Chemical, microbial and antibiotic susceptibility analyses of groundwater after a major flood event in Chennai

System-wide approaches to antimicrobial therapy and antimicrobial resistance in the UK: the AMR-X framework

Antimicrobial resistance (AMR) threatens human, animal, and environmental health. Acknowledging the urgency of addressing AMR, an opportunity exists to extend AMR action-focused research beyond the confines of an isolated biomedical paradigm. An AMR learning system, AMR-X, envisions a national network of health systems creating and applying optimal use of antimicrobials on the basis of their data collected from the delivery of routine clinical care. AMR-X integrates traditional AMR discovery, experimental research, and applied research with continuous analysis of pathogens, antimicrobial uses, and clinical outcomes that are routinely disseminated to practitioners, policy makers, patients, and the public to drive changes in practice and outcomes. AMR-X uses connected data-to-action systems to underpin an evaluation framework embedded in routine care, continuously driving implementation of improvements in patient and population health, targeting investment, and incentivising innovation. All stakeholders co-create AMR-X, protecting the public from AMR by adapting to continuously evolving AMR threats and generating the information needed for precision patient and population care.

Microbiological Hazards Associated with the Use of Oligocene Waters: A Study of Water Intakes in Warsaw, Poland

Oligocene waters are widely recognized as excellent sources of drinking water. Due to the belief in their good quality, the water from Oligocene intakes in Warsaw, Poland, is made available to users without prior treatment or disinfection. The present study aimed at assessing possible microbiological risks associated with the use of this water. The occurrence of microbiological contaminants in selected intakes was evaluated, in addition to an assessment of possible changes in the microbiological quality of the water under typical storage conditions. The possibility of antibiotic resistance in bacteria isolated from Oligocene water samples was also investigated, as was their sensitivity to selected disinfectants. A small number of bacteria-27.0 ± 60.8 CFU/cm³ and 3.0 ± 3.0 CFU/cm³-were found in Oligocene water intakes for psychrophilic and mesophilic bacteria, respectively. Fecal bacteria were not detected. Bacteria present in Oligocene waters showed the ability to multiply intensively during standard water storage; this was especially true for mesophilic bacteria in water stored at room temperature. In some samples, bacterial counts reached 10³-10⁴ CFU/cm³ after 48 h. Almost all bacterial isolates were resistant to the commonly used antibiotics: ampicillin, vancomycin and rifampicin. The bacteria were also insensitive to some disinfectants.

How Antimicrobial Resistance Is Linked to Climate Change: An Overview of Two Intertwined Global Challenges

Globally, antimicrobial resistance (AMR) and climate change (CC) are two of the top health emergencies, and can be considered as two interlinked public health priorities. The complex commonalities between AMR and CC should be deeply investigated in a One Health perspective. Here, we provided an overview of the current knowledge about the relationship between AMR and CC. Overall, the studies included pointed out the need for applying a systemic approach to planetary health. Firstly, CC increasingly brings humans and animals into contact, leading to outbreaks of zoonotic and vector-borne diseases with pandemic potential. Although it is well-established that antimicrobial use in human, animal and environmental sectors is one of the main drivers of AMR, the COVID-19 pandemic is exacerbating the current scenario, by influencing the use of antibiotics, personal protective equipment, and biocides. This also results in higher concentrations of contaminants (e.g., microplastics) in natural water bodies, which cannot be completely removed from wastewater treatment plants, and which could sustain the AMR spread. Our overview underlined the lack of studies on the direct relationship between AMR and CC, and encouraged further research to investigate the multiple aspects involved, and its effect on human health.

Acute health risks to community hand-pumped groundwater supplies following Cyclone Idai flooding

This longitudinal flood-relief study assessed the impact of the March 2019 Cyclone Idai flood event on E. coli contamination of hand-pumped boreholes in Mulanje District, Malawi. It established the microbiological water-quality safety of 279 community supplies over three phases, each comprising water-quality survey, rehabilitation and treatment verification monitoring. Phase 1 contamination three months after Idai was moderate, but likely underestimated. Increased contamination in Phase 2 at 9 months and even greater in Phase 3, a year after Idai was surprising and concerning, with 40% of supplies then registering E. coli contamination and 20% of supplies deemed 'unsafe'. Without donor support for follow-up interventions, this would have been missed by a typical single-phase flood-relief activity. Contamination rebound at boreholes successfully treated months earlier signifies a systemic problem from persistent sources intensified by groundwater levels likely at a decade high. Problem extent in normal, or drier years is unknown due to absence of routine monitoring of water point E. coli in Malawi. Statistical analysis was not conclusive, but was indicative of damaged borehole infrastructure and increased near-borehole pit-latrine numbers being influential. Spatial analysis including groundwater flow-field definition (an overlooked sector opportunity) revealed 'hit-and-miss' contamination of safe and unsafe boreholes in proximity. Hydrogeological control was shown by increased contamination near flood-affected area and in more recent recharge groundwater otherwise of good quality. Pit latrines are presented as credible e-coli sources in a conceptual model accounting for heterogeneous borehole contamination, wet season influence and rebound behavior. Critical to establish are groundwater level - flow direction, hand-pump plume draw, multiple footprint latrine sources - 'skinny' plumes, borehole short-circuiting and fast natural pathway (e.g. fracture flow) and other source influences. Concerted WASH (Water, Sanitation and Hygiene) sector investment in research and policy driving national water point based E. coli monitoring programs are advocated.

