Multidrug-Resistant Bacteria Isolated from Surface Water in Bassaseachic Falls National Park, Mexico

Metagenomic perspectives on antibiotic resistance genes in tap water: The environmental characteristic, potential mobility and health threat

As an emerging environmental contaminant, antibiotic resistance genes (ARGs) in tap water have attracted great attention. Although studies have provided ARG profiles in tap water, research on their abundance levels, composition characteristics, and potential threat is still insufficient. Here, 9 household tap water samples were collected from the Guangdong-Hong Kong-Macao Greater Bay Area (GBA) in China. Additionally, 75 sets of environmental sample data (9 types) were downloaded from the public database. Metagenomics was then performed to explore the differences in the abundance and composition of ARGs. 221 ARG subtypes consisting of 17 types were detected in tap water. Although the ARG abundance in tap water was not significantly different from that found in drinking water plants and reservoirs, their composition varied. In tap water samples, the three most abundant classes of resistance genes were multidrug, fosfomycin and MLS (macrolide-lincosamide-streptogramin) ARGs, and their corresponding subtypes ompR, fosX and macB were also the most abundant ARG subtypes. Regarding the potential mobility, vanS had the highest abundance on plasmids and viruses, but the absence of key genes rendered resistance to vancomycin ineffective. Generally, the majority of ARGs present in tap water were those that have not been assessed and are currently not listed as high-threat level ARG families based on the World Health Organization Guideline. Although the current potential threat to human health posed by ARGs in tap water is limited, with persistent transfer and accumulation, especially in pathogens, the potential danger to human health posed by ARGs should not be ignored.

Antimicrobial resistance, virulence genes, and ESBL (Extended Spectrum Beta-Lactamase) production analysis in E. coli strains from the Rio Grande/Rio Bravo River in Tamaulipas, Mexico

The Rio Grande/Rio Bravo River is used as a major water supply for diverse recreational, household, and industrial activities in Northeast Tamaulipas, Mexico, and South Texas. In this study, we sampled surface water from 38 sites along Rio Grande/Rio Bravo River (Díaz Ordaz, Reynosa and Matamoros). We isolated 105 E. coli strains that were molecularly and phenotypically characterized. The percentage of virulence genes detected in E. coli were: hlyA (15.23%), stx2 (11.42%), stx1 (9.52%), bfp (0.95%), and eae (0.0) and combinations of stx1/stx2 (2.85%), stx2/hlyA (1.90%), stx1/bfp (0.95%) and stx2/bfp (0.95%) were detected in these strains. Resistance to more than one antibiotic was detected in 85.71%, and 5.71% of strains were extended-spectrum β-lactamase-E. coli (ESBL-EC). These results indicate the presence of potentially pathogenic E. coli strains in the Rio Grande/Rio Bravo River; therefore, it can be considered a reservoir of pathogenic strains and represents a health risk for the population.

High Frequency of Antibiotic Resistance Genes (ARGs) in the Lerma River Basin, Mexico

The spread of beta-lactamase-producing bacteria is of great concern and the environment has been found to be a main source of contamination. Herein, it was proposed to determine the frequency of antimicrobial-resistant-Gram-negative bacteria throughout the Lerma River basin using phenotypic and molecular methods. Resistant bacteria were isolated with chromogenic media and antimicrobial susceptibility tests were used to characterize their resistance. ARGs for beta-lactams, aminoglycosides, and quinolones were detected by PCR. Species were identified by Sanger sequencing the 16S rRNA gene and the representative genomes of MDR strains were sequenced by NGS. A high variation in the number of isolates was observed in the 20 sampled sites, while observing a low diversity among the resistant bacteria. Of the 12 identified bacterial groups, C. freundii, E. coli, and S. marcescens were more predominant. A high frequency of resistance to beta-lactams, quinolones, and aminoglycosides was evidenced, where the bla_CTX,qnrB, qnrS y, and aac(6')lb-cr genes were the most prevalent. C. freundii showed the highest frequency of MDR strains. Whole genome sequencing revealed that S. marcescens and K. pneumoniae showed a high number of shared virulence and antimicrobial resistance genes, while E. coli showed the highest number of unique genes. The contamination of the Lerma River with MDR strains carrying various ARGs should raise awareness among environmental authorities to assess the risks and regulations regarding the optimal hygienic and sanitary conditions for this important river that supports economic activities in the different communities in Mexico.

Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition

The ability of extensively drug-resistant (XDR) Klebsiella pneumoniae to rapidly acquire resistance to novel antibiotics is a global concern. Moreover, Klebsiella clonal lineages that successfully combine resistance and hypervirulence have increasingly occurred during the last years. However, the underlying mechanisms of counteracting fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we investigated whether and how an XDR sequence type (ST)307 K. pneumoniae strain developed resistance against the novel drug combination ceftazidime-avibactam (CAZ-AVI) using experimental evolution. In addition, we performed in vitro and in vivo assays, molecular modeling, and bioinformatics to identify resistance-conferring processes and explore the resulting decrease in fitness and virulence. The subsequent amelioration of the initial costs was also addressed. We demonstrate that distinct mutations of the major nonselective porin OmpK36 caused CAZ-AVI resistance that persists even upon following a second experimental evolution without antibiotic selection pressure and that the Klebsiella strain compensates the resulting fitness and virulence costs. Furthermore, the genomic and transcriptomic analyses suggest the envelope stress response regulator rpoE and associated RpoE-regulated genes as drivers of this compensation. This study verifies the crucial role of OmpK36 in CAZ-AVI resistance and shows the rapid adaptation of a bacterial pathogen to compensate fitness- and virulence-associated resistance costs, which possibly contributes to the emergence of successful clonal lineages.

IMPORTANCE Extensively drug-resistant Klebsiella pneumoniae causing major outbreaks and severe infections has become a significant challenge for health care systems worldwide. Rapid resistance development against last-resort therapeutics like ceftazidime-avibactam is a significant driver for the accelerated emergence of such pathogens. Therefore, it is crucial to understand what exactly mediates rapid resistance acquisition and how bacterial pathogens counteract accompanying fitness and virulence costs. By combining bioinformatics with in vitro and in vivo phenotypic approaches, this study revealed the critical role of mutations in a particular porin channel in ceftazidime-avibactam resistance development and a major metabolic regulator for ameliorating fitness and virulence costs. These results highlight underlying mechanisms and contribute to the understanding of factors important for the emergence of successful bacterial pathogens.

Genomic Profiling of Antibiotic-Resistant Escherichia coli Isolates from Surface Water of Agricultural Drainage in North-Western Mexico: Detection of the International High-Risk Lineages ST410 and ST617

Aquatic environments are recognized as one of the main reservoirs for the emergence and dissemination of high-risk lineages of multidrug-resistant (MDR) bacteria of public health concern. However, the genomic characteristics of antibiotic-resistant Escherichia coli isolates from aquatic origins remain limited. Herein, we examined the antibiotic resistance and virulence genomic profiles of three E. coli recovered from surface water in northwest Mexico. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and in-depth in silico analysis were performed. Two E. coli exhibited MDR phenotypes. WGS-based typing revealed genetic diversity, and phylogenetic analysis corroborated a notable divergent relationship among the studied E. coli. One E. coli strain, harboring enterotoxigenic and extraintestinal pathogenic-associated virulence genes, was assigned to the ST4 lineage. MDR E. coli, belonging to the international high-risk clones ST410 and ST617, carried genes and mutations conferring resistance to aminoglycosides, β-lactams, quinolones, sulfonamides, tetracyclines, and trimethoprim. This study describes, for the first time, the detection and genomic profiling of high-risk lineages of E. coli ST410 and ST617 from surface water in Mexico. Additionally, our results underscore the role of surface water as a reservoir for critical pathogenic and MDR E. coli clones and the need for the surveillance and monitoring of aquatic environments via WGS from the One Health perspective.

