A national survey of antibacterial consumption in Sri Lanka

Rapid whole genome sequencing for AMR surveillance in low- and middle-income countries: Oxford Nanopore Technology reveals multidrug-resistant Enterobacter cloacae complex from dairy farms in Sri Lanka

BACKGROUND

Antimicrobial resistance (AMR) is a major global challenge that disproportionately affects low- and middle-income countries (LMICs). Environmental contamination by resistant bacteria from animal production facilities is a major driver of the spread of AMR through the food chain, requiring a robust one-health control approach. Traditional culture-based AMR surveillance is time-consuming and less sensitive, and fails to fully capture the spectrum of AMR, evolutionary trends, and epidemiological patterns of AMR spread. Whole-genome sequencing (WGS) has revolutionized AMR surveillance capabilities. Rapid WGS captures the full AMR spectrum with minimum samples, aids source attribution, and provides insights into trends in AMR spread. The portable Oxford Nanopore® Technology (ONT) platform, coupled with open-source software such as Galaxy and Konstanz Information Miner (KNIME), enables the establishment of a potentially portable, transferable workflow for low-resource settings. This study aimed to assess the AMR burden on four dairy farms in Kandy, Sri Lanka, via a resource-limited LMIC using a low-cost high-throughput screening assay and rapid WGS via ONT with Galaxy and KNIME processing to obtain full antibiotic resistomes.

RESULTS

The four isolates exhibiting the highest minimum inhibitory concentrations for amoxicillin were identified as Enterobacter cloacae and E. hormaechei by WGS. Chromosomes (4.8 to 4.9 Mb) carry the strain-specific resistance genes blaCMH-1, blaACT-25, fosA_7, and ramA, which are associated with diverse antibiotic classes. Plasmids, including IncFIB (pECLA), IncFII (pECLA), and IncX3, carry multiple resistance genes, including AAC(3)-IIe, AAC(6')-Ib-cr, APH(3″)-Ib, APH(6)-Id, blaCTX-M-15, blaNDM, blaOXA-1, blaTEM-1, dfrA14, QnrB17, catII, determinant-of-bleomycin-resistance, and sul2. Novel arrangements of insertion sequences were observed in E. hormaechei plasmids. The phenotypic resistance of all the isolates matched the genotypic MDR profiles, including resistance to chloramphenicol, gentamicin, tetracycline, and cotrimoxazole.

CONCLUSIONS

ONT WGS with Galaxy and KNIME processing may be a feasible option for AMR surveillance in resource-limited LMICs. To the best of our knowledge, this is the first in-house whole-genome analysis workflow in the country tailored for AMR surveillance. The presence of potentially pathogenic high-MIC, MDR Enterobacter spp. with wide resistomes, including the blaNDM gene, emphasizes the urgent need to address AMR in animal production facilities within a one-health framework.

Short- and long-read metagenomics uncover the mobile extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater in Sri Lanka

The antibiotic resistance issue in low- and middle-income countries has drawn global concern. This study presents the first metagenomic investigation of antibiotic resistance genes (ARGs) in hospital and municipal wastewater treatment plants (WWTPs) in Sri Lanka, using Illumina short-read and Nanopore long-read sequencing. Samples from three representative WWTPs receiving hospital and/or municipal wastewater (domestic generated) were collected from four districts in Sri Lanka, and as a comparison, wastewater directly discharged without treatment was also taken. ARG abundance was significantly higher in hospital wastewater (7.22 copies/cell) than in municipal wastewater (2.33 copies/cell), and greatly decreased by 82 % and 93 % after treatment processes, respectively. Similar trends were observed for mobile genetic elements. The prevalent subtypes of clinically relevant extended spectrum β-lactamase (ESBL) and carbapenemase genes in hospital wastewater were blaOXA, blaGES, blaVEB and blaTEM, whereas blaCTX-M and blaNDM were less dominant, which indicated the potential unique distribution pattern of ESBL and carbapenemase genes in Sri Lanka. Using long-read metagenomics, bacterial host range and genetic locations (plasmid or chromosome) of ARGs in sludge samples were predicted. Diverse pathogenic host taxa (Pseudomonas, Streptococcus, Salmonella and Escherichia) and a higher plasmid proportion were identified in the hospital WWTP (39.8 % vs. 21.5 % in the municipal WWTP). Detected mobile genetic contexts in this study, IS6100-sul1-blaOXA-329-blaGES-5-blaGES-5-intI1 and ISKpn6-blaKPC-2-ISKpn7-ISPsy42, were also common in antibiotic-resistant plasmids in Enterobacteriaceae from different countries. These data will serve to expand the inventory of global ARG epidemiology. Also, the finding emphasizes that the wastewater treatment projects, especially in healthcare facilities, are vital for reducing clinically relevant ARG discharge to the environment. Further monitoring using advanced meta-omics approaches is crucial to assess potential ARG risks and optimize control strategies for improving human and ecosystem health in Sri Lanka.