Remobilization of pollutants during extreme flood events poses severe risks to human and environmental health

While it is well recognized that the frequency and intensity of flood events are increasing worldwide, the environmental, economic, and societal consequences of remobilization and distribution of pollutants during flood events are not widely recognized. Loss of life, damage to infrastructure, and monetary cleanup costs associated with floods are important direct effects. However, there is a lack of attention towards the indirect effects of pollutants that are remobilized and redistributed during such catastrophic flood events, particularly considering the known toxic effects of substances present in flood-prone areas. The global examination of floods caused by a range of extreme events (e.g., heavy rainfall, tsunamis, extra- and tropical storms) and subsequent distribution of sediment-bound pollutants are needed to improve interdisciplinary investigations. Such examinations will aid in the remediation and management action plans necessary to tackle issues of environmental pollution from flooding. River basin-wide and coastal lowland action plans need to balance the opposing goals of flood retention, catchment conservation, and economical use of water.

Finite element modelling to assess the submarine groundwater discharge in an over exploited multilayered coastal aquifer

A three-dimensional variable-density finite element model was developed to quantify the impact of groundwater over use on submarine groundwater discharge (SGD). The model was applied to the Arani-Korttalaiyar river basin, north of Chennai, India. This region has an upper unconfined and lower semi-confined aquifer extending up to 30 km inland from the coast and beyond this distance; the two aquifers merge and become a single unconfined aquifer. The model simulated that during the period from 2000 to 2012, the flux of seawater to the aquifer has increased from 17,000 to 24,500 m³/day due to over-exploitation of groundwater from the semi-confined aquifer. Where as in the unconfined aquifer, SGD has been taking place. Scenarios showing the impact of newly constructed  managed aquifer recharge structures, 10% additional increase in rainfall recharge, and termination of pumping from five well-fields on the groundwater conditions in the area were studied. The model predicted a SGD of 85,243 m³/day from the unconfined aquifer and 22,414 m³/day from the semi-confined aquifer by the end of 2030. By adopting managed aquifer recharge methods, seawater intrusion (rate of 4,408 m³/day) can be reduced and SGD (rate of 22,414 m³/day) increased. The rate of SGD increase and the movement of seawater to aquifer can be completely prevented in the semi-confined aquifer by adopting these management options by 2030. Findings from this study have enhanced the understanding of SGD and water budget, which can be used by decision-makers for the sustainable management of groundwater resources in coastal aquifers.

Structural, functional, resistome and pathogenicity profiling of the Cooum river

The microbial community's structure and functions determine the health, quality, and anthropogenic conditions of the river ecosystems. The presence of Bacteria such as Arcobacter spp, Escherichia spp, and Campylobacters spp, have been shown to reflect the poor water quality of rivers. Apprehension of the microbial community in polluted water bodies is significant because it affects human health and the environment. Culture-independent metagenomic and metatranscriptomic approaches employed in the current study of the Cooum river unraveled the taxonomic classification of diverse microbes, including archaea, bacteria, viruses, and phages. The presence of abundant Macellibacteroides fermentans, Arcobacter bivolvorium, Arcobacter butzleri, Methanothrix soenhngeii, and Bacteroides graminisolvens were noted. Viruses and phages like Caudovirales, Human mastadenovirus C, Siphoviridae, Escherichia phage, Erwinia phage, Synechoccus phage, and Vibrio phage were relatively predominant. Various metabolic pathways like methane, sulfur, and nitrogen metabolism adopted by the microbiome confer dangerous gases. Mechanisms such as secretory systems, signal transduction, Chemotaxis, quorum sensing, transportation of chemicals and ions were significantly enriched. The microbes expressed antimicrobial resistance mechanisms as identified from the genes encoding beta-lactamase enzymes and aminoglycoside phosphotransferase enzymes. Metal resistance mechanisms against copper, tellurium, chromium, and cadmium were plentiful. Presence of human pathogens interactions with Yersinia pestis, Campylobacter jejuni, Escherichia coli, Helicobacter pylori, and Francisella tularensis subsp. tularensis suggested the possibilities of transmission of pathogenesis to humans. The current study is the first to apprehend the detailed microbiome composition of one of the highly polluted rivers in South India. The study elaborated the microbiome's structure, functions, and metabolic potential at a specific site of the polluted river.

