Evolution of antibiotic resistance at non-lethal drug concentrations

Antibiotic type and dose variably affect microbiomes of a disease-resistant Acropora cervicornis genotype

BACKGROUND

As coral diseases become more prevalent and frequent, the need for new intervention strategies also increases to counteract the rapid spread of disease. Recent advances in coral disease mitigation have resulted in increased use of antibiotics on reefs, as their application may halt disease lesion progression. Although efficacious, consequences of deliberate microbiome manipulation resulting from antibiotic administration are less well-understood- especially in non-diseased corals that appear visually healthy. Therefore, to understand how apparently healthy corals are affected by antibiotics, we investigated how three individual antibiotics, and a mixture of the three, impact the microbiome structure and diversity of a disease-resistant Caribbean staghorn coral (Acropora cervicornis) genotype. Over a 96-hour, aquarium-based antibiotic exposure experiment, we collected and processed coral tissue and water samples for 16S rRNA gene analysis.

RESULTS

We found that antibiotic type and dose distinctively impact microbiome alpha diversity, beta diversity, and community composition. In experimental controls, microbiome composition was dominated by an unclassified bacterial taxon from the order Campylobacterales, while each antibiotic treatment significantly reduced the relative abundance of this taxon. Those taxa that persisted following antibiotic treatment largely differed by antibiotic type and dose, thereby indicating that antibiotic treatment may result in varying potential for opportunist establishment.

CONCLUSION

Together, these data suggest that antibiotics induce microbiome dysbiosis- hallmarked by the loss of a dominant bacterium and the increase in taxa associated with coral stress responses. Understanding the off-target consequences of antibiotic administration is critical not only for informed, long-term coral restoration practices, but also for highlighting the importance of responsible antibiotic dissemination into natural environments.

Historical distribution and multi-dimensional environmental risk assessments of antibiotics in coastal sediments affected by land-based human activities

Coastal sediment cores provide important records of land-based antibiotics' deposition. This study examined sediment cores from the Hangzhou Bay, East China Sea, dating back to 1980-2020 using 210Pbex. The 40-year analysis revealed a mismatch between sediment depth and age. Wastewater treatment facilities have significantly reduced antibiotics discharge into the sea. We identified 27 antibiotics, with enrofloxacin (ERFX) and nadifloxacin (NDFX) exhibiting the highest average concentrations of 84.9 and 83.4 ng/g, respectively. Quinolones (QNs) were prominent, displaying strong co-occurrence and similar distribution patterns shaped by comparable soil-water distribution coefficient (Kd). QNs correlated positively with total antibiotic concentration, serving as indicators. We proposed a multi-dimensional risk assessment of antibiotics, encompassing ecological and antimicrobial resistance (AMR) risks, complementing each other. The assessment revealed antibiotics with distinct risks: sulfacetamide (SCM) and clindamycin (CLIN) exhibited high ecological risks, while ERFX, ciprofloxacin (CFX), norfloxacin (NFX), gatifloxacin (GTFX), moxifloxacin (MXFX), and marbofloxacin (MBFX) presented high AMR risks.

Occurrence, Removal, and Risk Assessment of Antimicrobials and Their Transformation Products in Effluent from Australian Wastewater Treatment Plants

Despite Australia's high antimicrobial use, their residues in wastewater and their impacts on receiving waters remain largely unknown. This study assessed the occurrence, removal, and risk for antimicrobial resistance (AMR) of 102 antimicrobial substances and selected transformation products (TPs) in wastewater effluent from 47 wastewater treatment plants (WWTPs) across Australia. Thirty-two antimicrobials and 13 TPs were detected, with 14 analytes occurring at >80% frequencies. Ampicillin, penicillin V, penicilloic V acid, fluconazole, and tazobactam M1 were observed with high median concentrations of >0.2 μg/L. Collectively, the WWTPs released 5.4 kg/day or 0.54 g/day/1000 inhabitants of antimicrobials/TPs into natural waters, with β-lactams, quinolones, nitroimidazoles/azoles, and sulfonamides comprising high volumes, which was correlated with the population's socioeconomic statuses. Thirty-seven analytes were removed at rates >80% post-treatment, whereas quinolones, nitroimidazoles/azoles, lincosamides, and macrolide TPs were observed with poor removal efficiencies, which were affected by treatment processes and regional climate. Comparing measured concentrations with the predicted no-effect concentrations for AMR selection (PNECAMR), 7 antimicrobials exerted selection risk for resistant bacteria. Concerningly, ciprofloxacin posed medium/high risk in most of the assessed WWTPs. The accumulative effects of antimicrobial classes and certain TPs might further aggravate adverse impacts on AMR development. Our study provides insights into the presence and AMR implications of antimicrobials in treated wastewater, aiming to safeguard public health and ecosystems.

Multi-compartment impact of micropollutants and particularly antibiotics on bacterial communities using environmental DNA at river basin-level

Bacterial communities respond to environmental conditions with diverse structural and functional changes depending on their compartment (water, biofilm or sediment), type of environmental stress, and type of pollution to which they are exposed. In this study, we combined amplicon sequencing of bacterial 16S rRNA genes from water, biofilm, and sediment samples collected in the anthropogenically impacted River Aconcagua basin (Central Chile, South America), in order to evaluate whether micropollutants alter bacterial community structure and functioning based on the type and degree of chemical pollution. Furthermore, we evaluated the potential of bacterial communities from differently polluted sites to degrade contaminants. Our results show a lower diversity at sites impacted by agriculture and urban areas, featuring high loads of micropollution with pesticides, pharmaceuticals and personal care products as well as industrial chemicals. Nutrients, antibiotic stress, and micropollutant loads explain most of the variability in the sediment and biofilm bacterial community, showing a significant increase of bacterial groups known for their capabilities to degrade various organic pollutants, such as Nitrospira and also selecting for taxa known for antibiotic resistance such as Exiguobacterium and Planomicrobium. Moreover, potential ecological functions linked to the biodegradation of toxic chemicals at the basin level revealed significant reductions in ecosystem-related services in sites affected by agriculture and wastewater treatment plant (WWTP) discharges across all investigated environmental compartments. Finally, we suggest transitioning from simple concentration-based assessments of environmental pollution to more meaningful toxic pressure values, measured environmental concentrations normalised by effect information, in order to comprehensively evaluate the role of micropollutants at the ecological (biodiversity) level.

Extended-spectrum β-lactamase production and antimicrobial resistance among Enterobacteriaceae causing clinical infections in Africa: a systematic review and meta-analysis (2012-2020)

BACKGROUND

Worldwide, antimicrobial resistance (AMR) has grown to represent a serious threat to the diagnosis, management, and prevention of bacterial diseases. Due to their multidrug resistance attributes, the WHO has classified extended-spectrum-β-lactamase-producing Enterobacteriaceae (ESBL-PE)-associated infections as infections of critical significance, posing a serious risk to human health. Thus, the goal of this systematic review and meta-analysis was to assess the pooled prevalence of ESBL-PE and AMR among strains causing clinical infections in Africa.

METHODS

In this systematic review and meta-analysis, two investigators independently made an electronic search in Google Scholar and PubMed databases using related keywords and corresponding "MeSH." terms for the PubMed. The accessed studies were screened, assessed for eligibility, and critically evaluated as per the PRISMA guidelines. The prevalence and 95% confidence intervals (CI) for ESBL-PE in Africa were evaluated using a random-effects model of a meta-analysis. As a visual and statistical way assessment, the funnel plot and Egger's test were utilized to assess the risk of bias or publication bias, with a statistically significant level of bias being determined at p < 0.05.

RESULTS

Twenty-six studies were included in the meta-analysis. Among the included studies done in Africa, the overall pooled proportion of ESBL-PE was reported to be 28% (95% CI 25-31%). ESBL-PE prevalence differed by region, the pooled estimates for East and North Africa were 29% (95% CI 20-38%) and 19% (95% CI 6-33%), respectively. The greatest sub-group analysis of pooled estimates among bacterial isolates was found in Klebsiella. pneumoniae, at 73% (95% CI 62-85%), while Proteus mirabilis had the lowest, at 40% (95% CI 1-81%).

CONCLUSIONS

In Africa, ESBL-PE is noticeably prevalent. The included studies demonstrated a significant variation in ESBL-PE resistance among the countries. This illustrates the necessity of actively monitoring antimicrobial resistance in Africa to develop interventions aimed at halting the spread of ESBL-PE.

Carbapenem-Resistant E. coli Adherence to Magnetic Nanoparticles

Carbapenem-resistant Enterobacterales (CRE) is an emerging global concern. Specifically, carbapenemase-producing (CP) E. coli strains in CRE have recently been found in clinical, environmental, and food samples worldwide, causing many hospitalizations and deaths. Their rapid identification and characterization are paramount in control, management options, and treatment choices. Thus, this study aimed to characterize the cell surface properties of carbapenem-resistant (R) E. coli isolates and their interaction with glycan-coated magnetic nanoparticles (gMNPs) compared with carbapenem-susceptible (S) E coli. This study used two groups of bacteria: The first group included E. coli (R) isolates harboring carbapenemases and had no antibiotic exposure. Their initial gMNP-cell binding capacity, with cell surface characteristics, was assessed. In the second group, one of the E. coli (R) isolates and E. coli (S) had long-term serial antibiotic exposure, which we used to observe their cell surface characteristics and gMNP interactions. Initially, cell surface characteristics (cell morphology and cell surface charge) of the E. coli isolates were evaluated using confocal laser scanning microscope (LSCM) and a Zetasizer, respectively. The interaction of gMNPs with the E. coli isolates was assessed through LSCM and transmission electron microscope (TEM). Further, the gMNP-cell attachment was quantified as a concentration factor (CF) through the standard plating method. The results showed that the CF values of all E. coli (R) were significantly different from those of E. coli (S), which could be due to the differences in cell characteristics. The E. coli (R) isolates displayed heterogeneous cell shapes (rod and round cells) and lower negative zeta potential (cell surface charge) values compared to E. coli (S). Further, this research identified the differences in the cell surface characteristics of E. coli (S) under carbapenem exposure, compared to unexposed E. coli (S) that impact their attachment capacity. The gMNPs captured more E. coli (S) cells compared to carbapenem-exposed E. coli (S) and all E. coli (R) isolates. This study clearly found that differences in cell surface characteristics impact their interaction with magnetic nanoparticles. The gained insights aid in further understanding adhesion mechanisms to develop or improve bacterial isolation techniques and diagnostic and treatment methods for CRE.

