6% (6/44) of the studies (Supplementary Table S2).
On Mayotte Island, only two studies have reported CRE (Figure 3; Supplementary Table S2).A three-year study conducted between 2015 and 2017 identified 14 patients carrying CRE (CRE carriers rate: 0.9%) (8).Another study conducted over 16 months between 2015 and 2017 reported the presence of 18 isolates of E. cloacae ST820 that harbored the bla IMI-1 gene, which was carried on the integrative mobile element EcloIMEX-8 (14).
For Sri Lanka, a total of 15 studies addressed the presence of CRE in the country (Figure 3; Supplementary Table S2).In 2012, a four-month study detected 22 K. pneumoniae isolates belonging to ST14, ST147, ST380, carrying bla OXA-181 and bla NDM-1 genes in a hospital (21).In early 2013, one isolate of K. pneumoniae ST394 with bla NDM-1 on a IncHI plasmid, which included the insertion sequence ISAba125 upstream, was detected (22).Throughout the 2013 year, four E. coli isolates (resistance rate: 7.5%) and ten K. pneumoniae isolates (resistance rate: 40.0%) were identified in a tertiary hospital  and bla KPC genes (35).
For Mauritius, three studies were included (Figure 4; Supplementary Table S2).In 2010 and 2014, the resistance rates for Acinetobacter spp.isolates were 68.0 and 74.0%respectively, indicating that a majority of the isolates were carbapenem-resistant in hospitalized patients (11,12).Another retrospective study conducted between July 2015 and December 2016 identified 32 CRAB isolates, with a resistance rate of 86.5% (13).
On Mayotte Island, one study mentioned the detection of two CRAB isolates in May and August 2011 (Figure 4; Supplementary Table S2).These isolates belonged to ST23 and carried the bla OXA-58 gene on the bacterial chromosome, with the insertion sequence ISAba3 downstream (40).It was suggested that these isolates likely originated from the Comoros archipelago, specifically from Grande Comore and Mohéli islands (40).
On Reunion Island, a comparative study conducted between 1997 and 2005 revealed a decrease in carbapenem resistance for A. baumannii from 12.9 to 8.3% (41).Another study reported the presence of a CRAB isolate belonging to ST2 and carrying the bla OXA- 23-like gene in hospital (Figure 4; Supplementary Table S2) (42).In 2017, a woman who had previously traveled to Saudi Arabia was found to have a OXA-23 carbapenemase-producing A. baumannii (17).More recently, during an outbreak from April 2019 and June 2020, CRAB isolates were obtained from 13 patients.The isolates belonged to ST Pas 1/ST Ox 231 clonal complex and carried the bla NDM-1 and bla OXA-23 With further details, CPE were the bacteria for which more data were available.They were relatively widespread and were detected in two-thirds of the investigated territories.Six resistance genes families were associated with resistance mechanisms; however, the bla NDM and bla OXA-48-like families were the most represented, supporting the trend observed worldwide (49)(50)(51).Interestingly, during our literature screening, emerging high-risk clones were detected.Specifically, K. pneumoniae ST307/ST147 or E. coli ST167/ST405/ST410 were reported on Reunion Island and/or Sri Lanka (19, 21,26,28).These clones are considered a significant threat to public health due to their propensity to harbor multiple-resistance genes, promoting their spread (particularly in regions where antibiotic use is poorly controlled); and because they can be involved in serious infections, as limited therapeutic options exist to treat infected patients (52,53).Their presence on these islands might likely originate from importation from territories on which they already circulate.For instance, K. pneumonia ST147 might have been imported from India, where it has been previously reported (52), and for which extensive human traveling exchanges exist between the Indian subcontinent and the SWIO region.Carbapenem-resistant Acinetobacter spp.and Pseudomonas spp.were detected in half of the investigated territories.However, compared to CPE, the number of studies and available information were less extensive.A. baumannii was the dominant species, and resistance mechanisms were only associated with bla NDM and bla OXA genes.For Pseudomonas spp., the main represented species was P. aeruginosa and bla VIM was the main gene involved in the resistance mechanisms.Finally, the bacteria that had the least number of available studies was Enterococcus spp.resistant to vancomycin.These bacteria were reported only in one third of the targeted territories.Both E. faecalis and E. faecium were identified and only the vanA gene was found to be associated with resistance to glycopeptides (47,48).The contrasting level of information found between the four bacterial groups may be due to a bias in investigation and should be interpreted with caution when assessing the epidemiology of these critical and high-priority pathogens.It is possible that CPE has been the main focus for both scientific and medical communities in recent years, which may explain why there are more studies investigating their circulation compared to the other groups.However, these discrepancies might also originate from the socio-economic context of the region.The selected islands belong to eight countries with highly disparate gross domestic product per capita and healthcare systems.Health policies and resources allocated to investigate AMR, particularly through antimicrobial susceptibility testing, are not equal across these territories (Supplementary Table S2).For instance, bacterial involving colorimetric/ biochemical methodologies might be less precise than new approaches such as Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry (54).Similarly, the use of traditional molecular biology test (PCRs) and limited access to sequencing analysis capabilities hinder performing Next Generation Sequencing for resistome/bacterial genotyping (55) may explain the scarcity of data regarding the localization of resistance genes.
Variations in the number of available studies across the nine investigated territories could also be attributed to the socio-economic context.Additionally, in regions with limited resources, the use of broad-spectrum antibiotic molecules like third generation cephalosporins or carbapenems as probabilistic treatments may contribute to the selection and proliferation of these resistant isolates.More globally, these socio-economic disparities and contact with highly endemic regions could also drive the spread of AMR through population movements, such as tourism or medical evacuation, as observed in many published examples (18,19,40).However, collaborative efforts with the IOC provide opportunities for multicenter studies to overcome recruitment biases.It is worth noting that veterinary surveillance targeting these critical and high priority pathogens is scarce, and that no "One Health" study has looked at the cross-compartmental spread of these pathogens in this geographical area, indicating a need for improvement that should be highlighted.
In conclusion, our review highlights a growing interest in studying AMR in the SWIO region.The identification of critical and high priority pathogens emphasizes the alarming progression of this global silent pandemic, even in insular ecosystems, and provides an overview of the regional epidemiology.Nevertheless, the available information is still lacking consistency among these territories.Furthermore, there is shortage of research on resistance mechanisms and genotyping analyses.It is, therefore, necessary to enhance the diagnostic capabilities of laboratories to collect more comprehensive data in the future.Now more than ever, it is crucial to set up a regional surveillance network to prevent the spread of these pathogens.This should be done alongside implementing strict and uniform infection control measures, as well as effective antibiotics stewardship.

FIGURE 1
FIGURE 1Number of studies identifying critical and high priority antibiotic-resistant bacteria in the Southwest Indian Ocean, per year, from 2010 to November 2023.

FIGURE 3
FIGURE 3Distribution of carbapenem-resistant Enterobacterales and genes associated with resistance mechanisms in the Southwest Indian Ocean Islands.

FIGURE 6
FIGURE 6Distribution of vancomycin-resistant Enterococcus spp.and genes associated with resistance mechanisms in the Southwest Indian Ocean Islands.