Impact of flooding on urban soils: Changes in antibiotic resistance and bacterial community after Hurricane Harvey

Major perturbations in soil and water quality are factors that can negatively impact human health. In soil environments of urban areas, changes in antibiotic-resistance profiles may represent an increased risk of exposure to antibiotic-resistant bacteria via oral, dermal, or inhalation routes. We studied the perturbation of antibiotic-resistance profiles and microbial communities in soils following a major flooding event in Houston, Texas, caused by Hurricane Harvey. The main objective of this study was to examine the presence of targeted antibiotic-resistance genes and changes in the diversity of microbial communities in soils a short time (3-5 months) and a long time (18 months) after the catastrophic flooding event. Using polymerase chain reaction, we surveyed fourteen antibiotic-resistance elements: intI1, intI2, sul1, sul2, tet(A) to (E), tet(M), tet(O), tet(W), tet(X), and bla_CMY-2. The number of antibiotic-resistance genes detected were higher in short-time samples compared to samples taken a long time after flooding. From all the genes surveyed, only tet(E), bla_CMY-2, and intI1 were prevalent in short-time samples but not observed in long-time samples; thus, we propose these genes as indicators of exogenous antibiotic resistance in the soils. Sequencing of the V3-V4 region of the bacterial 16S rRNA gene was used to find that flooding may have affected bacterial community diversity, enhanced differences among bacterial lineages profiles, and affected the relative abundance of Actinobacteria, Verrucomicrobia, and Gemmatimonadetes. A major conclusion of this study is that antibiotic resistance profiles of soil bacteria are impacted by urban flooding events such that they may pose an enhanced risk of exposure for up to three to five months following the hurricane. The occurrence of targeted antibiotic-resistance elements decreased eighteen months after the hurricane indicating a reduction of the risk of exposure long time after Harvey.

Microbial contamination and its associations with major ions in shallow groundwater along coastal Tamil Nadu

Microbes in groundwater play a key role in determining the drinking water quality of the water. The study aims to interpret the sources of microbes in groundwater and its relationship to geochemistry. The study was carried out by collecting groundwater samples and analyzed to obtain various cations and anions, where HCO₃^-, Cl^- and NO₃^- found to be higher than permissible limits in few samples. Microbial analysis, like total coliform (TC), total viable counts (TVC), fecal coliforms (FC), Vibrio cholera (V. cholerae) and total Streptococci (T. streptococci) were analyzed, and the observations reveal that most of the samples were found to be above the permissible limits adopted by EU, BIS, WHO and USEPA standards. Correlation analysis shows good correlation between Mg²⁺-HCO₃^-, K⁺-NO₃^-, TVC- V. cholerae and T. streptococci-FC. Major ions like Mg⁺, K⁺, NO₃, Ca²⁺ and PO₄ along with TS and FC were identified to control the geochemical and microbial activities in the region. The magnesium hardness in the groundwater is inferred to influence the TVC and V. cholerae. The mixing of effluents from different sources reflected the association of Cl with TC. Population of microbes T. streptococci and FC was mainly associated with Ca and Cl content in groundwater, depicting the role of electron acceptors and donors. The sources of the microbial population were observed with respect to the land use pattern and the spatial distribution of hydrogeochemical factors in the region. The study inferred that highest microbial activity in the observed in the residential areas, cultivated regions and around the landfill sites due to the leaching of sewage water and fertilizers runoff into groundwater. The concentrations of ions and microbes were found to be above the permissible limits of drinking water quality standards. This may lead to the deterioration in the health of particular coastal region.