Antibiotic contaminants and their impact in Gingee River, Puducherry: insights from SPE-UPLC-MS/MS and zebrafish study

The accumulation of antibiotic residues in ecosystems is intricately tied to the proliferation of bacterial resistance to antibiotics, with far-reaching consequences for the health and welfare of both humans and animal well-being. The analytical approach integrates solid phase extraction (SPE) with ultra performance liquid chromatography-mass spectrometry (UPLC-MS/MS) for quantification of multiclass antibiotic residues. Upon applying the aforementioned method to analyse water samples collected from the Gingee River, revealed the existence of five distinct antibiotics. This is the first study reporting antibiotic concentration in the Gingee River, Puducherry. The concentrations of nalidixic acid, sulfamethoxazole, and tetracycline were determined to be 8.5, 6.9, and 4.8 μg/L, respectively. Metronidazole and trimethoprim were detected at concentrations below the quantifiable limit. The microbial study of water samples also indicated that Shigella sp. and Acinetobacter sp. were the most predominant bacterial species present. Our preliminary observation underscores the importance of comprehending the intricate relationship between the presence of antibiotics in water and the concurrent proliferation of antibiotic-resistant bacteria within bacterial populations in the Gingee River. Further, we evaluated the developmental toxicity of environmentally relevant concentrations of antibiotics in zebrafish. The zebrafish model confirms that these antibiotics are sublethally hazardous to human health at environmentally relevant concentrations. This integrated approach allows unique views on the environmental impact of antibiotic residues, their role in the evolution of antibiotic resistance, and their impact on human health.

A critical meta-analysis of predicted no effect concentrations for antimicrobial resistance selection in the environment

Antimicrobial resistance (AMR) is one of the greatest threats to human health with a growing body of evidence demonstrating that selection for AMR can occur at environmental antimicrobial concentrations. Understanding the concentrations at which selection for resistance may occur is critical to help inform environmental risk assessments and highlight where mitigation strategies are required. A variety of experimental and data approaches have been used to determine these concentrations. However, there is minimal standardisation of existing approaches and no consensus on the relative merits of different methods. We conducted a semi-systematic literature review to collect and critically appraise available minimal selective concentration (MSC) and predicted no effect concentration for resistance (PNECR) data and the approaches used to derive them. There were 21 relevant articles providing 331 selective concentrations, ranging from 0.00087 µg/L (ciprofloxacin) to 2000 µg/L (carbenicillin). Meta-analyses of these data found that selective concentrations are highly compound-dependent, and only a subset of all antimicrobials have been the focus of most of the research. The variety of approaches that have been used, knowledge gaps and future research priorities were identified, as well as recommendations for those considering the selective risks of antimicrobials in the environment.

Impact of salmon farming in the antibiotic resistance and structure of marine bacterial communities from surface seawater of a northern Patagonian area of Chile

BACKGROUND

Aquaculture and salmon farming can cause environmental problems due to the pollution of the surrounding waters with nutrients, solid wastes and chemicals, such as antibiotics, which are used for disease control in the aquaculture facilities. Increasing antibiotic resistance in human-impacted environments, such as coastal waters with aquaculture activity, is linked to the widespread use of antibiotics, even at sub-lethal concentrations. In Chile, the world's second largest producer of salmon, aquaculture is considered the primary source of antibiotics residues in the coastal waters of northern Patagonia. Here, we evaluated whether the structure and diversity of marine bacterial community, the richness of antibiotic resistance bacteria and the frequency of antibiotic resistance genes increase in communities from the surface seawater of an area with salmon farming activities, in comparison with communities from an area without major anthropogenic disturbance.

RESULTS

The taxonomic structure of bacterial community was significantly different between areas with and without aquaculture production. Growth of the culturable fraction under controlled laboratory conditions showed that, in comparison with the undisturbed area, the bacterial community from salmon farms displayed a higher frequency of colonies resistant to the antibiotics used by the salmon industry. A higher adaptation to antibiotics was revealed by a greater proportion of multi-resistant bacteria isolated from the surface seawater of the salmon farming area. Furthermore, metagenomics data revealed a significant higher abundance of antibiotic resistant genes conferring resistance to 11 antibiotic families in the community from salmon farms, indicating that the proportion of bacteria carrying the resistance determinants was overall higher in salmon farms than in the undisturbed site.

CONCLUSIONS

Our results revealed an association between bacterial communities and antibiotic resistance from surface seawater of a coastal area of Chile. Although the total bacterial community may appear comparable between sites, the cultivation technique allowed to expose a higher prevalence of antibiotic resistant bacteria in the salmon farming area. Moreover, we demonstrated that metagenomics (culture-independent) and phenotypic (culture-dependent) methods are complementary to evaluate the bacterial communities' risk for antibiotic resistance, and that a human-influenced environment (such as salmon farms) can potentiate bacteria to adapt to environmental stresses, such as antibiotics.

Interspecies interactions alter the antibiotic sensitivity of Pseudomonas aeruginosa

Polymicrobial infections are infections that are caused by multiple pathogens and are common in patients with cystic fibrosis (CF). Although polymicrobial infections are associated with poor treatment responses in CF, the effects of the ecological interactions between co-infecting pathogens on antibiotic sensitivity and treatment outcome are poorly characterized. To this end, we systematically quantified the impact of these effects on the antibiotic sensitivity of Pseudomonas aeruginosa for nine antibiotics in medium conditioned by 13 secondary cystic fibrosis-associated bacterial and fungal pathogens through time-kill assays. We fitted pharmacodynamic models to these kill curves for each antibiotic-species combination and found that interspecies interactions changing the antibiotic sensitivity of P. aeruginosa are abundant. Interactions that lower antibiotic sensitivity are more common than those that increase it, with generally more substantial reductions than increases in sensitivity. For a selection of co-infecting species, we performed pharmacokinetic-pharmacodynamic modeling of P. aeruginosa treatment. We predicted that interspecies interactions can either improve or reduce treatment response to the extent that treatment is rendered ineffective from a previously effective antibiotic dosing schedule and vice versa. In summary, we show that quantifying the ecological interaction effects as pharmacodynamic parameters is necessary to determine the abundance and the extent to which these interactions affect antibiotic sensitivity in polymicrobial infections.IMPORTANCEIn cystic fibrosis (CF) patients, chronic respiratory tract infections are often polymicrobial, involving multiple pathogens simultaneously. Polymicrobial infections are difficult to treat as they often respond unexpectedly to antibiotic treatment, which might possibly be explained because co-infecting pathogens can influence each other's antibiotic sensitivity, but it is unknown to what extent such effects occur. To investigate this, we systematically quantified the impact of co-infecting species on antibiotic sensitivity, focusing on P. aeruginosa, a common CF pathogen. We studied for a large set co-infecting species and antibiotics whether changes in antibiotic response occur. Based on these experiments, we used mathematical modeling to simulate P. aeruginosa's response to colistin and tobramycin treatment in the presence of multiple pathogens. This study offers comprehensive data on altered antibiotic sensitivity of P. aeruginosa in polymicrobial infections, serves as a foundation for optimizing treatment of such infections, and consolidates the importance of considering co-infecting pathogens.

Combined ozonation-biological activated carbon process for antibiotic resistance control in treated effluent from wastewater treatment plant

Biological activated carbon (BAC) treatment plays a crucial role in wastewater treatment plants due to its economic and effective promotion of organic matter degradation or mineralization. However, whether the changes in antibiotic resistance (AR) resulting from BAC or O3-BAC treatment are related to environmental factors remains unclear, as previous studies have primarily focused on isolated aspects, or have combined these aspects without systematically comparing the BAC and O3-BAC treatment processes or analyzing their interrelationships. In this study, to gain a clearer understanding of the factors related to AR during the BAC treatment, the treatment process of BAC and O3-BAC were comprehensively compared, including antibiotics removal, wastewater matrix changes, antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and bacterial community characteristics. The roles of O3 pretreatment and the bed depth of BAC were also clarified. ARGs were found to be not as sensitive to ozone as ARB. In addition, further strengthening of control measures should be needed for trimethoprim and tetracycline, due to their low removal efficiencies by ozone pretreatment, and their close relationship with the increased AR. Besides, 2 mg/L ozonation pretreatment could significantly influence the microbial community composition of wastewater and biofilm samples, while 1 mg/L ozonation could not. Finally, the correlation of environmental factors, bacterial communities, and ARGs revealed that to reduce the AR risks of O3-BAC treatment, antibiotics in wastewater should be strictly controlled, since they were positively correlated with the accumulation of ARGs and Pseudomonadota, Actinomycetota, and Bacteroidota, which were responsible for carrying and disseminating ARGs. The results showed that higher dose ozonation pre-treatment and longer bed depth of BAC process could help control the AR of BAC.