Penicillin Allergy Management in India and Sri Lanka: Current Challenges

Data regarding Penicillin allergy labels (PALs) from India and Sri Lanka are sparse. Emerging data suggests that the proportion of patients declaring an unverified PAL in secondary care in India and Sri Lanka (1%-4%) is lesser than that reported in High Income Countries (15%-20%). However, even this relatively small percentage translates into a large absolute number, as this part of the world accounts for approximately 25% of the global population. There is a huge unmet need for allergy specialists in India and Sri Lanka. Penicillin allergy management is further compromised by unavailability of skin test reagents, lack of formal training in drug allergy, pre-emptive, non-standardised and unregulated skin testing by untrained operators and a weak health service framework. This has an adverse impact on antimicrobial stewardship, particularly in the management of rheumatic fever, rheumatic heart disease, bacterial endocarditis, syphilis and other sexually transmitted infections. This narrative review highlights the burden of PALs in India and Sri Lanka, as well as gaps in the published literature. It describes current challenges and a pragmatic, cautious and staged bespoke mitigation approach to improve and standardise antimicrobial stewardship in accordance with the World Health Organisation AWaRe guidance.

Increasing the use of the WHO AWaRe system in antibiotic surveillance and stewardship programmes in low- and middle-income countries

Introduction

Antimicrobial resistance (AMR) presents a major global health threat, driven in part by the inappropriate use of antibiotics including in low- and middle-income countries (LMICs). Improving the quality of antibiotic use is a key rationale for the development of the WHO's AWaRe (Access, Watch and Reserve) system. There is a need to review the uptake of the AWaRe system since its launch to guide future practice.

Methods

A literature search was conducted between 2017, the launch of AWaRe, and 2024. Inclusion criteria were studies that reported on antibiotic use in LMICs using the AWaRe system.

Results

Eighty-five studies were included in the review, of which 56.4% focused on antibiotic use trends, with 28.2% reporting on prescribing patterns; 51.7% of the studies included inpatients. Only 14.1% of studies reported meeting the 2024 United Nations General Assembly (UNGA) AMR recommended target of at least 70% of human antibiotic use being Access antibiotics, with a concerning trend of overuse of Watch antibiotics (68.2% of studies). Dispensing practices revealed significant dispensing of antibiotics without prescriptions especially in Pakistan and Bangladesh. Watch antibiotics were more available but also more expensive than Access antibiotics.

Conclusions

Encouragingly, many LMICs are now reporting antibiotic use via the AWaRe system, including in antimicrobial stewardship programmes (ASPs). Wide variation exists in the proportion of AWaRe antibiotics used across LMICs, with overuse of Watch antibiotics. There is an urgent need for targeted AWaRe-based ASPs in LMICs to meet recent UNGA recommendations. Improving the use, availability and affordability of Access antibiotics is essential to combat AMR.

Phenotypic and genotypic landscape of antibiotic resistance through One Health approach in Sri Lanka: A systematic review

OBJECTIVES

Antibiotic resistance (ABR) constitutes a significant burden to economies in developing countries. In the 'One-Health' concept, ABR in human, animals, and environment is interconnected. The aim of this study was to critically appraise literature on ABR in all three domains in One Health, within the Sri Lankan geographical context.

METHODS

The protocol was registered with PROSPERO and followed PRISMA 2020 guidelines. A comprehensive electronic literature search was conducted in PubMed, Scopus, Web of Science databases and grey literature via Google Scholar. Out of 298 abstracts, 37 articles were selected following screening. A risk of bias assessment was conducted using Joanna Briggs Institute tools. Following blinded data extraction, descriptive data analysis and narrative synthesis were performed.

