Impact of urban contamination of the La Paz River basin on thermotolerant coliform density and occurrence of multiple antibiotic resistant enteric pathogens in river water, irrigated soil and fresh vegetables

Occurrence and dissemination of antibiotics and antibiotic resistance in aquatic environment and its ecological implications: a review

The occurrence of antibiotics and antibiotic-resistant bacteria (ARBs), genes (ARGs), and mobile genetic elements (MGEs) in aquatic systems is growing global public health concern. These emerging micropollutants, stemming from improper wastewater treatment and disposal, highlight the complex and evolving nature of environmental pollution. Current literature reveals potential biases, such as a geographical focus on specific regions, leading to an insufficient understanding of the global distribution and dynamics of antibiotic resistance in aquatic systems. There is methodological inconsistency across studies, making it challenging to compare findings. Potential biases include sample collection inconsistencies, detection sensitivity variances, and data interpretation variability. Gaps in understanding include the need for comprehensive, standardized long-term monitoring programs, elucidating the environmental fate and transformation of antibiotics and resistance genes. This review summarizes current knowledge on the occurrence and dissemination of emerging micropollutants, their ecological impacts, and the global health implications of antimicrobial resistance. It highlights the need for interdisciplinary collaborations among researchers, policymakers, and stakeholders to address the challenges posed by antibiotic resistance in aquatic resistance in aquatic systems effectively. This review highlights widespread antibiotic and antibiotic resistance in aquatic environment, driven by human and agricultural activities. It underscores the ecological consequences, including disrupted microbial communities and altered ecosystem functions. The findings call for urgent measures to mitigate antibiotics pollution and manage antibiotic resistance spread in water bodies.

Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective

Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.

Circulation of enterotoxigenic Escherichia coli (ETEC) isolates expressing CS23 from the environment to clinical settings

IMPORTANCE

The importance of clean water cannot be overstated. It is a vital resource for maintaining health and well-being. Unfortunately, water sources contaminated with fecal discharges from animal and human origin due to a lack of wastewater management pose a significant risk to communities, as they can become a means of transmission of pathogenic bacteria like enterotoxigenic E. coli (ETEC). ETEC is frequently found in polluted water in countries with a high prevalence of diarrheal diseases, such as Bolivia. This study provides novel insights into the circulation of ETEC between diarrheal cases and polluted water sources in areas with high rates of diarrheal disease. These findings highlight the Choqueyapu River as a potential reservoir for emerging pathogens carrying antibiotic-resistance genes, making it a crucial area for monitoring and intervention. Furthermore, the results demonstrate the feasibility of a low-cost, high-throughput method for tracking bacterial pathogens in low- and middle-income countries, making it a valuable tool for One Health monitoring efforts.

Conjugative transfer of multi-drug resistance IncN plasmids from environmental waterborne bacteria to Escherichia coli

Watersheds contaminated with municipal, hospital, and agricultural residues are recognized as reservoirs for bacteria carrying antibiotic resistance genes (ARGs). The objective of this study was to determine the potential of environmental bacterial communities from the highly contaminated La Paz River basin in Bolivia to transfer ARGs to an Escherichia coli lab strain used as the recipient. Additionally, we tested ZnSO4 and CuSO4 at sub-inhibitory concentrations as stressors and analyzed transfer frequencies (TFs), diversity, richness, and acquired resistance profiles. The bacterial communities were collected from surface water in an urban site close to a hospital and near an agricultural area. High transfer potentials of a large set of resistance factors to E. coli were observed at both sites. Whole-genome sequencing revealed that putative plasmids belonging to the incompatibility group N (IncN, IncN2, and IncN3) were predominant among the transconjugants. All IncN variants were verified to be mobile by a second conjugation step. The plasmid backbones were similar to other IncN plasmids isolated worldwide and carried a wide range of ARGs extensively corroborated by phenotypic resistance patterns. Interestingly, all transconjugants also acquired the class 1 integron intl1, which is commonly known as a proxy for anthropogenic pollution. The addition of ZnSO4 and CuSO4 at sub-inhibitory concentrations did not affect the transfer rate. Metal resistance genes were absent from most transconjugants, suggesting a minor role, if any, of metals in the spread of multidrug-resistant plasmids at the investigated sites.