Flumequine, a fluoroquinolone in disguise

Fluoroquinolone resistance in E. coli isolates from livestock in Europe remains high despite EMA restrictions on fluoroquinolone use in animals. However, flumequine, a quinolone not classified as a fluoroquinolone by various regulatory bodies, is still used in livestock in the Netherlands, Belgium, Greece and France. We investigated whether flumequine selects for the same resistance mechanisms in E. coli. Resistant and non-resistant E. coli isolates were obtained from caecal fermentation assays and broilers exposed to concentrations of flumequine and enrofloxacin. Flumequine usage leads to an approximately 3-fold increase in resistant E. coli in the caecal fermentation, similar to enrofloxacin. In vitro exposure to both flumequine and enrofloxacin revealed the same amino acid substitutions (S83L, D87G) in GyrA. Additionally, the same resistance-causing substitutions were found in phenotypically resistant E. coli isolates from broilers treated with either enrofloxacin or flumequine. Flumequine induces similar resistance mechanisms as enrofloxacin, warranting equivalent restrictions on its use.

Spatiotemporal variations and priority ranking of emerging contaminants in nanwan reservoir: A case study from the agricultural region in huaihe river basin in China

The presence of emerging contaminants (ECs) in drinking water sources is an increasing concern, yet limited data exists on their occurrence and risk in the upper Huaihe River Basin, an important agricultural region in Central China. This study investigated 70 ECs, including pesticide and antibiotics in surface water from drinking water source areas in Nanwan Reservoir along the upper reaches of the Huaihe River Basin to prioritize the ECs based on ecological risk and health risk assessment. A total of 66 ECs were detected in the surface water at least once at the selected 38 sampling sites, with concentrations ranging from 0.04 to 2508 ng/L. Ecological risk assessment using the risk quotient (RQ) method revealed high risks (RQ > 1) from 7 ECs in the dry season and 15 ECs in the wet season, with triazine pesticides as the main contributors. Non-carcinogenic risks were below negligible levels, but carcinogenic risks from neonicotinoid and carbamate pesticides and macrolide antibiotics were concerning for teenagers. Ciprofloxacin exhibited a high level of resistance risk during the wet season. A multi-indicator prioritization approach integrating occurrence, risk, and chemical property data ranked 6 pesticides and 3 antibiotics as priority pollutants. The results highlight EC contamination of drinking water sources in this agriculturally-intensive region and the need for targeted monitoring and management to protect water quality.

Cell morphology as biomarker of carbapenem exposure

Characterizing the physiological response of bacterial cells to antibiotics is crucial for designing diagnostic techniques, treatment choices, and drug development. While bacterial cells at sublethal doses of antibiotics are commonly characterized, the impact of exposure to high concentrations of antibiotics on bacteria after long-term serial exposure and their effect on withdrawal need attention for further characterization. This study investigated the effect of increasing imipenem concentrations on carbapenem-susceptible (S) and carbapenem-resistant (R) E. coli on their growth adaptation and cell surface structure. We exposed the bacterial population to increasing imipenem concentrations through 30 exposure cycles. Cell morphology was observed using a 3D laser scanning confocal microscope (LSCM) and transmission electron microscope (TEM). Results showed that the exposure resulted in significant morphological changes in E. coli (S) cells, while minor changes were seen in E. coli (R) cells. The rod-shaped E. coli (S) gradually transformed into round shapes. Further, the exposed E. coli (S) cells' surface area-to-volume ratio (SA/V) was also significantly different from the control, which is non-exposed E. coli (S). Then, the exposed E. coli (S) cells were re-grown in antibiotic-free environment for 100 growth cycles to determine if the changes in cells were reversible. The results showed that their cell morphology remained round, showing that the cell morphology was not reversible. The morphological response of these cells to imipenem can assist in understanding the resistance mechanism in the context of diagnostics and antibacterial therapies.

Subminimum Inhibitory Concentrations Tetracycline Antibiotics Induce Biofilm Formation in Minocycline-Resistant Klebsiella pneumonia by Affecting Bacterial Physical and Chemical Properties and Associated Genes Expression

Biofilm formation of Klebsiella pneumoniae can protect bacteria from antibiotics and is difficult to eradicate. Thus, the influence of subinhibitory concentrations of antibiotics on bacteria is becoming increasingly important. Our study showed that subminimum inhibitory concentrations (sub-MICs) of tetracycline antibiotics can increase biofilm formation in minocycline-resistant Klebsiella pneumoniae clinical strains. However, in the bacterial adhesion and invasion experiments, the adhesion and invasion ability decreased and the survival rate of Galleria mellonella increased. Under sub-MICs of tetracycline antibiotics treatment, abnormal stretching of bacteria was observed by scanning electron microscopy. Treatment with sub-MICs of tetracyclines leads to increased surface hydrophobicity and eDNA content and decreased outer membrane permeability. The expression levels of the fimA, luxS, qseB, and qseC genes decreased, the expression level of mrkA increased, and the expression level of acrA was inconsistent under different tetracycline antibiotics treatments. Together, our results suggested that the increase in Klebsiella pneumoniae biofilm formation caused by sub-MICs of tetracycline antibiotics may occur by affecting bacterial physical and chemical properties and associated genes expression.

Unveiling the ecological landscape of bacterial β-lactam resistance in Delhi-national capital region, India: An emerging health concern

Inappropriate antibiotic use not only amplifies the threat of antimicrobial resistance (AMR), moreover exacerbates the spread of resistant bacterial strains and genes in the environment, underscoring the critical need for effective research and interventions. Our aim is to assess the prevalence and resistance characteristics of β-lactam resistant bacteria (BLRB) and β-lactamase resistant bacterial genes (BLRBGs) under various environmental conditions within Delhi NCR, India. Using a culture-dependent method, we isolated 130 BLRB from 75 different environmental samples, including lakes, ponds, the Yamuna River, agricultural soil, aquatic weeds, drains, dumping yards, STPs, and gaushalas. Tests for antibiotic susceptibility were conducted in addition to phenotypic and genotypic identification of BLs and integron genes. The water and sediment samples recorded an average bacterial abundance of 3.6 × 106 CFU/mL and an average ampicillin-resistant bacterial count of 2.2 × 106 CFU/mL, which can be considered a potent reservoir of BLRB and BLRBGs. The majority of the BLRB discovered are opportunistic pathogens from the Bacillus, Aeromonas, Pseudomonas, Enterobacter, Escherichia, and Klebsiella genera, with Multiple Antibiotic Resistance (MAR) index ≥0.2 against a wide variety of β-lactams and β-lactamase (BLs) inhibitor combinations. The antibiotic resistance pattern was similar in the case of bacteria isolated from STPs. Meanwhile, bacteria isolated from other sources were diverse in their antibiotic resistance profile. Interestingly, we discovered that 10 isolates of various origins produce both Extended Spectrum BLs and Metallo BLs, as well as found harboring blaTEM, blaCTX, blaOXA, blaSHV, int-1, and int-3 genes. Enterobacter cloacae (S50/A), a common nosocomial pathogen isolated from Yamuna River sediment samples at Nizamuddin point, possesses three BLRBGs (blaTEM, blaCTX, and blaOXA) and a MAR index of 1.0, which is a major cause for concern. Therefore, identifying the source, origin and dissemination of BLRB and BLRGs in the environment is of the utmost importance for designing effective mitigation approaches to reduce a load of antimicrobial resistance factors in the environmental settings.

Determination of antibiotics during treatment of hospital wastewater using automated solid-phase extraction followed by UHPLC-MS: occurrence, removal and environmental risks

The extent of removal of pharmaceuticals by African-based wastewater treatment plants (WWTPs) is relatively unknown with various studies observing high concentrations in effluents. This is mainly due to WWTPs still utilising the traditional treatment methods which are known to be less effective. In this study, 15 selected antibiotics (amoxicillin, ampicillin, azithromycin, ciprofloxacin, doxycycline, erythromycin, gentamicin, metronidazole, norfloxacin, ofloxacin, penicillin, sulfamethoxazole, sulfapyridine, tetracycline and trimethoprim) were monitored in wastewater as it goes through sedimentation (primary and secondary), aeration and chlorination stages of a WWTP. Analytical method involved solid-phase extraction followed by liquid chromatographic determination. Removal efficiencies during sedimentation were generally positive with doxycycline achieving 80-95.8%, while negative removal efficiencies were observed for penicillin V (-46.4 to -17.1%) and trimethoprim (-26.2 to -18.9%). The aeration and agitation stage resulted in concentration enhancement for several antibiotics with seven of them ranging between -273 and -15.5%. This stage was responsible for the relatively low overall removal efficiencies in which only 4 antibiotics (doxycycline, tetracycline, ciprofloxacin, and erythromycin) experienced overall removal efficiencies above 50%. The recorded effluent concentrations ranging between 0.0130 and 0.383 ng/mL were translated to low potential for development of antibiotic resistance genes in the receiving environments while ecotoxicity risk was high for only amoxicillin, ampicillin and sulfapyridine. The study has provided an overview of the performance of common wastewater treatment processes in South Africa and hopes that more monitoring and environmental risk data can be made available towards drafting of antibiotic priority lists that cater for Africa.

Co-selection for antibiotic resistance by environmental contaminants

The environment is increasingly recognised as a hotspot for the selection and dissemination of antibiotic resistant bacteria and antibiotic resistance genes. These can be selected for by antibiotics and non-antibiotic agents (such as metals and biocides), with the evidence to support this well established by observational and experimental studies. However, there is emerging evidence to suggest that plant protection products (such as herbicides), and non-antibiotic drugs (such as chemotherapeutic agents), can also co-select for antibiotic resistance. This review aims to provide an overview of four classes of non-antibiotic agents (metals, biocides, plant protection products, and non-antibiotic drugs) and how they may co-select for antibiotic resistance, with a particular focus on the environment. It also aims to identify key knowledge gaps that should be addressed in future work, to better understand these potential co-selective agents.