Coastal Surveillance and Water Quality monitoring in the Rejiche Sea-Tunisia

The aim of this study is to determine physiochemical and bacteriological properties of seawater and sediments from the coast of Tunisia during six successive months. The conductivity was measured using previously calibrated Hach Conductivity meter. Total suspended solid was determined using Whatman GF/C glass fiber filter (Sigma Aldrich), and the turbidity was assessed using a spectrophotometer (UV/Vis). The pH was measured using pH electrodes. Other physiochemical parameters were determined using Pastel UV multiparameter water analyzer (Secomam, aqualabo). Bacterial analysis was displayed by membrane filtration method, and isolates were identified to the species level by Api strips. Susceptibility to antibiotics was determined by disk diffusion methods. Total suspended solid, turbidity, adsorbable organic halogen, chemical oxygen demand, and biochemical oxygen demand were higher than accepted norms in Tunisia. Enterococcus faecalis was detected in all the sites indicating a human fecal contamination, and all the isolates were highly resistant to rifampicin, gentamicin, chloramphenicol, ampicillin, and azithromycin. The situation in Mahdia coast is alarming particularly with the isolation of multidrug resistance strains. It is recommended that the local government provide restrict policies for the treatment and the assessment of municipal wastewater before its discharge into sea. PRACTITIONER POINTS: Coastal Surveillance and Water Quality monitoring in the Rejiche Sea - Tunisia is crucial. Enterococcus faecalis was detected in sea water and sediment samples in the coast of Rejiche. Isolated strains were highly resistant to rifampicin, gentamicin, chloramphenicol, ampicillin and azithromycin.

Anthropogenic Activities and the Problem of Antibiotic Resistance in Latin America: A Water Issue

Antibiotics revolutionized modern medicine and have been an excellent tool to fight infections. However, their overuse and misuse in different human activities such as health care, food production and agriculture has resulted in a global antimicrobial resistance crisis. Some regions such as Latin America present a more complex scenario because of the lack of resources, systematic studies and legislation to control the use of antimicrobials, thus increasing the spread of antibiotic resistance. This review aims to summarize the state of environmental antibiotic resistance in Latin America, focusing on water resources. Three databases were searched to identify publications on antimicrobial resistance and anthropogenic activities in relation to natural and artificial water ecosystems. We found that antibiotic resistant bacteria, mainly against beta lactam antibiotics, have been reported in several Latin American countries, and that resistant bacteria as well as resistant genes can be isolated from a wide variety of aquatic environments, including drinking, surface, irrigation, sea and wastewater. It is urgent to establish policies and regulations for antibiotic use to prevent the increase of multi-drug resistant microorganisms in the environment.

Diversity of Multidrug-Resistant Bacteria in an Urbanized River: A Case Study of the Potential Risks from Combined Sewage Overflows

Wastewater contamination and urbanization contribute to the spread of antibiotic resistance in aquatic environments. This is a particular concern in areas receiving chronic pollution of untreated waste via combined sewer overflow (CSO) events. The goal of this study was to expand knowledge of CSO impacts, with a specific focus on multidrug resistance. We sampled a CSO-impacted segment of the James River (Virginia, USA) during both clear weather and an active overflow event and compared it to an unimpacted upstream site. Bacteria resistant to ampicillin, streptomycin, and tetracycline were isolated from all samples. Ampicillin resistance was particularly abundant, especially during the CSO event, so these isolates were studied further using disk susceptibility tests to assess multidrug resistance. During a CSO overflow event, 82% of these isolates were resistant to five or more antibiotics, and 44% were resistant to seven or more. The latter statistic contrasts starkly with the upstream reference site, where only 4% of isolates displayed resistance to more than seven antibiotics. DNA sequencing (16S rRNA gene) revealed that ~35% of our isolates were opportunistic pathogens, comprised primarily of the genera Stenotrophomonas, Pseudomonas, and Chryseobacterium. Together, these results demonstrate that CSOs can be a significant source of viable clinically-relevant bacteria to the natural environment and that multidrug resistance is an important understudied component of the environmental spread of antibiotic resistance.

