Profiles of antibiotic resistome and microbial community in groundwater of CKDu prevalence zones in Sri Lanka

Ferric chloride further simplified the horizontal gene transfer network of antibiotic resistance genes in anaerobic digestion

The role of ferric chloride (FC) on the reduction of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) system was investigated from the perspective of vertical (VGT) and horizontal gene transfer (HGT) network through the high-throughput qPCR (HT-qPCR). Although FC showed limited impacts on methane production in AD of swine manure, the tetracycline and MLSB resistance genes were specifically reduced at the end, where tetQ of antibiotic target protection and ermF of antibiotic target alteration contributed the most to the reduction. Both VGT and HGT network were divided into three modules, and the complexity of HGT network was largely reduced along with AD, where the HGT connection was reduced from 683 (Module III) to 172 (Module I), and FC addition could further reduce the relative abundance of ARG hosts in Module I. The contribution of VGT and HGT to the changes of ARGs in AD was further deciphered, and although the VGT reflected by the changes of microbial community contributed the most to the dynamics of ARGs (68.0 %), the HGT contribution could further be reduced by the FC addition. This study provided a new perspective on the fate of ARGs response to the FC addition in the AD system.

Shifts of Antibiotic Resistomes in Soil Following Amendments of Antibiotics-Contained Dairy Manure

Dairy manure is a nutrition source for cropland soils and also simultaneously serves as a contamination source of antibiotic resistance genes (ARGs). In this study, five classes of antibiotics including aminoglycosides, beta-lactams, macrolides, sulfonamides, and tetracyclines, were spiked in dairy manure and incubated with soil for 60 days. The high throughput qPCR and 16S rRNA amplicon sequencing were used to detect temporal shifts of the soil antibiotic resistomes and bacterial community. Results indicated dairy manure application increased the ARG abundance by 0.5-3.7 times and subtype numbers by 2.7-3.7 times and changed the microbial community structure in soils. These effects were limited to the early incubation stage. Selection pressure was observed after the addition of sulfonamides. Bacterial communities played an important role in the shifts of ARG profiles and accounted for 44.9% of the resistome variation. The incubation period, but not the different antibiotic treatments, has a strong impact on the bacteria community. Firmicutes and Bacteroidetes were the dominant bacterial hosts for individual ARGs. This study advanced our understanding of the effect of dairy manure and antibiotics on the antibiotic resistome in soils and provided a reference for controlling ARG dissemination from dairy farms to the environment.

Characterization of metal(loid)s and antibiotic resistance in bacteria of human gut microbiota from chronic kidney disease subjects

BACKGROUND

Human Gut Microbiota (HGM) is composed of more than one thousand species, playing an important role in the health status of individuals. Dysbiosis (an HGM imbalance) is augmented as chronic kidney disease (CKD) progresses, as loss of kidney function accelerates. Increased antibiotic use in CKD subjects and consumption of nephrotoxic heavy metals and metalloids such as lead, cadmium, arsenic, and mercury in tap water increases the dysbiosis state. Studies in people with stage 3 CKD are complex to carry out, mainly because patients are self-reliant who rarely consult a specialist. The current work focused on this type of patient.

RESULTS

Lead and arsenic-resistant bacteria were obtained from self-reliant (that stands on its own) stage 3 CKD subjects. Pathogen-related Firmicutes and Proteobacteria genus bacteria were observed. Resistance and potentiation of antibiotic effects in the presence of metal(loid)s in vitro were found. Furthermore, the presence of the following genes markers for antibiotic and metal(loid) resistance were identified by qPCR: oxa10, qnrB1, mphB, ermB, mefE1, arr2, sulll, tetA, floR, strB, dhfr1, acrB, cadA2k, cadA3k, arsC, pbrA. We observed a decrease in the number of metal resistance markers.

CONCLUSIONS

The presence of cadA and arsC genetic markers of antibiotics and metal(loid)s resistance were detected in samples from stage 3 CKD subjects. Lower gene amplification in advanced stages of CKD were also observed, possibly associated with a decrease in resident HGM during kidney disease progression.