Seasonal contamination of well-water in flood-prone colonias and other unincorporated U.S. communities

Many of the six million residents of unincorporated communities in the United States depend on well-water to meet their needs. One group of unincorporated communities is the colonias, located primarily in several southwestern U.S. states. Texas is home to the largest number of these self-built communities, of mostly low-income families, lacking basic infrastructure. While some states have regulations that mandate minimum infrastructure for these communities, water and sewage systems are still lacking for many of their residents. Unprotected wells and self-built septic/cesspool systems serve as the primary infrastructure for many such colonias. This research was designed to probe how wells and septic/cesspool systems are influenced by heavy rainfall events. Such events are hypothesized to impact water quality with regard to human health. Inorganic and microbiological water quality of the wells in nine colonias located in Nueces County, Texas, were evaluated during dry and wet periods. Nueces County was selected as an example based on its flooding history and the fact that many colonias there depend entirely on well-water and septic/cesspool systems. The results demonstrate that well-water quality in these communities varies seasonally with respect to arsenic (up to 35 μg/L) and bacterial contamination (Escherichia coli), dependent on the amount of rainfall, which leaves this population vulnerable to health risks during both wet and dry periods. Microbial community analyses were also conducted on selected samples. To explore similar seasonal contamination of well-water, an analysis of unincorporated communities, flooding frequency, and arsenic contamination in wells was conducted by county throughout the United States. This nationwide analysis indicates that unincorporated communities elsewhere in the United States are likely experiencing comparable challenges for potable water access because of a confluence of socioeconomic, infrastructural, and policy realities.

Determination of the Microbial and Chemical Loads in Rivers from the Quito Capital Province of Ecuador (Pichincha)-A Preliminary Analysis of Microbial and Chemical Quality of the Main Rivers

Contamination of natural water sources is one of the main health problems worldwide, which could be caused by chemicals, metals, or microbial agents. This study aimed to analyze the quality of 18 rivers located in Quito, the capital province of Pichincha, Ecuador, through physico-chemical and microbial parameters. The E. coli and total coliforms assessments were performed by a counting procedure in growth media. Polymerase chain reaction (PCR) was realized to detect several microbial genera, as well as Candida albicans, two parasites (Cryptosporidium and Giardia spp.) and E. coli pathotypes: enterohemorrhagic E. coli (EHEC), enteroaggregative E. coli (EAEC), enteroinvasive E. coli (EIEC) and enteropathogenic E. coli (EPEC). Additionally, physico-chemical parameters and major and trace metals were analyzed in each surface water sample. Our results demonstrated that most of the rivers analyzed do not comply with the microbial, physico-chemical, and metal requirements established by the Ecuadorian legislation. In terms of microbial pollution, the most polluted rivers were Monjas, Machángara, Pisque, and Pita Rivers. Furthermore, three out of four analyzed E. coli pathotypes (EIEC, EHEC, and EAEC) were detected in certain rivers, specifically: Monjas River showed the presence of EIEC and EHEC; in the Machángara River, EAEC and EIEC were detected; and finally, EIEC was present in the Guayllabamba River. Several physico-chemical parameters, such as pH, COD_total, and TSS values, were higher than the Ecuadorian guidelines in 11, 28, and 28% of the rivers, respectively. Regarding heavy metals, Zn, Cu, Ni, Pb, Cd, and Mn surpassed the established values in 94, 89, 61, 22, 22, and 17% of the rivers, respectively. Machangara River was the only one that registered higher Cr concentrations than the national guidelines. The values of Al and Fe were above the recommended values in 83 and 72% of the rivers. Overall, based on the physical-chemical and microbiological parameters the most contaminated rivers were Machángara and Monjas. This study revealed severe contaminations in Ecuadorean Rivers; further studies should evaluate the sources of contamination and their impact on public health.

Insights into the Bacterial Profiles and Resistome Structures Following the Severe 2018 Flood in Kerala, South India

Extreme flooding is one of the major risk factors for human health, and it can significantly influence the microbial communities and enhance the mobility of infectious disease agents within the affected areas. The flood crisis in 2018 was one of the severe natural calamities recorded in the southern state of India (Kerala) that significantly affected its economy and ecological habitat. We utilized a combination of shotgun metagenomics and bioinformatics approaches to understand the bacterial profile and the abundance of pathogenic and antibiotic-resistant bacteria in extremely flooded areas of Kuttanad, Kerala (4-10 feet below sea level). Here we report the bacterial profiles of flooded sites that are abundant with virulent and resistant bacteria. The flooded sites were heavily contaminated with faecal contamination indicators such as Escherichia coli and Enterococcus faecalis and multidrug-resistant strains of Pseudomonas aeruginosa, Salmonella typhi/typhimurium, Klebsiella pneumoniae, Vibrio cholerae. The resistome of the flooded sites contains 103 known resistant genes, of which 38% are plasmid-encoded, where most of them are known to be associated with pathogenic bacteria. Our results reveal an overall picture of the bacterial profile and resistome of sites following a devastating flood event, which might increase the levels of pathogens and its associated risks.