Detection and Quantification of Enteric Pathogens in Aerosols Near Open Wastewater Canals in Cities with Poor Sanitation

Urban sanitation infrastructure is inadequate in many low-income countries, leading to the presence of highly concentrated, uncontained fecal waste streams in densely populated areas. Combined with mechanisms of aerosolization, airborne transport of enteric microbes and their genetic material is possible in such settings but remains poorly characterized. We detected and quantified enteric pathogen-associated gene targets in aerosol samples near open wastewater canals (OWCs) or impacted (receiving sewage or wastewater) surface waters and control sites in La Paz, Bolivia; Kanpur, India; and Atlanta, USA, via multiplex reverse-transcription qPCR (37 targets) and ddPCR (13 targets). We detected a wide range of enteric targets, some not previously reported in extramural urban aerosols, with more frequent detections of all enteric targets at higher densities in La Paz and Kanpur near OWCs. We report density estimates ranging up to 4.7 × 10² gc per m_air³ across all targets including heat-stable enterotoxigenic Escherichia coli, Campylobacter jejuni, enteroinvasive E. coli/Shigella spp., Salmonella spp., norovirus, and Cryptosporidium spp. Estimated 25, 76, and 0% of samples containing positive pathogen detects were accompanied by culturable E. coli in La Paz, Kanpur, and Atlanta, respectively, suggesting potential for viability of enteric microbes at the point of sampling. Airborne transmission of enteric pathogens merits further investigation in cities with poor sanitation.

Detection and assessment of the antibiotic resistance of Enterobacteriaceae recovered from bioaerosols in the Choqueyapu River area, La Paz - Bolivia

As a highly contaminated waterway flowing through a densely populated urban area, microbiological pollution associated with the Choqueyapu River and the absence of a wastewater treatment plant in La Paz city threatens public health. We collected air samples adjacent to this river using impingement. Laboratory analyses identified the presence of Enterobacteriaceae, reporting a maximum concentration of 86,11 CFU/m³ of sampled air. Positive samples were tested for antibiotic susceptibility against the antibiotics amoxicillin-clavulanic acid, ciprofloxacin, gentamicin, meropenem, sulfamethoxazole-trimethoprim and tetracycline via disk diffusion. The highest percentages of antibiotic resistance were registered for tetracycline (50% of isolates) and sulfamethoxazole-trimethoprim (38,9%), while the lowest resistance profile was reported for meropenem (5,6%). A comparison of results obtained on the pilot studies [elaborated during the wet season of 2018 by Chavez, 2019 and Salazar et al., 2020] and the present study has been done, highlighting seasonal effects over airborne Enterobacteriaceae concentration. Also, it was determined an increase of antibiotic resistance for tetracycline, gentamicin and ciprofloxacin; and a reduction for sulfamethoxazole-trimethoprim, meropenem and amoxicillin-clavulanic acid.

Antimicrobial resistance genes are enriched in aerosols near impacted urban surface waters in La Paz, Bolivia

Antibiotic resistance poses a major global health threat. Understanding emergence and dissemination of antibiotic resistance in environmental media is critical to the design of control strategies. Because antibiotic resistance genes (ARGs) may be aerosolized from contaminated point sources and disseminated more widely in localized environments, we assessed ARGs in aerosols in urban La Paz, Bolivia, where wastewater flows in engineered surface water channels through the densely populated urban core. We quantified key ARGs and a mobile integron (MI) via ddPCR and E. coli spp. as a fecal indicator by culture over two years during both the rainy and dry seasons in sites near wastewater flows. ARG targets represented major antibiotic groups-tetracyclines (tetA), fluoroquinolines (qnrB), and beta-lactams (blaTEM)-and an MI (intI1) represented the potential for mobility of genetic material. Most air samples (82%) had detectable targets above the experimentally determined LOD: most commonly blaTEM and intI1 (68% and 47% respectively) followed by tetA and qnrB (17% and 11% respectively). ARG and MI densities in positive air samples ranged from 1.3 × 101 to 6.6 × 104 gene copies/m3 air. Additionally, we detected culturable E. coli in the air (52% of samples <1 km from impacted surface waters) with an average density of 11 CFU/m3 in positive samples. We observed decreasing density of blaTEM with increasing distance up to 150 m from impacted surface waters. To our knowledge this is the first study conducting absolute quantification and a spatial analysis of ARGs and MIs in ambient urban air of a city with contaminated surface waters. Environments in close proximity to urban wastewater flows in this setting may experience locally elevated concentrations of ARGs, a possible concern for the emergence and dissemination of antimicrobial resistance in cities with poor sanitation.