Groundwater-Based Drinking Water Supply in Sri Lanka: Status and Perspectives

Drinking water is largely from groundwater in Sri Lanka, so quality management is of great concern. In order to achieve the 6th goal of United Nations (UN) Sustainable Development Goals (SDG), more efforts are being undertaken to secure drinking water quality. In this paper, the current status, challenges and opportunities of groundwater quality management and improvement in Sri Lanka were reviewed and discussed, based on previous studies. There are Ca-HCO3 type, Ca–Mg-HCO3 type and Na–SO4–Cl type groundwater dominated in the wet zone, intermediate and the dry zone, respectively. Elevated levels of hardness, fluoride, DOC, and alkalinity, and salinity are reported in the groundwater in the dry zone controlled by geology and arid climate. Although groundwater in some regions contain significant levels of nitrates, arsenic, cadmium and lead, the majority remain at acceptable levels for drinking purposes. As for treatment technologies, existing membrane-based drinking water treatment technologies such as RO (Reverse Osmosis) stations can produce safe and clean drinking water to the community, but this has still a limited coverage. To achieve a safe drinking water supply for all, especially in rural communities of Sri Lanka under the 6th goal of the UN SDG, more efforts in building up the infrastructure and man power are needed to monitor and assess groundwater quality regularly so as to develop management strategies. Research and development can be directed towards more cost-effective water treatment technologies. Protection of groundwater from being polluted, and educational and awareness programs for the stakeholders are also essential tasks in the future.

Chronic kidney disease of unknown etiology in India: a comparative study with Mesoamerican and Sri Lankan nephropathy

Chronic kidney disease of unknown etiology [CKDu] is a condition characterized by decline in kidney function and is not associated with diabetic nephropathy or hypertensive nephropathy. In this review, we have done a detailed literature analysis on CKDu in India, and then had a comparison with that of Mesoamerica and Sri Lanka. In India, CKDu became the second most common type of CKD after diabetic nephropathy. Silica was seen in the groundwater of both India and Sri Lanka, whereas in Mesoamerica silica exposure through particulate matter was seen among CKDu communities. DDE is a common agrochemical seen in both India and Sri Lanka. The risk factors vary from region to region and it is important to categorize CKDu population based on the risk factors to avoid misinterpretation of the condition as non-CKDu category and to evade further complications. More studies have to be conducted to reveal the detailed pathophysiological mechanisms and its relation with irrational exploitation of environmental resources.

Zero valent iron improved methane production and specifically reduced aminoglycoside and tetracycline resistance genes in anaerobic digestion

It is unadvisable to discuss the antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) system neglecting its main purpose-methane production. The methane production improvement coupling with antibiotic resistance genes (ARGs) reduction in anaerobic digestion (AD) by zero valent iron (ZVI) were simultaneously investigated. Whether the role of ZVI on the ARGs fate was random or specific was clarified through the high-throughput qPCR (HT-qPCR). Results indicated that ZVI improved methane production and ARGs reduction by 23.9% and 25.0%, respectively. The improved methane production was associated with chemical reaction and variances of microbial community caused by ZVI, where DIET between Petrimonas, Clostridium and Syntrophomonas, Methanosarcina was established along with ACAS being enriched. ZVI specifically, not randomly, facilitated the reduction of aminoglycoside resistance genes of antibiotic inactivation and tetracycline resistance genes of ribosomal protection proteins. The specifical reduction could be attributed to enzyme activity inhibition and intracellular ionic disturbance caused by higher amounts of ZVI, although most of ARGs fate could be well explained by microbial community which contributed the most to ARGs dynamics as a whole. ZVI-based AD was a promising way for the improvement of methane production coupling ARGs reduction.

Groundwater as a potential cause of Chronic Kidney Disease of unknown etiology (CKDu) in Sri Lanka: a review

The cause of Chronic Kidney Disease of unknown etiology (CKDu) in the rural dry zone of Sri Lanka remains unidentified, despite vast research efforts that brought about an extensive list of potential risk factors. Among these, the long-term exposure to various nephrotoxic elements through drinking groundwater was widely suspected owing to the unique geographical distribution of the disease. This review focuses on such well-known hypotheses suspecting the relations with fluoride, hardness, major ions, heavy metals, metalloids, organic matter, agrochemical residues, pathogens, and bacterial toxins in the groundwaters of the CKDu-endemic region. It was comprehensively discussed why each of these constituents was considered a risk factor of CKDu, how could they possibly trigger the pathogenesis of the disease, what was the evidence that supported or failed each hypothesis, and whether providing safe drinking water had been effective at mitigating the progression of the disease. Although plenty of circumstantial evidence supported an etiology related to groundwater for CKDu, it was impossible to elucidate the cause-effect relationships between drinking impaired groundwater and the occurrence of the disease. Future research should be effectively designed to clarify the role of groundwater in the onset of CKDu by taking into account the gaps in past research.