The Beta-Lactam Resistome Expressed by Aerobic and Anaerobic Bacteria Isolated from Human Feces of Healthy Donors

Antibiotic resistance is a major health problem worldwide, causing more deaths than diabetes and cancer. The dissemination of vertical and horizontal antibiotic resistance genes has been conducted for a selection of pan-resistant bacteria. Here, we test if the aerobic and anaerobic bacteria from human feces samples in health conditions are carriers of beta-lactamases genes. The samples were cultured in a brain–heart infusion medium and subcultured in blood agar in aerobic and anaerobic conditions for 24 h at 37 °C. The grown colonies were identified by their biochemical profiles. The DNA was extracted and purified by bacterial lysis using thermal shock and were used in the endpoint PCR and next generation sequencing to identify beta-lactamase genes expression (OXA, VIM, SHV, TEM, IMP, ROB, KPC, CMY, DHA, P, CFX, LAP, and BIL). The aerobic bacterias Aeromonas hydrophila, Citrobacter freundii, Proteus mirabilis, Providencia rettgeri, Serratia fonticola, Serratia liquefaciens, Enterobacter aerogenes, Escherichia coli, Klebsiella pneumoniae, Pantoea agglomerans, Enterococcus faecalis, and Enterobacter cloacae, the anaerobic bacteria: Capnocytophaga species, Bacteroides distasonis, Bifidobacterium adolescentis, Bacteroides ovatus, Bacteroides fragilis, Eubacterium species, Eubacterium aerofaciens, Peptostreptococcus anaerobius, Fusobacterium species, Bacteroides species, and Bacteroides vulgatus were isolated and identified. The results showed 49 strains resistant to beta-lactam with the expression of blaSHV (10.2%), blaTEM (100%), blaKPC (10.2%), blaCYM (14.3%), blaP (2%), blaCFX (8.2%), and blaBIL (6.1%). These data support the idea that the human enteric microbiota constitutes an important reservoir of genes for resistance to beta-lactamases and that such genes could be transferred to pathogenic bacteria.

Structure of Bacterial Community with Resistance to Antibiotics in Aquatic Environments. A Systematic Review

Aquatic environments have been affected by the increase in bacterial resistant to antibiotics. The aim of this review is to describe the studies carried out in relation to the bacterial population structure and antibiotic resistance genes in natural and artificial water systems. We performed a systematic review based on the PRISMA guideline (preferred reporting items for systematic reviews and meta-analyzes). Articles were collected from scientific databases between January 2010 and December 2020. Sixty-eight papers meeting the inclusion criteria, i.e., "reporting the water bacterial community composition", "resistance to antibiotics", and "antibiotic resistance genes (ARG)", were evaluated according to pre-defined validity criteria. The results indicate that the predominant phyla were Firmicutes and Bacteroidetes in natural and artificial water systems. Gram-negative bacteria of the family Enterobacteraceae with resistance to antibiotics are commonly reported in drinking water and in natural water systems. The ARGs mainly reported were those that confer resistance to β-lactam antibiotics, aminoglycosides, fluoroquinolones, macrolides and tetracycline. The high influence of anthropogenic activity in the environment is evidenced. The antibiotic resistance genes that are mainly reported in the urban areas of the world are those that confer resistance to the antibiotics that are most used in clinical practice, which constitutes a problem for human and animal health.

Evaluation of recreational risks due to exposure of antibiotic-resistance bacteria from environmental water: A proposed framework