RESULTS

This review included studies published between 2016-2023. Of the included studies, 17 (45.9%) reported data on samples obtained from humans, 9 (24.3%) from animals, and 6 (16.2%) from environmental sources, two studies (5.4%) from humans and animals, one study on animal and environment; whereas two studies including all three domains. ABR of 32 different bacteria (Gram negative⸺17, Gram positive⸺14) was retrieved; E. coli was the most frequently studied bacteria followed by MRSA and ESBL. For E. coli, a median resistance over 50% was reported for sulfamethoxazole (88.8%), trimethoprim (79.1%), ampicillin (60%) and tetracycline (50.3%) with the highest resistance for erythromycin (98%). Of a total of 21 antibiotic-resistance genes in E. coli, the highest genotypic resistance was for tet-A (48.5%).

CONCLUSIONS

A comprehensive description of ABR for a total of 32 bacteria, 62 antibiotics and 46 ABR genes is presented. This review discusses the contemporary ABR landscape in Sri Lanka through the One Health lens, highlighting key methodological and empirical research gaps.

Ethiopian antimicrobial consumption trends in human health sector: A surveillance report 2020-2022

BACKGROUND

Antimicrobial resistance (AMR) poses a severe global health threat, driven by the overuse and misuse of antimicrobials across the human, agricultural, and veterinary sectors. To combat this, global and national AMR prevention and containment strategies have been implemented, necessitating continuous monitoring of antimicrobial consumption (AMC) as an integral part of antimicrobial stewardship interventions.

OBJECTIVE

This study aims to assess and analyze trends in AMC in Ethiopia from 2020 to 2022, with the goal of informing national and sub-national strategies to combat AMR.

METHODS

A three-year AMC surveillance was conducted from 2020 to 2022. Data on locally manufactured and imported antimicrobials were collected from local manufacturers and Ethiopian Food and Drug Authority (EFDA)-regulated ports of entry. AMC was analyzed using the WHO GLASS AMC tool, with antimicrobials categorized using the WHO Anatomical Therapeutic Chemical (ATC) classification system. Consumption was measured in Defined Daily Doses (DDDs) and DDD per 1,000 inhabitants per day (DID), normalized using population estimates from the World Population Prospects for Ethiopia.

RESULTS

The total AMC in Ethiopia increased from 432 million DDDs in 2020 to 485 million DDDs in 2022. The DID rose from 10.63 in 2020 to 11.34 in 2022. Antibacterials dominated consumption, comprising 98.87% in 2020, 95.96% in 2021, and 99.79% in 2022. Penicillins (J01C) and quinolones (J01M) were the most consumed antimicrobials. As per the Ethiopian AWaRe classification, the majority of antibacterial agents consumed were in the Access group, accounting for 71.14% in 2020, 70.65% in 2021, and 74.2% in 2022. Oral formulations consistently made up over 87% of the total consumption each year. Reliance on imported antimicrobials remained high, with imports comprising 64.76% in 2020 and 74.47% in 2022.

CONCLUSION

The increasing trend in AMC in Ethiopia from 2020 to 2022 underscores the urgent need to establish and strengthen national, sub-national, and facility-level surveillance and reporting systems to better monitor and ensure rational antimicrobial use.

Pharmacogenomic profiling of variants affecting efficacy and toxicity of anti-infective medicines in a south Asian population from Sri Lanka

BACKGROUND

Anti-infective medicines are crucial for treating infections, but improper dosing can cause toxicity, resistance and treatment failure. Pharmacogenomics can address genetic variations affecting drug efficacy and safety. Despite the high burden of diseases like TB and HIV in Sri Lanka and South Asia, pharmacogenomic data for these populations are limited. This study aims to fill this gap by investigating pharmacogenomic variants in a South Asian population from Sri Lankan.

METHODS

Pharmacogenomic data on anti-infective medicines were obtained from the PharmGKB database, selecting variants with evidence levels 1 A, 1B, 2 A, and 2B. Sri Lankan genetic data were sourced from an anonymized database of 670 Sri Lankans maintained by the Centre for Genetics and Genomics, Faculty of Medicine, University of Colombo. MAFs were compared between Sri Lankan sub-populations and global data from gnomAD, with statistical significance set at p < 0.05.