Antibiotic resistance determinants among carbapenemase producing bacteria isolated from wastewaters of Kathmandu, Nepal

The emergence of carbapenem resistant bacteria (CRB) possesses a remarkable threat to the health of humans. CRB and carbapenem resistance genes (CRGs) have frequently been reported in clinical isolates from hospitals, however, their occurrence and distribution in wastewaters from various sources and river water have not been emphasized in Nepal. So, this study aimed to detect carbapenem resistant bacterial isolates and their resistance determinants in river water and different types of wastewaters. River water and both untreated and treated wastewater samples from hospitals, pharmaceutical industries, and municipal sewage were collected in summer and winter seasons. From 68 grab wastewater samples, CRB were detected only in 16 samples, which included eight hospital wastewater, and four each from untreated municipal sewage and river water. A total of 25 CRB isolates were detected with dominance of E. coli (44.0%) and K. pneumoniae (24.0%). The majority of the isolates harbored blaNDM-1 (76.0%), followed by blaOXA (36.0%) and blaKPC (20.0%) genes. Hospital wastewater majorly contributed to the presence of blaNDM-1, blaKPC, and blaOXA along with intI1 genes compared to river water and untreated municipal sewage, especially during the winter season. However, CRB were not detected in treated effluents of hospitals and municipal sewage, and both influents and effluents from pharmaceutical industries. The combined presence of each blaNDM-1 & blaOXA and blaKPC & blaOXA occurred in 16.0% of the bacterial isolates. The increased minimum inhibitory concentration (MIC) of meropenem was significantly associated with the presence of CRGs. The results of this study highlight the significance of carbapenem resistance in bacteria isolated from wastewater and river water, and underscore the necessity for efficient monitoring and control strategies to prevent the dispersion of carbapenem resistance in the environment and its potential consequences on human health.

The Mechanism of Tigecycline Resistance in Acinetobacter baumannii under Sub-Minimal Inhibitory Concentrations of Tigecycline

The presence of sub-minimal inhibitory concentration (sub-MIC) antibiotics in our environment is widespread, and their ability to induce antibiotic resistance is inevitable. Acinetobacter baumannii, a pathogen known for its strong ability to acquire antibiotic resistance, has recently shown clinical resistance to the last-line antibiotic tigecycline. To unravel the complex mechanism of A. baumannii drug resistance, we subjected tigecycline-susceptible, -intermediate, and -mildly-resistant strains to successive increases in sub-MIC tigecycline and ultimately obtained tigecycline-resistant strains. The proteome of both key intermediate and final strains during the selection process was analyzed using nanoLC-MS/MS. Among the more than 2600 proteins detected in all strains, we found that RND efflux pump AdeABC was associated with the adaptability of A. baumannii to tigecycline under sub-MIC pressure. qRT-PCR analysis also revealed higher expression of AdeAB in strains that can quickly acquire tigecycline resistance compared with strains that displayed lower adaptability. To validate our findings, we added an efflux pump inhibitor, carbonyl cyanide m-chlorophenyl hydrazine (CCCP), to the medium and observed its ability to inhibit tigecycline resistance in A. baumannii strains with quick adaptability. This study contributes to a better understanding of the mechanisms underlying tigecycline resistance in A. baumannii under sub-MIC pressure.

Dynamic responses of Salmonella Typhimurium to re-exposure to sublethal ciprofloxacin

This study was designed to evaluate the history-dependent behaviors of Salmonella Typhimurium re-exposed to sublethal levels of ciprofloxacin. The S. Typhimurium cells were pre-exposed to 0 (CON), 1/16 (LOW), 1/8 (MED), and 1/4 (HIGH) minimum inhibitory concentrations (MICs) of ciprofloxacin, followed by re-exposure to the same concentrations. The bacterial growth, postantibiotic effect (PAE), relative fitness, and swimming motility of treatments were evaluated in the absence of ciprofloxacin. The lag phase duration (LPD) was estimate to assess bacterial recovery under ciprofloxacin exposure. A disk diffusion assay was used to determine the cross-resistance and collateral sensitivity of CON, LOW, MED, and HIGH treatments to ciprofloxacin (CIP), ceftriaxone (CEF), erythromycin (ERY), gentamicin (GEN), and polymyxin B (POL). The S. Typhimurium cells pre-exposed to ciprofloxacin were susceptible in antibiotic-free media, showing delayed growth. The highest PAE (>1 h) and bacterial fluctuation (CV = 5%) were observed at the High treatment compared to the CON. The HIGH treatment had the lowest relative fitness levels (0.87) and swimming motility (55 mm). The LPD was significantly decreased at the LOW treatment (1.8 h) when re-exposed to 1/16 × MIC of ciprofloxacin. The LOW, MED, and HIGH treatments showed the cross-resistance to POL and the collateral sensitivity to CEF, ERY, and GEN. The pre-exposure to ciprofloxacin could induce phenotypic diversity, corresponding to the history-dependent behaviors. These results provide important insights for the dynamic nature of bacterial populations when re-exposed to sublethal concentrations of antibiotics.

Convergence of resistance and evolutionary responses in Escherichia coli and Salmonella enterica co-inhabiting chicken farms in China

Sharing of genetic elements among different pathogens and commensals inhabiting same hosts and environments has significant implications for antimicrobial resistance (AMR), especially in settings with high antimicrobial exposure. We analysed 661 Escherichia coli and Salmonella enterica isolates collected within and across hosts and environments, in 10 Chinese chicken farms over 2.5 years using data-mining methods. Most isolates within same hosts possessed the same clinically relevant AMR-carrying mobile genetic elements (plasmids: 70.6%, transposons: 78%), which also showed recent common evolution. Supervised machine learning classifiers revealed known and novel AMR-associated mutations and genes underlying resistance to 28 antimicrobials, primarily associated with resistance in E. coli and susceptibility in S. enterica. Many were essential and affected same metabolic processes in both species, albeit with varying degrees of phylogenetic penetration. Multi-modal strategies are crucial to investigate the interplay of mobilome, resistance and metabolism in cohabiting bacteria, especially in ecological settings where community-driven resistance selection occurs.

An update on the prevalence of colistin and carbapenem-resistant Gram-negative bacteria in aquaculture: an emerging threat to public health

Aquaculture has been recognized as a hotspot for the emergence and spread of antimicrobial resistance genes conferring resistance to clinically important antibiotics. This review gives insights into studies investigating the prevalence of colistin and carbapenem resistance (CCR) among Gram-negative bacilli in aquaculture. Overall, a high incidence of CCR has been reported in aquatic farms in several countries, with CCR being more prevalent among opportunistic human pathogens such as Acinetobacter nosocomialis, Shewanella algae, Photobacterium damselae, Vibrio spp., Aeromonas spp., as well as members of Enterobacteriaceae family. A high proportion of isolates in these studies exhibited wide-spectrum profiles of antimicrobial resistance, highlighting their multidrug-resistance properties (MDR). Several mobile colistin resistance genes (including, mcr-1, mcr-1.1, mcr-2, mcr-2.1, mcr-3, mcr-3.1, mcr-4.1, mcr-4.3, mcr-5.1, mcr-6.1, mcr-7.1, mcr-8.1, and mcr-10.1) and carbapenemase encoding genes (including, blaOXA-48, blaOXA-55, blaNDM, blaKPC, blaIMI, blaAIM, blaVIM, and blaIMP) have been detected in aquatic farms in different countries. The majority of these were carried on MDR Incompatibility (Inc) plasmids including IncA/C, and IncX4, which have been associated with a wide host range of different sources. Thus, there is a risk for the possible spread of resistance genes between fish, their environments, and humans. These findings highlight the need to monitor and regulate the usage of antimicrobials in aquaculture. A multisectoral and transdisciplinary (One Health) approach is urgently needed to reduce the spread of resistant bacteria and/or resistance genes originating in aquaculture and avoid their global reach.

Public health trends in neurologically relevant infections: a global perspective

Neuroinfectious diseases represent a growing threat to public health globally. Infections of the central nervous system remain challenging to diagnose and treat, partially driven by the fact that a high proportion of emerging pathogens are capable of causing neurological disease. Many of the trends driving the emergence of novel pathogens, including climate change, ecological degradation, urbanization, and global travel, have accelerated in recent years. These circumstances raise concern for the potential emergence of additional pathogens of pandemic potential in the coming years, necessitating a stronger understanding of the forces that give rise to the emergence and spread of neuroinvasive pathogens and a commitment to public health infrastructure to identify and treat these diseases. In this review, we discuss the clinical and epidemiological features of three types of emerging neuroinvasive pathogens of significant public health consequences that are emblematic of key ongoing trends in global health. We first discuss dengue viruses in the context of climate change, considering the environmental factors that allow for the expansion of the geographic range and seasonal population of the viruses' vector. We then review the rising prevalence of fungal meningitis secondary to medical tourism, a trend representative of the highly globalized nature of modern healthcare. Lastly, we discuss the increasing prevalence of antibiotic-resistant neurological infections driven by the intersection of antibiotic overuse in medical and agricultural settings. Taken together, the rising prevalence of these conditions necessitates a recommitment to investment in public health infrastructure focused on local and global infectious disease surveillance coupled with ongoing development of novel therapeutics and vaccines for emerging pathogens. Such emerging threats also obviate the need to address the root causes driving the emergence of novel infectious diseases, including a sustained effort to address anthropogenic climate change and environmental degradation.