This research provides a framework for the human health risk assessment due to exposure of AR (antibiotic resistance) E. coli from recreational water (swimming activity). Literature-based epidemiological studies were used for f-value formulation (i.e., AR E. coli/total number of E. coli isolates) and the theoretical calculation of AR and non-AR E. coli concentrations. Risk was estimated using calculated values by considering four different dose-response (D-R) scenarios with known characteristics due to current lack of availability of D-R for AR bacteria. f-values ranged between 0.14 and 0.59 and the order of calculated theoretical values of maximum AR E. coli are as follows: ampicillin or amoxicillin (38 CFU/dip) > co-trimoxazole (19 CFU/dip) ~ tetracycline (18 CFU/dip) > ceftriaxone or cefotaxime or ceftazidime (10 CFU/dip) ~ ciprofloxacin or ofloxacin (9 CFU/dip). The risk of infection was considerably high for theoretical calculated concentration values regardless of the chosen D-R model (annual risk of infection (95th percentile) = 1, Spearman's rank correlation coefficient = -0.06 to 0.94), under the conditions studied. Further, AR levels of human gastrointestinal-tract were determined using literature-reported data in stool samples and indicated that the resistance level was very high in healthy human (range: 3.7 × 10⁷-8.4 × 10⁷ CFU/g of wet lumen content). The maximum allowable concentration values for AR E. coli and non-ARB (0.0075 CFU/dip and 2.56 CFU/dip) were found to be smaller than the USEPA recreational water quality guidelines (≤126 CFU/100 mL), which can help the USEPA and other regulatory bodies in revisiting the current guidelines. So based on the noted results, we can conclude that the maintenance of inventory of actual measured concentration of ARB in the recreational water sites is needed to prevent unwanted complication related to the treatment of infectious sustained by resistant microbes.

Detection of extended-spectrum beta-lactamase-producing E. coli and Klebsiella spp. in effluents of different hospitals sewage in Biratnagar, Nepal

Objective

This study was aimed to determine prevalence and resistance pattern like multidrug resistant (MDR) or ESBL nature of E. coli and Klebsiella spp. from various sewage drain samples with an idea to deliver baseline information that could be utilized for defining guidelines for the treatment of hospital sewages.

Results

Of 10 sewage samples analyzed, 7 (70%) contained E. coli while 6 (60%) contained Klebsiella. Except one sample, all positive samples contained both E. coli and Klebsiella spp. E. coli isolates were resistant to ampicillin, amoxicillin, cefoxitin, cefuroxime, and cefpodoxime; while 85.7% were resistant to amoxicillin/clavulanate, ceftazidime, cefotaxime and ceftriaxone. 71.4%, 57.1%, 42.9%, and 28.6% were resistant to aztreonam, trimethoprim/sulfamethoxazole, nitrofurantoin, and gentamicin. Most were sensitive to chloramphenicol, ofloxacin, ciprofloxacin, and azithromycin. 85.7% and 57.1% of E. coli were MDR and ESBL isolates, respectively. Klebsiella were resistant to ampicillin, amoxicillin, and amoxicillin/clavulanate. 83.4% of Klebsiella were resistant to cefoxitin. 66.7% of strains were resistant to cefuroxime, ceftazidime, cefotaxime, ceftriaxone, and cefpodoxime. Klebsiella showed 50% resistant to aztreonam and trimethoprim/sulfamethoxazole, while 33.3% were resistant to chloramphenicol, nitrofurantoin, ofloxacin, and ciprofloxacin. Klebsiella were sensitive to azithromycin and gentamicin. 66.7% and 33.3% of Klebsiella were MDR and ESBL isolates, respectively.

Occurrence of β-Lactamase-Producing Gram-Negative Bacterial Isolates in Water Sources in Cali City, Colombia

Introduction

Pollution by domestic, industrial, and hospital wastes of the artificial and natural waters of the city of Cali led us to investigate the presence of Gram-negative bacteria resistant to antibiotics in these aquatic ecosystems.

Material and methods

We used culture-dependent methods and molecular techniques to investigate the prevalence and dynamics of β-lactamase producing Gram-negative bacteria in five areas located in channels and rivers that cross the city of Cali in January (dry season) and May (wet season). The association between the variables was determined by the chi-square test, using the statistical package SPSS vs 23.0.

Results

The main species being Escherichia coli and Pseudomonas spp. with associated resistance to both cefoxitin and cefotaxime were observed in 73.3% isolates during the dry season. Most of the isolates belonged to antibiotype 3 (with resistance to 6 antibiotics), 51.2% in the dry season and 48.9% in the wet season, and they were found especially in the artificial waters of “Intersector Canal (CVC) Sur”.