RESULTS

MAFs of NAT2 gene rs1041983 and rs1799931 variants were, 43.7% (95%CI:41.1-46.4), 7.3% (95%CI:6.0-8.8), respectively. The UGT1A1 rs4148323 variant had a MAF of 3.5% (95%CI:2.6-4.6). In the CYP2B6 gene, 109 individuals were homozygous for the rs3745274 (poor metaboliser) variant, with a MAF of 39.6% (95%CI:37.0-42.3), while the rs34097093 and rs28399499 variants had no individuals homozygous for the variant (MAF: 0.2% [95%CI:0-0.5] (poor/intermediate metaboliser), and 0.1% [95%CI:0-0.4] (poor/intermediate metaboliser), respectively). The MAFs of the CYP2C19 rs12769205 (poor/intermediate metaboliser), rs4244285 (poor/intermediate metaboliser), rs3758581 (poor/intermediate metaboliser), and rs4986893 (poor/intermediate metaboliser) variants were 41.9% (95%CI:39.3-44.6), 41.9% (95%CI:39.2-44.7), 9.7% (95%CI:8.2-11.4), and 0.5% [(95%CI:0.2-1.1), respectively. Most variants showed significant differences compared to global populations, with some exhibiting higher frequencies, particularly when compared to Europeans. CYP2C19 rs12769205 and rs4244285 exhibited higher MAFs in Sri Lankans compared to both other South Asians and Europeans. The NAT2 rs1041983, NAT2 rs1799931, CYP2C19 rs4986893, CYP2C19 rs3758581, and CYP2B6 rs3745274 variants demonstrated significantly higher MAFs than in Europeans but not significantly different from South Asians.

CONCLUSION

This preliminary study identifies variants in NAT2, UGT1A1, CYP2B6, and CYP2C19 genes relevant to the metabolism of anti-TB drugs, antiretrovirals, and voriconazole among Sri Lankans. Several variants, including CYP2C19 rs12769205 and rs4244285, showed higher MAFs, particularly in comparison to European populations, indicating potential differences in drug response. However, the nature of the study limits the ability to explore clinical correlations with the genotypes, therefore further research focusing on clinical correlation and functional validation is required.

A Review of the Dissemination of Antibiotic Resistance through Wastewater Treatment Plants: Current Situation in Sri Lanka and Future Perspectives

The emergence of antibiotic resistance (AR) poses a significant threat to both public health and aquatic ecosystems. Wastewater treatment plants (WWTPs) have been identified as potential hotspots for disseminating AR in the environment. However, only a limited number of studies have been conducted on AR dissemination through WWTPs in Sri Lanka. To address this knowledge gap in AR dissemination through WWTP operations in Sri Lanka, we critically examined the global situation of WWTPs as hotspots for transmitting antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs) by evaluating more than a hundred peer-reviewed international publications and available national publications. Our findings discuss the current state of operating WWTPs in the country and highlight the research needed in controlling AR dissemination. The results revealed that the impact of different wastewater types, such as clinical, veterinary, domestic, and industrial, on the dissemination of AR has not been extensively studied in Sri Lanka; furthermore, the effectiveness of various wastewater treatment techniques in removing ARGs requires further investigation to improve the technologies. Furthermore, existing studies have not explored deeply enough the potential public health and ecological risks posed by AR dissemination through WWTPs.

Antibiotic resistance through the lens of One Health: A study from an urban and a rural area in Sri Lanka

This study aimed to investigate and compare the proportion of AMR Escherichia coli (E. coli) between urban (Dompe in the Western province) and rural (Dambana in the Sabaragamuwa province) areas in Sri Lanka. The overall hypothesis of the study is that there is a difference in the proportion of AMR E. coli between the urban and the rural areas. Faecal samples were collected from healthy humans (n = 109), dairy animals (n = 103), poultry (n = 35), wild mammals (n = 81), wild birds (n = 76), soil (n = 80) and water (n = 80) from both areas. A total of 908 E. coli isolates were tested for susceptibility to 12 antimicrobials. Overall, E. coli isolated from urban area was significantly more likely to be resistant than those isolated from rural area. The human domain of the area had a significantly higher prevalence of AMR E. coli, but it was not significantly different in urban (98%) and rural (97%) areas. AMR E. coli isolated from dairy animals, wild animals and water was significantly higher in the urban area compared with the rural area. There was no significant difference in the proportion of multidrug resistance (MDR) E. coli isolated from humans, wild animals and water between the two study sites. Resistant isolates found from water and wild animals suggest contamination of the environment. A multi-sectorial One Health approach is urgently needed to control the spread of AMR and prevent the occurrences of AMR in Sri Lanka.