Need for standardization in sub-lethal antibiotics research

While monitoring and managing resistant and persistent microbes is of utmost importance and should not be glossed over, one must also focus on mitigating the microbe's ability to cause harm. Exploring the concept of lowering or even suppressing the microbe's virulence with sub-Minimum Inhibitory Concentration (MIC) antibiotics holds promise and warrants further investigation. At present, such antibiotic concentrations have mostly been studied to cover the side-effects of gradient exposure, overlooking the possibility of utilizing them to influence not only bacterial virulence, but also colonization, fitness and collateral sensitivities. This review focuses on conflicting findings of studies demonstrating both increased and decreased virulence in microbes under sub-MIC antibiotic exposure. It identifies lack of standardization in this field of research as one of the main culprits for discordant results across numerous studies on virulence. It critically discusses important terminology related to bacterial traits and existing methods to determine MIC and sub-MIC ranges. Lastly, possible directions toward standardized sub-MIC profiling and thereby tailored treatment options in the future are explored.

Descriptive analyses of bacterial communities in marine sediment microcosms spiked with fish wastes, emamectin benzoate, and oxytetracycline

In marine sediments surrounding salmon aquaculture sites, organic matter (OM) enrichment has been shown to influence resident bacterial community composition; however, additional effects on these communities due to combined use of the sea-lice therapeutant emamectin benzoate (EMB) and the widely used antibiotic oxytetracycline (OTC) are unknown. Here, we use sediment microcosms to assess the influence of OM, EMB, and OTC on benthic bacterial communities. Microcosms consisted of mud or sand sediments enriched with OM (fish and feed wastes) and spiked with EMB and OTC at environmentally-relevant concentrations. Samples were collected from initial matrices at the initiation of the trial and after 110 days for 16 S rRNA gene sequencing of the V3-V4 region and microbiome profiling. The addition of OM in both mud and sand sediments reduced alpha diversities; for example, an average of 1106 amplicon sequence variants (ASVs) were detected in mud with no OM addition, while only 729 and 596 ASVs were detected in mud with low OM and high OM, respectively. Sediments enriched with OM had higher relative abundances of Spirochaetota, Firmicutes, and Bacteroidota. For instance, Spirochaetota were detected in sediments with no OM with a relative abundance range of 0.01-1.2%, while in sediments enriched with OM relative abundance varied from 0.16% to 26.1%. In contrast, the addition of EMB (60 ng/g) or OTC (150 ng/g) did not result in distinct taxonomic shifts in the bacterial communities compared to un-spiked sediments during the timeline of this experiment. EMB and OTC concentrations may have been below effective inhibitor concentrations for taxa in these communities; further work should explore gene content and the presence of antibiotic resistance genes (ARGs) in sediment-dwelling bacteria.

Environmental concentrations of antibiotics, biocides, and heavy metals fail to induce phenotypic antimicrobial resistance in Escherichia coli

Most anthropogenically affected environments contain mixtures of pollutants from different sources. The impact of these pollutants is usually the combined effect of the individual polluting constituents. However, how these stressors contribute to the development of antimicrobial resistance in environmental microorganisms is poorly understood. Thus, a 30-day exposure experiment to environmental and sub-inhibitory concentrations of oxytetracycline, amoxicillin, zinc, copper, BAC (benzalkonium chloride) 10 and DADMAC (diallyldimethylammonium chloride) 12, was conducted using fully susceptible E. coli ATCC 25922 to ascertain any development of phenotypic or genotypic resistance. Furthermore, wild-type isolates were collected from the same aquatic environment as the stressors, analysed for phenotypic resistance using the disk diffusion method and genotypically through whole genome sequencing. Exposure to the various concentrations and combinations of the stressors did not trigger phenotypic resistance in the experimental bacteria. Furthermore, genotypic analysis of the WGS on the exposed isolates only found the macrolide resistance mdf(A) gene (also present in the control strain) and the disinfectant resistance gene sitABCD. With further analysis for single nucleotide variants (SNV), mutations were detected for 19 genes that encoded for oxidative stress, DNA repair, membrane proteins efflux systems, growth and persister formations except for the robA, a transcription protein subset of the ArcC/XylS family of proteins, which confer multidrug resistance in E. coli. This indicates that exposure to sub-inhibitory concentrations of antibiotics, heavy metals and biocide residues in the aquatic environmental concentrations of the stressors identified in the current study could not induce phenotypic or genotypic resistance but encoded for genes responsible for the development of persistence and tolerance in bacteria, which could be a precursor to the development of resistance in environmental bacteria.

Spatial distribution of antibiotics and antibiotic resistance genes in tidal flat reclamation areas in China

Tidal flat areas are important resources for land development and are becoming antibiotic resistance receivers that trigger major health concerns. The spatial distributions of forty-nine antibiotics, nine antibiotic resistance genes (ARGs), one mobile gene element (MGE) gene, and nine available metals in the soils and sediments along the coastlines of the Yellow Sea in China were quantified. Hierarchical linear model analysis was used to explore relationships between the antibiotics and ARGs across multiple effects resulting from human activities and environmental factors. Fish farm sediments and farmland soils showed high levels of quinolones (QNs) (maximum 637 ng·g-1), sulfonamides (SAs) (maximum 221 ng·g-1), and corresponding ARGs. Significant positive correlations (P from 5.47 × 10-14 to 0.0487) were observed between the antibiotics (QNs, SAs, and chlortetracycline) and their corresponding ARGs (qnrA, qnrD, aac(6')-Ib-cr, dfrA, sul2, and tetA), indicating the selective pressure from antibiotics in soils and sediments. Nine available metals had positive correlations with at least one ARG, indicating heavy metal pollution could enhance the ARGs. Sheep and poultry husbandry and marine aquaculture contribute the most to the antibiotic resistance in the coastlines. In conclusion, antibiotic pollutions have promoting effects at sub-inhibitory concentrations and more attention should be given to inhibit the enrichment of ARGs during tidal flat reclamation processes. The study also suggests the induction effects from metal pollutions, MGE spread, and the antibiotic pollutions from the usage in livestock and aquaculture.

Occurrence and prevalence of antibiotics in wastewater treatment plants and effluent receiving rivers in South Africa using UHPLC-MS determination

The increased usage of antibiotics over the recent years has led to an increased interest in monitoring their presence in wastewater all over the world. In this study the occurrence of sixteen (16) selected antibiotics (amoxicillin, ampicillin, azithromycin, ciprofloxacin, doxycycline, erythromycin, gentamicin, metronidazole, norfloxacin, ofloxacin, penicillin, sulfamethoxazole, sulfapyridine, sulfamethizole, tetracycline and trimethoprim) were determined in two wastewater treatment plants and two effluent receiving rivers in Northern part of Pretoria, South Africa. Targeted screening and identification of antibiotics was done using ultra high-performance liquid chromatography coupled with mass spectrometry after sample clean-up and pre-concentration using solid phase extraction. The concentrations of the targeted antibiotics detected in influent samples ranged between 0.78 and 96.8 ng mL-1 and those in effluent were between 0.12 and 9.89 ng mL-1. The highest recorded concentrations in all samples were those of doxycycline (30.9-120 ng mL-1) and sulfamethoxazole (2.52-96.8 ng mL-1) in effluent and influent samples, respectively. The concentrations of antibiotics in the rivers receiving effluents were between 0.03 and 72.8 ng mL-1 in upstream samples and 0.008-76.8 ng mL-1 in downstream samples, indicating that there is other source of contaminate to these rivers other than the treatment plants. Risk assessment using the hazard quotients ranged between 0.24 and 889 indicating that the presence of these antibiotics and antibiotic mixtures posed higher ecological risks to aquatic organisms. From the study, it could be concluded that wastewater treatment plants were releasing antibiotics to the environment and posing a risk to the aquatic ecosystem and public health. Therefore, there is a need to research into developing more efficient conventional wastewater treatment technologies that can completely remove antibiotics from wastewater.

Water brownness regulates the bioavailability of a fluoroquinolone antibiotic: UV-absorbance as a predictor of ciprofloxacin ecotoxicity

Dissolved organic carbon (DOC) is a powerful regulator of the ecotoxicity of ciprofloxacin (CIP), a widely applied fluoroquinolone antibiotic. In this study, we investigated the impact of DOC from a variety of sources on CIP bioavailability, using a cyanobacteria growth inhibition test with Microcystis aeruginosa. We analyzed the impact from two perspectives: (1) DOC concentration, and (2) water brownness, defined in this work as the light absorbance of DOC solutions. The toxicity tests were conducted with (1) unprocessed freshwater DOC in the naturally occurring state, (2) DOC extracted from a freshwater stream (Schwarzbach stream, Küchelscheid, Belgium), and (3) the commercial DOC product Suwannee River organic matter. Across all DOC sources investigated, a strong negative correlation was observed between CIP ecotoxicity and light absorbance at four wavelengths across the ultraviolet-visible range (e.g., A350), whereas CIP ecotoxicity correlated poorly with the DOC concentration. In addition, the interactions between CIP and DOC were modelled as a CIP-DOC binding process to allow the quantification of the inhibitory effects of DOC on CIP toxicity via binding constants (Kd,CIPx, with x being the ionic charge + or +/-, L g-1). Processed DOC sources showed higher binding potency than most of the unprocessed DOC sources, suggesting that toxicity tests employing only processed DOC potentially overestimates the impact of DOC in natural environments. Nonetheless, the light absorption coefficient (i.e., ε350) appeared a reliable predictor of the Kd,CIP+/- (and thus of the potential of the DOC source to reduce ecotoxicity of CIP) of both processed and unprocessed DOC. The relationship can be further incorporated into model simulations to estimate CIP bioavailability in dynamic environments. It is concluded that the brownness of water is a better predictor of the impact of DOC on CIP bioavailability than the DOC concentration itself.