Conclusion

These results indicate that β-lactamase-producing Gram-negative bacteria are widespread in the environment in the aquatic ecosystem of Cali city. The artificial and natural waters that cross the city are finally discharged into the Rio Cauca; this river can then be considered as a medium for the spread of bacterial antibiotic resistance genes.

High level of drug resistance by gram-negative bacteria from selected sewage polluted urban rivers in Addis Ababa, Ethiopia

OBJECTIVE

The aim of this study was to determine the level of drug resistance by gram-negative bacteria isolated from selected sewage polluted urban rivers in Addis Ababa, Ethiopia.

RESULTS

From a total of 94 river water samples, 90 medically important gram-negative bacterial isolates were recovered to the species level. The predominant bacteria isolated were E. coli. 23 (26%) followed by K. pneumoniae 18 (20%), K. oxytoca 17 (19%). E. coli showed a high level of resistance to ampicillin 21 (91.3%), cefalotin, cefuroxime, ceftriaxone and cefepime 16 (70%). Both K. pneumoniae and K. oxytoca showed high resistance to ampicillin 16 (94%) and 17 (95%) respectively. Among identified bacterial species, most of them showed a multidrug-resistant pattern. Providential retigerri showed 100% multidrug resistance followed by P. alkalificiens (90%), E. coli (78%), M. morgani (75%), and C. frundi (60%).

Antibiotic Use in Agriculture and Its Consequential Resistance in Environmental Sources: Potential Public Health Implications

Due to the increased demand of animal protein in developing countries, intensive farming is instigated, which results in antibiotic residues in animal-derived products, and eventually, antibiotic resistance. Antibiotic resistance is of great public health concern because the antibiotic-resistant bacteria associated with the animals may be pathogenic to humans, easily transmitted to humans via food chains, and widely disseminated in the environment via animal wastes. These may cause complicated, untreatable, and prolonged infections in humans, leading to higher healthcare cost and sometimes death. In the said countries, antibiotic resistance is so complex and difficult, due to irrational use of antibiotics both in the clinical and agriculture settings, low socioeconomic status, poor sanitation and hygienic status, as well as that zoonotic bacterial pathogens are not regularly cultured, and their resistance to commonly used antibiotics are scarcely investigated (poor surveillance systems). The challenges that follow are of local, national, regional, and international dimensions, as there are no geographic boundaries to impede the spread of antibiotic resistance. In addition, the information assembled in this study through a thorough review of published findings, emphasized the presence of antibiotics in animal-derived products and the phenomenon of multidrug resistance in environmental samples. This therefore calls for strengthening of regulations that direct antibiotic manufacture, distribution, dispensing, and prescription, hence fostering antibiotic stewardship. Joint collaboration across the world with international bodies is needed to assist the developing countries to implement good surveillance of antibiotic use and antibiotic resistance.

Depth and Well Type Related to Groundwater Microbiological Contamination

Use of groundwater from private wells in households has increased considerably, owing to a better cost/benefit ratio than that of water provided by local utilities for a fee. However, this water is usually untreated, which makes it a vehicle for diseases. Thus, monitoring this water is necessary to ensure its integrity and quality. We aimed to evaluate the physical, chemical, and microbiological parameters of untreated groundwater drawn from different types of wells, and the antimicrobial susceptibility profile of the bacteria isolated from this water. Wellwater samples were collected in two Brazilian cities. Although physical and chemical parameters of the water were suitable for drinking, Escherichia coli was detected in 33% of the samples. E. coli contaminated 65% of dug wells and 10.25% of drilled wells. Many bacteria isolated were resistant to multiple antibacterial agents, including β-lactams. Microbial contamination of this water was related to the well depth, and was more common in dug wells, making this water unfit for human consumption. Consumption of such contaminated and untreated water is a public health concern. Thus, individuals who regularly use such water must be alerted so they may either take preventive measures or connect to the water distribution system operated by local utilities.