Response to antimicrobial resistance in South-East Asia Region

Antimicrobial resistance (AMR) inflicts significant mortality, morbidity and economic loss in the 11 countries in the WHO South-East Asia Region (SEAR). With technical assistance and advocacy from WHO, all countries have developed their respective National Action Plans on AMR that are aligned with the Global Action Plan. Historically, the WHO Regional Office has been proactive in advocacy at the highest political level. The past decade has seen an enhancement of the country's capacity to combat AMR through national efforts catalyzed and supported through several WHO initiatives at all levels-global, regional and country levels. Several countries including Bangladesh, India, Indonesia, Nepal, Sri Lanka and Thailand have observed a worrying trend of increasing drug resistance, despite heightened awareness and actions. Recent AMR data generated by the countries are indicative of fragmented progress. Lack of technical capacity, financial resources, weak regulatory apparatus, slow behavioural changes at all levels of the antimicrobial stewardship landscape and the COVID-19 pandemic have prevented the effective application of several interventions to minimize the impact of AMR.

A model for analysis of antibiotic usage in low-income settings

OBJECTIVES

Quantification of antibiotic usage is an important component of antimicrobial stewardship programmes. We aimed to estimate institutional antibiotic usage and costs using methodology and metrics applicable to low-income settings without electronic health records.

METHODS

The DDD per 100 patient-days (DDDs/100 PDs) of antibiotics used in a calendar year was calculated retrospectively from ward registers and inpatient drug records in general surgical wards of a tertiary hospital. The antibiotics were categorized using the Access, Watch, Reserve classification. The annual expenditure on antibiotics was estimated from price lists of the state medication procurer.

RESULTS

Annual usage of IV co-amoxiclav, cefuroxime and metronidazole was significantly higher than other antibiotics and certain wards showed outlier use of the same. The IV formulations of co-amoxiclav (5-fold), metronidazole (3-fold) and ciprofloxacin (2-fold) were used in excess of the oral formulation. Proportionate antibiotic usage based on the AWaRe category did not vary significantly between wards. Two wards were outliers for annual expenditure/100 PDs. IV clindamycin and meropenem combined accounted for 43.8% of expenditure on antibiotics.

CONCLUSIONS

This study demonstrated intra-institutional variations of annual antibiotic usage and related costs. The metric DDD/100 PDs and the methodology used here are suitable for intra- and inter-institutional analyses of antibiotic usage, particularly in low-income settings.

One Health Surveillance of Antimicrobial Use and Resistance: Challenges and Successes of Implementing Surveillance Programs in Sri Lanka

Background: Sri Lanka is a low-income country, as defined by the World Bank. The country suffered further economic downturn during the COVID-19 pandemic. This situation adversely affected the prioritization of policies and programs around healthcare and public health. In particular, inflation, fuel prices, and shortage of food supplies increased struggles to implement antimicrobial resistance (AMR) programs. However, in the long run, it is crucial to gather data and evidence to plan AMR policies and track interventions. (1) Aim: To establish and reiterate the importance of prioritizing AMR programs in the One Health framework, the Fleming Fellows collected and studied antimicrobial use/consumption (AMU/AMC) and resistance (AMR) in humans, food-producing animals, and the environment. (2) Methods: A systematic and cross-sectional study was conducted between 2019 and 2021. By way of coordinating an AMU/AMC and AMR prevalence study across six agencies from human health and food-producing animal sectors, the authors established a field epidemiology study, laboratory testing, and data processing at their institutions. AMU/AMC patterns were surveyed using questionnaires and interviews, while AMR samples were collected for antibiotic susceptibility tests and genomic tests. Samples were tested for phenotypic and genotypic resistance. (3) Results: In human samples, resistance was highest to beta-lactam antibiotics. In non-human samples, resistance was highest to erythromycin, a highest-priority, critically important antibiotic defined by the World Health Organization. From government records, tylosin was sold the most in the food-producing animal sector. (4) Conclusions: Sri Lanka AMU and AMR trends in human and non-human sectors can be ascertained by a One Health framework. Further coordinated, consistent, and sustainable planning is feasible, and can help implement an AMU/AMR surveillance system in Sri Lanka.