Rapid Isolation of Low-Level Carbapenem-Resistant E. coli from Water and Foods Using Glycan-Coated Magnetic Nanoparticles

Carbapenem-resistant Enterobacterales (CRE) are one of the major global issues needing attention. Among them, carbapenemase-producing (CP) E. coli strains are commonly found in clinical and biological samples. Rapid and cost-effective detection of such strains is critical in minimizing their deleterious impact. While promising progress is being made in rapid detection platforms, separation and enrichment of bacteria are required to ensure the detection of low bacterial counts. The current separation methods, such as centrifugation, filtration, electrophoresis, and immunomagnetic separation, are often tedious, expensive, or ineffective for clinical and biological samples. Further, the extraction and concentration of antimicrobial-resistant bacteria (ARB) are not well documented. Thus, this study assessed the applicability of cost-effective glycan-coated magnetic nanoparticles (gMNPs) for simple and rapid extraction of CP E. coli. The study included two resistant (R)strains: Klebsiella pneumoniae carbapenemase (KPC)-producing E. coli (R: KPC) and New Delhi metallo-β-lactamase (NDM)-producing E. coli (R: NDM). A susceptible E. coli (S) strain was used as a control, a reference bacterium. The gMNPs successfully extracted and concentrated E. coli (R) and E. coli (S) at low concentrations from large volumes of buffer solution, water, and food samples. The gMNPs concentrated up to two and five times their initial concentration for E. coli (R) and E. coli (S) in the buffer solution, respectively. In water and food samples, the concentration of E. coli (S) and E. coli (R) were similar and ranged 1-3 times their initial inoculation. A variation in the concentration from different food samples was seen, displaying the impact of food microstructure and natural microflora. The cost-effective and rapid bacterial cell capture by gMNPs was achieved in 15 min, and its successful binding to the bacterial cells in the buffer solution and food matrices was also confirmed using Transmission Electron Microscopy (TEM). These results show promising applications of gMNPs to extract pathogens and ARB from biological samples.

Potential selection and maintenance of manure-originated multi-drug resistant plasmids at sub-clinical concentrations for tetracycline family antibiotics

The goal of this study was to (a) determine the minimum selection concentrations of tetracycline family antibiotics necessary to maintain plasmids carrying tetracycline-resistant genes and (b) correlate these results to environmental hotspot concentrations reported in previous studies. This study used two plasmids (pT295A and pT413A) originating from dairy manure in a surrogate Escherichia coli host CV601. The minimum selection concentrations of antibiotics tested in nutrient-rich medium were determined as follows: 0.1 mg/L for oxytetracycline, 0.45 mg/L for chlortetracycline, and 0.13-0.25 mg/L for tetracycline. Mixing oxytetracycline and chlortetracycline had minimum selection concentration values increased 2-fold compared to those in single antibiotic tests. Minimum selection concentrations found in this study were lower than reported environmental hotspot concentrations, suggesting that tetracycline family antibiotics were likely to be the driver for the selection and maintenance of these plasmids. Relatively high plasmid loss rates (>90%) were observed when culturing a strain carrying a tetracycline-resistant plasmid in antibiotic-free nutrient-rich and nutrient-defined media. Overall, results suggested that these plasmids can be maintained at concentrations environmentally relevant in wastewater treatment plants, sewage, manure, and manured soil; however, they are unstable and easily lost in the absence of antibiotics.

Screening of priority antibiotics in Chinese seawater based on the persistence, bioaccumulation, toxicity and resistance

Antibiotics are emerging pollutants that have detrimental effects on both target and non-target organisms in the environment. However, current methods for environmental risk assessment primarily focus on the risk to non-target organisms in ecosystems, overlooking a crucial risk of antibiotics - the induction of resistance in targeted bacteria. To address this oversight, we have incorporated resistance (R) risk with persistence, bioaccumulation and toxicity (PBT) to establish a more comprehensive PBTR (persistence, bioaccumulation, toxicity, and resistance) framework for antibiotic-specific risk assessment. Using the PBTR framework, we evaluated 74 antibiotics detected in Chinese seawater from 2000 to 2021, and identified priority antibiotics. Our analysis revealed that the priority antibiotics with R risk accounted for the largest proportion (50% to 70%), followed by P risk (40% to 58%), T risk (16% to 35%) and B risk (0 to 13%). To further categorize these priority antibiotics, we assigned them a risk level according to their fulfillment of criteria related to P, B, T, and R. Antibiotics meeting all four indicators were classified as Grade I, representing the highest risk level. Grade II and Grade III were assigned to antibiotics meeting three or two indicators, respectively. Antibiotics meeting only one indicator were classified as Grade IV, representing the lowest risk level. The majority of priority antibiotics fell into Grade IV, indicating low risk (55% to 79%), followed by Grade III (16% to 45%). The highest risk antibiotic identified in this study was clindamycin (CLIN), categorized as Grade II, in the East China Sea. Our findings aligned with previous studies for 25 antibiotics, affirming the validity of the PBTR framework. Moreover, we identified 13 new priority antibiotics, highlighting the advancement of this approach. This study provides a feasible screening strategy and monitoring recommendations for priority antibiotics in Chinese seawater.

Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies

This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.

Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities

The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure-function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.

Towards monitoring of antimicrobial resistance in the environment: For what reasons, how to implement it, and what are the data needs?

Antimicrobial resistance (AMR) is a global threat to human and animal health and well-being. To understand AMR dynamics, it is important to monitor resistant bacteria and resistance genes in all relevant settings. However, while monitoring of AMR has been implemented in clinical and veterinary settings, comprehensive monitoring of AMR in the environment is almost completely lacking. Yet, the environmental dimension of AMR is critical for understanding the dissemination routes and selection of resistant microorganisms, as well as the human health risks related to environmental AMR. Here, we outline important knowledge gaps that impede implementation of environmental AMR monitoring. These include lack of knowledge of the 'normal' background levels of environmental AMR, definition of high-risk environments for transmission, and a poor understanding of the concentrations of antibiotics and other chemical agents that promote resistance selection. Furthermore, there is a lack of methods to detect resistance genes that are not already circulating among pathogens. We conclude that these knowledge gaps need to be addressed before routine monitoring for AMR in the environment can be implemented on a large scale. Yet, AMR monitoring data bridging different sectors is needed in order to fill these knowledge gaps, which means that some level of national, regional and global AMR surveillance in the environment must happen even without all scientific questions answered. With the possibilities opened up by rapidly advancing technologies, it is time to fill these knowledge gaps. Doing so will allow for specific actions against environmental AMR development and spread to pathogens and thereby safeguard the health and wellbeing of humans and animals.

A Review of Carbapenem Resistance in Enterobacterales and Its Detection Techniques

Infectious disease outbreaks have caused thousands of deaths and hospitalizations, along with severe negative global economic impacts. Among these, infections caused by antimicrobial-resistant microorganisms are a major growing concern. The misuse and overuse of antimicrobials have resulted in the emergence of antimicrobial resistance (AMR) worldwide. Carbapenem-resistant Enterobacterales (CRE) are among the bacteria that need urgent attention globally. The emergence and spread of carbapenem-resistant bacteria are mainly due to the rapid dissemination of genes that encode carbapenemases through horizontal gene transfer (HGT). The rapid dissemination enables the development of host colonization and infection cases in humans who do not use the antibiotic (carbapenem) or those who are hospitalized but interacting with environments and hosts colonized with carbapenemase-producing (CP) bacteria. There are continuing efforts to characterize and differentiate carbapenem-resistant bacteria from susceptible bacteria to allow for the appropriate diagnosis, treatment, prevention, and control of infections. This review presents an overview of the factors that cause the emergence of AMR, particularly CRE, where they have been reported, and then, it outlines carbapenemases and how they are disseminated through humans, the environment, and food systems. Then, current and emerging techniques for the detection and surveillance of AMR, primarily CRE, and gaps in detection technologies are presented. This review can assist in developing prevention and control measures to minimize the spread of carbapenem resistance in the human ecosystem, including hospitals, food supply chains, and water treatment facilities. Furthermore, the development of rapid and affordable detection techniques is helpful in controlling the negative impact of infections caused by AMR/CRE. Since delays in diagnostics and appropriate antibiotic treatment for such infections lead to increased mortality rates and hospital costs, it is, therefore, imperative that rapid tests be a priority.

Comprehensive micropollutant characterization of wastewater during Covid-19 crisis in 2020: Suspect screening and environmental risk prioritization strategy

Micropollutants monitoring in wastewater can serve as a picture of what is consuming society and how it can impact the aquatic environment. In this work, a suspect screening approach was used to detect the known and unknown contaminants in wastewater samples collected from two wastewater treatment plants (WWTPs) located in the Basque Country (Crispijana in Alava, and Galindo in Vizcaya) during two weekly sampling campaigns, which included the months from April to July 2020, part of the confinement period caused by COVID-19. To that aim, high-resolution mass spectrometry was used to collect full-scan data-dependent tandem mass spectra from the water samples using a suspect database containing >40,000 chemical substances. The presence of > 80 contaminants was confirmed (level 1) and quantified in both WWTP samples, while at least 47 compounds were tentatively identified (2a). Among the contaminants of concern, an increase in the occurrence of some compounds used for COVID-19 disease treatment, such as lopinavir and hydroxychloroquine, was observed during the lockdown. A prioritization strategy for environmental risk assessment was carried out considering only the compounds quantified in the effluents of Crispijana and Galindo WWTPs. The compounds were scored based on the removal efficiency, estimated persistency, bioconcentration factor, mobility, toxicity potential and frequency of detection in the samples. With this approach, 33 compounds (e.g. amantadine, clozapine or lopinavir) were found to be considered key contaminants in the analyzed samples based on their concentration, occurrence and potential toxicity. Additionally, antimicrobial (RQ-AR) and antiviral (EDRP) risk of certain compounds was evaluated, where ciprofloxacin and fluconazole represented medium risk for antibiotic resistance (1 > RQ-AR > 0.1) in the aquatic ecosystems. Regarding mixture toxicity, the computed sum of toxic unit values of the different effluents (> 1) suggest that interactions between the compounds need to be considered for future environmental risk assessments.