The Composition of Microbial Communities in Six Streams, and Its Association With Environmental Conditions, and Foodborne Pathogen Isolation

Surface water used for produce production is a potential source of pre-harvest contamination with foodborne pathogens. Decisions on how to mitigate food safety risks associated with pre-harvest water use currently rely on generic Escherichia coli-based water quality tests, although multiple studies have suggested that E. coli levels are not a suitable indicator of the food safety risks under all relevant environmental conditions. Hence, improved understanding of spatiotemporal variability in surface water microbiota composition is needed to facilitate identification of alternative or supplementary indicators that co-occur with pathogens. To this end, we aimed to characterize the composition of bacterial and fungal communities in the sediment and water fractions of 68 agricultural water samples collected from six New York streams. We investigated potential associations between the composition of microbial communities, environmental factors and Salmonella and/or Listeria monocytogenes isolation. We found significantly different composition of fungal and bacterial communities among sampled streams and among water fractions of collected samples. This indicates that geography and the amount of sediment in a collected water sample may affect its microbial composition, which was further supported by identified associations between the flow rate, turbidity, pH and conductivity, and microbial community composition. Lastly, we identified specific microbial families that were weakly associated with the presence of Salmonella or Listeria monocytogenes, however, further studies on samples from additional streams are needed to assess whether identified families may be used as indicators of pathogen presence.

Fecal Pollution Drives Antibiotic Resistance and Class 1 Integron Abundance in Aquatic Environments of the Bolivian Andes Impacted by Mining and Wastewater

An increased abundance of antibiotic resistance genes (ARGs) in aquatic environments has been linked to environmental pollution. Mining polluted sites with high concentration of metals could favor the in situ coselection of ARGs, whereas wastewater discharges release fecal antibiotic resistant bacteria in the environment. To study the effect of human fecal contamination and mining pollution, water and sediment samples affected by mining activities and sewage discharges were collected from three lakes in Bolivia, the pristine Andean lake Pata Khota, the Milluni Chico lake directly impacted by acid mine drainage, and the Uru-Uru lake located close to Oruro city and highly polluted by mining activities and human wastewater discharges. Physicochemical parameters, including metal composition, were analyzed in water and sediment samples. ARGs were screened for and verified by quantitative polymerase chain reaction (PCR) together with the mobile element class 1 integron (intl1), as well as crAssphage, a marker of human fecal pollution. The gene intl1 was positively correlated with sul1, sul2, tetA, and bla_OXA-2. CrAssphage was only detected in the Uru-Uru lake, and its tributaries and significantly higher abundance of ARGs were found in these sites. Multivariate analysis showed that crAssphage abundance, electrical conductivity, and pH were positively correlated with higher levels of intl1 and ARGs. Taken together, our results suggest that fecal pollution is the major driver of higher levels of ARGs and intl1 in environments contaminated by wastewater and mining activities.

Effects of Cefazolin and Meropenem in Eradication Biofilms of Clinical and Environmental Isolates of Proteus mirabilis

Proteus mirabilis is an opportunistic Gram-negative bacterium belonging to the family Enterobacteriaceae and is known for its ability to cause urinary tract infections. The aim of this study was to determine the value of the minimum concentration of cefazolin and meropenem on biofilm eradication, as well as the resistance profiles and genetic diversity of clinical and environmental isolates of P. mirabilis. We compared the isolates collected from a hospital environment and from an urban stream impacted in Recife-Pernambuco, Brazil. Biochemical tests were performed to determine the profiles of susceptibility, hydrophobicity, biofilm formation and eradication. The genetic diversity was verified using the ERIC-PCR method. The results revealed that two clinical isolates (ICP4 and ICP5) were multi-drug resistant, whereas the environmental isolates showed resistance only to tetracycline, except for CP₅25S, which was resistant also to ampicillin. Of the isolates investigated, three were moderately hydrophobic, while the remaining were hydrophilic. Genetic diversity analysis verified the presence of clones indicating that the stream is harboring and disseminating bacteria of hospital origin. All isolates formed a biofilm, however, high concentrations of cefazolin and meropenem were required to eradicate the already formed biofilm. Our study analyzed the survival strategies of these bacteria in the environments investigated and corresponds to first report the use of these antibiotics to eliminate P. mirabilis biofilms.