Investigating the drivers for antibiotic use and misuse amongst medical undergraduates-perspectives from a Sri Lankan medical school

Medical undergraduates are a unique group who gain the theoretical knowledge on prescribing antibiotics but are not authorized to prescribe till full licensure. This unique situation may result in self-medication and unauthorized prescription of antibiotics. This cross-sectional study was conducted among medical students of the Faculty of Medicine, University of Peradeniya, Sri Lanka in 2021 to identify patterns and drivers for antibiotic use and misuse among medical undergraduates. A validated, self-administered Google forms-based online questionnaire was used to gather information on antibiotic use, misuse, and associated factors: demographics, knowledge and perceptions. Two scores; a practice score and a knowledge score were calculated to compare with the associated factors. The study population consisted of 347 medical students with a mean age of 24 (SD1.7) years and 142/347 (40.9%) were male participants. The patterns of misuses identified included; use of antibiotics without a prescription (161/347, 46.4%), keeping left-over antibiotics for future use (111/347, 32.0%), not completing the course of antibiotics (81/347, 23.3%), use of left-over antibiotics (74/347, 21.3%), prescribing to animals (61/347, 17.6%), prescribing antibiotics to family members or friends (51/347, 14.7%), antibiotic self-medication (25/347, 7.2%) and not following the dosage regime prescribed (24/347, 6.9%). The practice score ranged from 33% to 100% (median 87%, IQR 80.0-93.3) and did not differ significantly with either the gender or the year of study. The knowledge score ranged from 4% to 100% (median 87%, IQR: 71.5-95.4) differing significantly according to the year of study. Antibiotic prescription by medical undergraduates was perceived as unacceptable (329/347, 94.8%) by the majority. Individual misuse patterns were associated favourably or unfavourably with gender, year of study, having a health care worker at home and knowledge score. The knowledge score increased with the advancement in training at the medical school while the practice score remained indifferent, highlighting the need to identify the additional drivers of antibiotic misuse among medical undergraduates.

Consumption of systemic antibiotics in India in 2019

BACKGROUND

Inappropriate use of antibiotics is a significant driver of antibiotic resistance in India. Largely unrestricted over-the-counter sales of most antibiotics, manufacturing and marketing of many fixed-dose combinations (FDC) and overlap in regulatory powers between national and state-level agencies complicate antibiotics availability, sales, and consumption in the country.

METHODS

We analyzed cross-sectional data from PharmaTrac, a nationally representative private-sector drug sales dataset gathered from a panel of 9000 stockists across India. We used the AWaRe (Access, Watch, Reserve) classification and the defined daily dose (DDD) metrics to calculate the per capita private-sector consumption of systemic antibiotics across different categories: FDCs vs single formulations; approved vs unapproved; and listed vs not listed in the national list of essential medicines (NLEM).

FINDINGS

The total DDDs consumed in 2019 was 5071 million (10.4 DDD/1000/day). Watch contributed 54.9% (2783 million) DDDs, while Access contributed 27.0% (1370 million). Formulations listed in the NLEM contributed 49.0% (2486 million DDDs); FDCs contributed 34.0% (1722 million), and unapproved formulations contributed 47.1% (2408 million DDDs). Watch antibiotics constituted 72.7% (1750 million DDDs) of unapproved products and combinations discouraged by the WHO constituted 48.7% (836 million DDDs) of FDCs.

INTERPRETATION

Although the per-capita private-sector consumption rate of antibiotics in India is relatively low compared to many countries, India consumes a large volume of broad-spectrum antibiotics that should ideally be used sparingly. This, together with significant share of FDCs from formulations outside NLEM and a large volume of antibiotics not approved by the central drug regulators, call for significant policy and regulatory reform.

FUNDING

Not applicable.