Induced development of oxytetracycline tolerance in bacterial communities from soil amended with well-aged cow manure

The use of animal manure as organic fertilizer is a common agricultural practice that can improve soil health and crop yield. However, antibiotics and their metabolites are often present in animal manure and, hence, in manure-amended soil. The aim of this study was to assess the induced development of oxytetracycline (OTC) tolerance in soil bacterial communities as a result of the addition of OTC to soil amended with well-aged cow manure. To this purpose, soil amended with well-aged cow manure was repeatedly - three times - spiked with different OTC concentrations (0, 2, 20, 60, 150, and 500 mg OTC kg^-1 dry weight soil, each time) according to a pollution-induced community tolerance (PICT) assay. The PICT detection phase was conducted in Biolog EcoPlates^TM in the presence of the following OTC concentration gradient in the wells: 0, 5, 20, 40, 60, and 100 mg L^-1. For all treatments, the application of OTC in the PICT selection phase resulted in lower values of bacterial metabolic activity (i.e., lower values of average well color development) in the PICT detection phase. A significant increase in OTC tolerance was observed in soil bacterial communities that had been exposed three times to ≥ 20 mg OTC kg^-1 DW soil during the PICT selection phase. In general, higher levels of OTC exposure during the PICT selection phase resulted in bacterial tolerance to higher OTC concentrations during the PICT detection phase, pointing to a dose-dependent induced tolerance. It is important to (i) rationalize the amount of antibiotics administered to livestock, and (ii) treat properly the antibiotic-containing manure before its application to agricultural soil as fertilizer.

Modeling Antibiotic Concentrations in the Vicinity of Antibiotic-Producing Bacteria at the Micron Scale

It is generally thought that antibiotics confer upon the producing bacteria the ability to inhibit or kill neighboring microorganisms, thereby providing the producer with a significant competitive advantage. Were this to be the case, the concentrations of emitted antibiotics in the vicinity of producing bacteria might be expected to fall within the ranges of MICs that are documented for a number of bacteria. Furthermore, antibiotic concentrations that bacteria are punctually or chronically exposed to in environments harboring antibiotic-producing bacteria might fall within the range of minimum selective concentrations (MSCs) that confer a fitness advantage to bacteria carrying acquired antibiotic resistance genes. There are, to our knowledge, no available in situ measured antibiotic concentrations in the biofilm environments that bacteria typically live in. The objective of the present study was to use a modeling approach to estimate the antibiotic concentrations that might accumulate in the vicinity of bacteria that are producing an antibiotic. Fick's law was used to model antibiotic diffusion using a series of key assumptions. The concentrations of antibiotics within a few microns of single producing cells could not reach MSC (8 to 16 μg/L) or MIC (500 μg/L) values, whereas the concentrations around aggregates of a thousand cells could reach these concentrations. The model outputs suggest that single cells could not produce an antibiotic at a rate sufficient to achieve a bioactive concentration in the vicinity, whereas a group of cells, each producing the antibiotic, could do so. IMPORTANCE It is generally assumed that a natural function of antibiotics is to provide their producers with a competitive advantage. If this were the case, sensitive organisms in proximity to producers would be exposed to inhibitory concentrations. The widespread detection of antibiotic resistance genes in pristine environments suggests that bacteria are indeed exposed to inhibitory antibiotic concentrations in the natural world. Here, a model using Fick's law was used to estimate potential antibiotic concentrations in the space surrounding producing cells at the micron scale. Key assumptions were that per-cell production rates drawn from the pharmaceutical manufacturing industry are applicable in situ, that production rates were constant, and that produced antibiotics are stable. The model outputs indicate that antibiotic concentrations in proximity to aggregates of a thousand cells can indeed be in the minimum inhibitory or minimum selective concentration range.

Trends in removal of pharmaceuticals in contaminated water using waste coffee and tea-based materials with their derivatives

The introduction of large amounts of pharmaceuticals into the environmental waters is well-documented in literature with their occurrence reported in all different water matrices accessible to humans and animals. At the same time, the increasing consumption of coffee and tea-based beverages results in the generation of solid waste, which is mostly disposed-off in the environment. To minimize environmental pollution, coffee and tea-based materials have been proposed as suitable options to remove pharmaceuticals in environmental waters. Therefore, this article provides a critical review on the preparation and applications of coffee and tea-based materials in removing pharmaceuticals from contaminated water. In this context, most studies in literature focused on the applications of these materials as adsorbents, while only limited work on their role in degradation of pharmaceuticals is discussed. The successful application in adsorption studies is attributed to high surface areas of adsorbents and the ability to easily modify the adsorbent surfaces by incorporating functional groups that provide additional oxygen atoms, which promote easy interactions with pharmaceuticals. Hence, the adsorption mechanisms are mostly described by hydrogen bonding, electrostatic and π-π interactions with sample pH playing a dominant role in the adsorption process. Overall, the present article focused on the developments, trends and future research direction on the preparations and applications of coffee and tea-based materials for efficient removal of pharmaceuticals in water. PRACTITIONER POINTS: Review of tea and coffee wastes application for removal of pharmaceuticals in water Key applications in adsorption and degradation of pharmaceuticals in water Removal mostly explained by hydrogen bonding, electrostatic, and π-π interactions Trends, gaps, and future research to be explored are reviewed and highlighted.

Structure and Microbiological Activity of 1H-benzo[d]imidazole Derivatives

Three new crystal structures of 1H-benzo[d]imidazole derivatives were determined. In the structures of these compounds, an identical system of hydrogen bonds, C(4), was observed. Solid-state NMR was applied for testing the quality of the obtained samples. All of these compounds were tested for in vitro antibacterial activity against Gram-positive bacteria and Gram-negative bacteria, as well as antifungal activity, by checking their selectivity. ADME calculations indicate that the compounds can be tested as potential drugs.

The Effects of Antibiotic Combination Treatments on Pseudomonas aeruginosa Tolerance Evolution and Coexistence with Stenotrophomonas maltophilia

The Pseudomonas aeruginosa bacterium is a common pathogen of cystic fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. While P. aeruginosa resistance evolution is well-characterized in monocultures, it is less well-understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-minimum inhibitory concentration (MIC) doses, both alone and in combination, shaped the tolerance evolution of P. aeruginosa (PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species, Stenotrophomonas maltophilia. The increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and, when combined, the selected antibiotics increased the MICs for all of the antibiotics. Though the presence of S. maltophilia did not affect the tolerance or the MIC evolution, it drove P. aeruginosa into extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast, P. aeruginosa dominated and drove S. maltophilia extinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multispecies communities. IMPORTANCE Cystic fibrosis (CF) is a genetic condition that results in thick mucus secretions in the lungs that are susceptible to chronic bacterial infections. The bacterial pathogen Pseudomonas aeruginosa is often associated with morbidity in CF and is difficult to treat due to its high resistance to antibiotics. The resistance evolution of Pseudomonas aeruginosa is poorly understood in polymicrobial infections that are typical of CF. To study this, we exposed P. aeruginosa to sublethal concentrations of ciprofloxacin, colistin, or tobramycin antibiotics in the absence and presence of a commonly co-occurring CF species, Stenotrophomonas maltophilia. We found that low-level antibiotic concentrations selected for high-level antibiotic resistance. While P. aeruginosa dominated in most antibiotic treatments, S. maltophilia drove it into extinction in the presence of tobramycin due to an innately higher tobramycin resistance. Our findings suggest that, besides driving high-level antibiotic tolerance evolution, sublethal antibiotic exposure can magnify competition in bacterial communities, which can lead to target pathogen extinctions in multispecies communities.

Exploring the in situ evolution of nitrofurantoin resistance in clinically derived uropathogenic Escherichia coli isolates

BACKGROUND

Nitrofurantoin has been re-introduced as a first-choice antibiotic to treat uncomplicated acute urinary tract infections in England and Wales. Highly effective against common uropathogens such as Escherichia coli, its use is accompanied by a low incidence (<10%) of antimicrobial resistance. Resistance to nitrofurantoin is predominantly via the acquisition of loss-of-function, step-wise mutations in the nitroreductase genes nfsA and nfsB.

OBJECTIVE

To explore the in situ evolution of NitR in E. coli isolates from 17 patients participating in AnTIC, a 12-month open label randomized controlled trial assessing the efficacy of antibiotic prophylaxis in reducing urinary tract infections (UTIs) incidence in clean intermittent self-catheterizing patients.

METHODS

The investigation of NitR evolution in E. coli used general microbiology techniques and genetics to model known NitR mutations in NitSE. coli strains.

RESULTS

Growth rate analysis identified a 2%-10% slower doubling time for nitrofurantoin resistant strains: NitS: 20.8 ± 0.7 min compared to NitR: 23 ± 0.8 min. Statistically, these data indicated no fitness advantage of evolved strains compared to the sensitive predecessor (P-value = 0.13). Genetic manipulation of E. coli to mimic NitR evolution, supported no fitness advantage (P-value = 0.22). In contrast, data argued that a first-step mutant gained a selective advantage, at sub-MIC (4-8 mg/L) nitrofurantoin concentrations.