Diarrheal bacterial pathogens and multi-resistant enterobacteria in the Choqueyapu River in La Paz, Bolivia

Water borne diarrheal pathogens might accumulate in river water and cause contamination of drinking and irrigation water. The La Paz River basin, including the Choqueyapu River, flows through La Paz city in Bolivia where it is receiving sewage, and residues from inhabitants, hospitals, and industry. Using quantitative real-time PCR (qPCR), we determined the quantity and occurrence of diarrheagenic Escherichia coli (DEC), Salmonella enterica, Klebsiella pneumoniae, Shigella spp. and total enterobacteria in river water, downstream agricultural soil, and irrigated crops, during one year of sampling. The most abundant and frequently detected genes were gapA and eltB, indicating presence of enterobacteria and enterotoxigenic E. coli (ETEC) carrying the heat labile toxin, respectively. Pathogen levels in the samples were significantly positively associated with high water conductivity and low water temperature. In addition, a set of bacterial isolates from water, soil and crops were analyzed by PCR for presence of the genes blaCTX-M, blaKPC, blaNDM, blaVIM and blaOXA-48. Four isolates were found to be positive for blaCTX-M genes and whole genome sequencing identified them as E. coli and one Enterobacter cloacae. The E. coli isolates belonged to the emerging, globally disseminated, multi-resistant E. coli lineages ST648, ST410 and ST162. The results indicate not only a high potential risk of transmission of diarrheal diseases by the consumption of contaminated water and vegetables but also the possibility of antibiotic resistance transfer from the environment to the community.

Relationships between Microbial Indicators and Pathogens in Recreational Water Settings

Fecal pollution of recreational waters can cause scenic blight and pose a threat to public health, resulting in beach advisories and closures. Fecal indicator bacteria (total and fecal coliforms, Escherichia coli, and enterococci), and alternative indicators of fecal pollution (Clostridium perfringens and bacteriophages) are routinely used in the assessment of sanitary quality of recreational waters. However, fecal indicator bacteria (FIB), and alternative indicators are found in the gastrointestinal tract of humans, and many other animals and therefore are considered general indicators of fecal pollution. As such, there is room for improvement in terms of their use for informing risk assessment and remediation strategies. Microbial source tracking (MST) genetic markers are closely associated with animal hosts and are used to identify fecal pollution sources. In this review, we examine 73 papers generated over 40 years that reported the relationship between at least one indicator and one pathogen group or species. Nearly half of the reports did not include statistical analysis, while the remainder were almost equally split between those that observed statistically significant relationships and those that did not. Statistical significance was reported less frequently in marine and brackish waters compared to freshwater, and the number of statistically significant relationships was considerably higher in freshwater (p < 0.0001). Overall, significant relationships were more commonly reported between FIB and pathogenic bacteria or protozoa, compared to pathogenic viruses (p: 0.0022⁻0.0005), and this was more pronounced in freshwater compared to marine. Statistically significant relationships were typically noted following wet weather events and at sites known to be impacted by recent fecal pollution. Among the studies that reported frequency of detection, FIB were detected most consistently, followed by alternative indicators. MST markers and the three pathogen groups were detected least frequently. This trend was mirrored by reported concentrations for each group of organisms (FIB > alternative indicators > MST markers > pathogens). Thus, while FIB, alternative indicators, and MST markers continue to be suitable indicators of fecal pollution, their relationship with waterborne pathogens, particularly viruses, is tenuous at best and influenced by many different factors such as frequency of detection, variable shedding rates, differential fate and transport characteristics, as well as a broad range of site-specific factors such as the potential for the presence of a complex mixture of multiple sources of fecal contamination and pathogens.

Water Quality Assessment of the Pardo River Basin, Brazil: A Multivariate Approach Using Limnological Parameters, Metal Concentrations and Indicator Bacteria

Located in the southeast of Brazil, the Pardo River Basin has a large population and an economy focused on agriculture, with a strong predominance of the sugarcane agro-industry. The purpose of the study was to assess the water quality of the Pardo River Basin under a multivariate approach using limnological parameters, metal concentrations, and indicator bacteria. Nine sampling campaigns were performed during both the dry and rainy seasons. Element concentrations were determined by inductively coupled plasma spectrometry (ICP-MS, Perkin Elmer Elan 6000). A battery of test to determine limnological parameters was performed (in situ). Total coliforms and Escherichia coli were detected and quantified using Defined Substrate Technology Colilert^® and multiple tube dilutions. Principal component analysis and hierarchical cluster analysis were used as multivariate exploratory analysis. In general, the results suggest the influence of rain, possible sewage discharges into the watercourse, and the input of organic matter in some sampling points in both seasons, besides the absence of riparian vegetation in much of the Pardo River. The likely influence of industrial activities that do not have great prominence in the region was supported by temporal/spatial assessment of Cr and V. The water quality monitoring of Pardo River is an important tool for environmental management, and its continuity is indicated to obtain a consistent series of systematic data and thereby support concretely the actions of planning and controlling the use of water from the Pardo River and soil around them.