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. 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. 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.

Methicillin-resistant Staphylococcus aureus (MRSA) can spread from animals to humans, but how it adapts to infect both is not fully understood. Our review aimed to determine the prevalence of MRSA in livestock, poultry, and companion animals in different countries, including Bangladesh, the Hong Kong SAR, Mainland China, and Sri Lanka. Articles were collected using PubMed, Embase, Web of Science, Scopus, CINAHL, and Google Scholar. Only prevalence studies that followed the PICO guidelines were included. A random-effects model meta-analysis was used to pool the data. The quality of the evidence and bias were assessed using the GRADEpro and Cochrane collaboration tools. Out of 1438 articles, 69 studies were eligible for meta-analysis. The studies showed significant heterogeneity (I² = 97.00%, p < 0.0001) in the prevalence of MRSA colonization. Therefore, a random-effects model was used to determine the pooled prevalence of MRSA colonization, which was found to be 4.92% (95% CI: 3.79% to 6.18%). Begg’s test (p = 0.0002) and Egger’s test (p = 0.0044) revealed publication bias. Subgroup analysis of the pooled prevalence of MRSA showed a significant difference (p < 0.00001) when the subgroups were divided by country, MRSA detection method, whether pre-enrichment was performed or not, study period, sample collection location, and study population. Although significant factors can partially explain the heterogeneity, it is crucial to recognize the heterogeneity within different subgroups. The pooled prevalence of MRSA was found to vary significantly (p < 0.00001) among the study periods and has increased since the study period of 2020. Therefore, it is crucial to continuously monitor and implement measures to control the spread of MRSA in animals to minimize the risk of transmission to humans.

Purpose: Sri Lankan dairy sector faces challenges due to seasonal variability and suboptimal quality of forage for dairy cattle feeding. While silage offers year-round availability of forage, concerns arise regarding potential quality degradation during forage ensiling. Microbial inoculants are utilized to expedite the ensiling and minimize quality deterioration. This study involves the isolation and characterization of lactic acid bacteria (LAB) from silage, with the aim of identifying potential candidates to be used as silage inoculants.Research Method: Lactobacillus were isolated from 10 silage samples of each forage type: sorghum, maize, and guinea grass. They were characterized using the 16S rRNA gene sequencing procedure. The anaerobic sugar fermentation ability of the isolated LAB was evaluated by inoculating them into sterilized sugar solutions, and measuring the titratable acidity (TA) and pH value over time.Findings: The isolates were identified to be non-motile, non-spore-forming and Gram-positive rods. Further, they tested negative for catalase, triple sugar iron, citrate, urease, indole, gelatine hydrolysis, motility, and oxidase tests. The LAB isolated from guinea grass, sorghum, and maize corresponded to Lactobacillus oris, Lactobacillus rhamnosus, and Lactobacillus plantarum, respectively. The TA in all inoculated solutions was higher compared to the control (0.55-0.66% vs. 0.48%), with L. plantarum showing the highest TA (0.66%) at 30 hours incubation. Additionally, all sugar solutions treated with LAB isolates exhibited a lower pH value at 30 hours compared to the control (4.70-5.07 vs. 5.75). Notably, L. plantarum demonstrated the most significant pH value reduction at 18 hours (5.85 vs. 6.29-6.64).Value: Lactobacillus oris, L. rhamnosus, and L. plantarum, isolated from guinea grass, sorghum, and maize silage, respectively, have the potential to be developed as inoculants for ensiling forage.

Antibiotic residues and bacteria resistant to antimicrobial have been found in poultry litter, which is popular low cost manure in agriculture. A study was conducted to investigate a pre-treatment method to reduce antibiotic resistant bacteria in poultry litter. Poultry litter was collected from eleven medium-scale broiler farms in Kandy. Total and antibiotic resistant (tetracycline and/or enrofloxacin) culturable bacteria were isolated using Tryptic Soy Agar supplemented with 0 or 100 ppm of each antibiotic. A fresh and a cured broiler litter sample were collected from one farm and treated with different temperatures (25 o C, 40 o C, 60 o C and 80 o C for 24 hours), neem seed extract (10 and 1000 ppm for 4 day) and neem dry leaves (10% w/w for 4 days) in triplicates. Total and antibiotic resistant bacteria in treated litter were assessed. Broiler litter from all farms contained tetracycline resistant bacteria. Heating at 80 o C reduced tetracycline resistant bacteria by 96-100% compared to 25 o C. Neem seed extract at 10 ppm reduced tetracycline resistant bacteria by 75-96%. Treating broiler litter with high temperature (>60 o C) and neem seed extract (10 ppm) could minimize spread of antibiotic resistant bacteria to the environment.

The aim of the study was to identify canine parvovirus type 2 (CPV-2) subtypes circulating among a selected population of domestic dogs and cats in Sri Lanka and to investigate the evolutionary patterns among Sri Lankan viruses in the context of contemporary global CPV-2 sequences. Altogether, 40/61 (65.6%) samples tested were positive for CPV-2 DNA, including 31/48 (64.6%) dogs and 9/13 (69%) cats. All three subtypes (CPV-2a, CPV-2b and CPV-2c) were detected, with CPV-2a being most common. International median joining haplotype network of 291 CPV-2 sequences suggested that there was little barrier for CPV-2 moving between different geographical regions worldwide, including Sri Lanka, and that there was no correlation between the genetic structure within the molecular network and the decade of sample collection. By contrast, there was correlation between CPV-2 subtype and genetic structure, both within the international network and within the network built from 31 Sri Lankan CPV-2 sequences only. The structure within the latter was not correlated with the location of the veterinary clinic where the samples were submitted, the age or species of the host. Altogether, we have shown that there is considerable variability of CPV-2 genotypes circulating in Sri Lanka, which is likely driven by both local evolution and introduction from other countries. The similarity of CPV-2 obtained from cats and dogs suggests that cats may play a role in the epidemiology of CPV-2 in Sri Lanka.