CONCLUSION

Correlation of these findings to nitrofurantoin pharmacokinetic data suggests that the low incidence of E. coli NitR, within the community, is driven by urine-based nitrofurantoin concentrations that selectively inhibit the growth of E. coli strains carrying the key first-step loss-of-function mutation.

Pheromone Activity after Stimulation with Ampicillin in a Plasmid-Free Enterococcus faecalis Strain

Enterococci exhibit clumping under the selective pressure of antibiotics. The aim of this study was to analyze the effect of supernatants from a plasmid-free clone (C29) of Enterococcus faecalis subjected to 0.25×, 0.5×, and 0.75× of the minimal inhibitory concentration (MIC) of ampicillin on the expression of an aggregation substance (AS) by a donor plasmid clone (1390R). A clumping assay was performed. The relative expression of prgB (gene that encodes AS) was determined and semiquantified in 1390R, and iad1 expression was determined and semiquantified in C29. AS expression was analyzed in the stimulated 1390R cells by confocal microscopy, flow cytometry, and ELISA. Adherence was also measured. Maximal clumping was observed with the pheromone medium 0.25×. Only the 1390R strain stimulated with the C29 supernatant without ampicillin and with 0.25× was able to express prgB. No expression of prgB was observed at 0.5× and 0.75×. The difference in relative expression (RE) of 1390R without ampicillin and with 0.25× was 0.5-fold. AS expression in 1390R showed the greatest increase upon stimulation with 0.25×. When 1390R was stimulated with 0.5× and 0.75×, AS expression was also observed but was significantly lower. Ampicillin stimulated C29 switch-off pheromone expression in recipient cells, which in turn switched off AS expression in donor cells. We observed that although prgB was switched off after 0.5× stimulation in C29, the supernatants induced expression in certain 1390R strains. In conclusion, ampicillin was able to modulate pheromone expression in free plasmid clones which, in turn, modulated AS expression in plasmid donor cells. The fact that PrgB gene expression was switched off after the ampicillin stimulus at 0.5× MIC, whereas AS proteins were present on the surface of the bacteria, suggested that a mechanism of rescue associated with mechanism pheromone sensing may be involved.

Antibiotic resistant bacteria: A bibliometric review of literature

Antibiotic-resistant bacteria (ARB) are a serious threat to the health of people and the ecological environment. With this problem becoming more and more serious, more countries made research on the ARB, and the research number has been sharply increased particularly over the past decade. Therefore, it is quite necessary to globally retrace relevant researches on the ARB published from 2010 to 2020. This will help researchers to understand the current research situation, research trends and research hotspots in this field. This paper uses bibliometrics to examine publications in the field of ARB from 2010 to 2020 that were retrieved from the Web of Science (WOS). Our study performed a statistical analysis of the countries, institutions, journals, authors, research areas, author keywords, Essential Science Indicators (ESI) highly cited papers, and ESI hotspots papers to provide an overview of the ARB field as well as research trends, research hotspots, and future research directions in the field. The results showed that the number of related studies is increasing year by year; the USA is most published in the field of ARB; China is the most active in this field in the recent years; the Chinese Acad Sci published the most articles; Sci. Total Environ. published the greatest number of articles; CM Manaia has the most contributions; Environmental Sciences and Ecology is the most popular research area; and "antibiotic resistance," "antibiotics," and "antibiotic resistance genes" were the most frequently occurring author keywords. A citation analysis showed that aquatic environment-related antibiotic resistance is a key research area in this field, while antimicrobial nanomaterial-related research is a recent popular topic.

Virulence Genes and In Vitro Antibiotic Profile of Photobacterium damselae Strains, Isolated from Fish Reared in Greek Aquaculture Facilities

Bacteria belonging to the species Photobacterium damselae are pathogens of cultured marine fish, causing diseases of high importance, such as Pasteurellosis. Thus, they are considered a major threat to the aquaculture sector. Despite the great importance of fish mariculture for the Greek economy, the distribution and abundance of these bacteria are not well documented in aquaculture units in Greece. Keeping this in mind, the scope of the present study was to investigate the presence, antibiotic profile, and virulence of Photobacterium bacteria originating from a representative sample of mariculture units throughout Greece. Samples were collected from diseased fish belonging to three different cultured fish species, namely Sparus aurata, Dicentrarchus labrax, and Pagrus pagrus, from both the Aegean and the Ionian Sea. Tissue samples were cultured in agar media, and bacteria were molecularly identified using both bacterial universal and species-specific primer pairs for Photobacterium spp. Additionally, the identified strains were characterized for the presence of virulence genes as well as antibiotic profiles. According to the results, the aforementioned bacteria are distributed in the Greek aquaculture units and are characterized by high pathogenicity based on the abundance of virulence genes. Furthermore, the majority of the detected strains exhibit some level of antibiotic resistance. In summary, our results indicate the need for systematic surveillance and study of their antibiotic profiles in Greek aquaculture since these bacteria constitute a major threat to the sector.

Aquatic Environments as Hotspots of Transferable Low-Level Quinolone Resistance and Their Potential Contribution to High-Level Quinolone Resistance

The disposal of antibiotics in the aquatic environment favors the selection of bacteria exhibiting antibiotic resistance mechanisms. Quinolones are bactericidal antimicrobials extensively used in both human and animal medicine. Some of the quinolone-resistance mechanisms are encoded by different bacterial genes, whereas others are the result of mutations in the enzymes on which those antibiotics act. The worldwide occurrence of quinolone resistance genes in aquatic environments has been widely reported, particularly in areas impacted by urban discharges. The most commonly reported quinolone resistance gene, qnr, encodes for the Qnr proteins that protect DNA gyrase and topoisomerase IV from quinolone activity. It is important to note that low-level resistance usually constitutes the first step in the development of high-level resistance, because bacteria carrying these genes have an adaptive advantage compared to the highly susceptible bacterial population in environments with low concentrations of this antimicrobial group. In addition, these genes can act additively with chromosomal mutations in the sequences of the target proteins of quinolones leading to high-level quinolone resistance. The occurrence of qnr genes in aquatic environments is most probably caused by the release of bacteria carrying these genes through anthropogenic pollution and maintained by the selective activity of antimicrobial residues discharged into these environments. This increase in the levels of quinolone resistance has consequences both in clinical settings and the wider aquatic environment, where there is an increased exposure risk to the general population, representing a significant threat to the efficacy of quinolone-based human and animal therapies. In this review the potential role of aquatic environments as reservoirs of the qnr genes, their activity in reducing the susceptibility to various quinolones, and the possible ways these genes contribute to the acquisition and spread of high-level resistance to quinolones will be discussed.

Chemical characterization of riverine sediments affected by wastewater treatment plant effluent discharge

This study was aimed at assessing the contribution of wastewater treatment effluents to the contamination profile of the sediments of receiving waterways. Three wastewater treatment plants (WWTP) were addressed, encompassing different population equivalent sizes, urbanization degrees and treatment methods translating differences in expected contamination patterns. Within each WWTP system, the assessment targeted the effluent and sediment samples collected upstream and downstream the effluent discharge point; contaminants belonging to several concerning chemical classes (metals and metalloids; pesticides; pharmaceuticals and personal care products, PPCPs; and polycyclic aromatic hydrocarbons, PAHs) were quantified both in effluent and sediment samples. Clear associations between contaminants present in the effluent and corresponding sediment samples were not always verified. In fact, a noticeable difference between the number or abundance of contaminants detected in effluents and in sediments, suggesting that effluents are not always the most likely source (e.g. PAHs). However, sediment contaminants that were likely sourced by the effluents were also identified (e.g. PPCPs). Sediment analysis offers an important historical view of contamination, especially in flowing recipient ecosystems where any characterization over the water matrix is ephemeral and linking exclusively to the moment of sampling. Hence, sediments should be considered for the establishment of WWTP operational benchmarks regulating the emission of contaminants, which is currently focused mostly on effluent composition thus potentially over/underestimating the longer-term impact of effluent discharge in the recipient waterways.

Whole-genome sequencing for surveillance of fluoroquinolone resistance in rifampicin-susceptible tuberculosis in a rural district of Shanghai: A 10-year retrospective study

Background

Fluoroquinolones (FQs) are the most important second-line anti-tuberculosis (anti-TB) drugs, primarily used for the treatment of multidrug- or rifampicin-resistant TB (MDR/RR-TB). However, FQs are also commonly used to treat other bacterial infections. There are few published data on the rates of FQ resistance among rifampicin-susceptible TB.

Methods

We used whole-genome sequencing (WGS) to determine the prevalence of FQ resistance among rifampicin-susceptible TB in a rural district of Shanghai. This was a population-based retrospective study of all culture-positive pulmonary TB patients diagnosed in the Chongming district of Shanghai, China during 2009-2018.

Results

The rate of FQ resistance was 8.4% (29/345) among TB, 6.2% (20/324) among rifampicin-susceptible TB, and 42.9% (9/21) among MDR/RR-TB. Transmission of FQ-resistant strains was defined as strains differing within 12 single-nucleotide polymorphisms (SNPs) based on WGS. Among the rifampicin-susceptible TB, 20% (4/20) of FQ resistance was caused by the transmission of FQ-resistant strains and 45% (9/20) of FQ resistance was identified as hetero-resistance.

Conclusions

The prevalence of FQ resistance in rifampicin-susceptible TB was higher than expected in Shanghai. Both the transmission and the selection of drug-resistant strains drive the emergence of FQ resistance in rifampicin-susceptible TB isolates. Therefore, the WGS-based surveillance system for TB should be urgently established and the clinical awareness of the rational use of FQs for respiratory infections should be enhanced to prevent the premature occurrence of FQ resistance.