Detection of carbapenem resistance genes and cephalosporin, and quinolone resistance genes along with oqxAB gene in Escherichia coli in hospital wastewater: a matter of concern

Barriers and pathways to environmental surveillance of antibiotic resistance in middle- and low-income settings: a qualitative exploratory key expert study

BACKGROUND

Local and global surveillance of antibiotic resistance (ABR) has proven a challenge to implement effectively in low- and middleincome (LMI) settings. Environmental surveillance solutions are increasingly highlighted as a strategy to help overcome such problems, and thus to promote global health as well as the local management of ABR in LMI countries. While technical and scientific aspects of such solutions are being probed continuously, no study has investigated their practical feasibility.

OBJECTIVE

Explore practical barriers for environmental surveillance of ABR in LMI countries, and pathways for surveillance experts to manage these.

METHODS

To start charting this unknown territory, we conducted an explorative, qualitative interview study with key informants, applying a constructivist grounded theory approach to analyze the results.

RESULTS

Barriers were identified across infrastructural, institutional and social dimensions, and pathways to manage them were mostly counterproductive from an ABR management perspective, including avoiding entire regions, applying substandard methods and failing to include local collaborators.

CONCLUSION

The research community as well as international agencies, organizations and states have key roles and responsibilities for improving the prospects of feasible environmental ABR surveillance in LMI-settings.

An overview on the prevalence and potential impact of antimicrobials and antimicrobial resistance in the aquatic environment of India

India at present is one of the leading countries in antimicrobial drug production and use, leading to increasing antimicrobial resistance (AMR) and public health problems. Attention has mainly been focused on the human and food animals' contribution to AMR neglecting the potential contribution of the perceptibly degraded aquatic environment in India. The paper reviews the available published literature in India on the prevalence of antimicrobial residues and their dissemination pathways in wastewater of pharmaceutical industries, sewage treatment plants, hospitals, riverine, community pond water, and groundwater. The prevalence of antimicrobial residue concentration, pathogenic and non-pathogenic bacteria antimicrobial resistant bacteria (ARB), their drug resistance levels, and their specific antimicrobial resistant genes (ARGs) occurring in various water matrices of India have been comprehensively depicted from existing literature. The concentration of some widely used antimicrobials recorded from the sewage treatment plants and hospital wastewater and rivers in India has been compared with other countries. The ecotoxicological risk posed by these antimicrobials in the various water matrices in India indicated high hazard quotient (HQ) values for pharmaceutical effluents, hospital effluents, and river water. The degraded aquatic environment exhibited the selection of a wide array of co-existent resistant genes for antibiotics and metals. The review revealed improper use of antibiotics and inadequate wastewater treatment as major drivers of AMR contaminating water bodies in India and suggestion for containing the challenges posed by AMR in India has been proposed.

Effects of sewer biofilms on the degradability of carbapenems in wastewater using laboratory scale bioreactors

Carbapenems are last-resort antibiotics used to treat bacterial infections unsuccessfully treated by most common categories of antibiotics in humans. Most of their dosage is secreted unchanged as waste, thereby making its way into the urban water system. There are two major knowledge gaps addressed in this study to gain a better understanding of the effects of their residual concentrations on the environment and environmental microbiome: development of a UHPLC-MS/MS method of detection and quantification from raw domestic wastewater via direct injection and study of their stability in sewer environment during the transportation from domestic sewers to wastewater treatment plants. The UHPLC-MS/MS method was developed for four carbapenems: meropenem, doripenem, biapenem and ertapenem, and validation was performed in the range of 0.5-10 μg/L for all analytes, with limit of detection (LOD) and limit of quantification (LOQ) values ranging from 0.2-0.5 μg/L and 0.8-1.6 μg/L respectively. Laboratory scale rising main (RM) and gravity sewer (GS) bioreactors were employed to culture mature biofilms with real wastewater as the feed. Batch tests were conducted in RM and GS sewer bioreactors fed with carbapenem-spiked wastewater to evaluate the stability of carbapenems and compared against those in a control reactor (CTL) without sewer biofilms, over a duration of 12 h. Significantly higher degradation was observed for all carbapenems in RM and GS reactors (60 - 80%) as opposed to CTL reactor (5 - 15%), which indicates that sewer biofilms play a significant role in the degradation. First order kinetics model was applied to the concentration data along with Friedman's test and Dunn's multiple comparisons analysis to establish degradation patterns and differences in the degradation observed in sewer reactors. As per Friedman's test, there was a statistically significant difference in the degradation of carbapenems observed depending on the reactor type (p = 0.0017 - 0.0289). The results from Dunn's test indicate that the degradation in the CTL reactor was statistically different from that observed in either RM (p = 0.0033 - 0.1088) or GS (p = 0.0162 - 0.1088), with the latter two showing insignificant difference in the degradation rates observed (p = 0.2850 - 0.5930). The findings contribute to the understanding about the fate of carbapenems in urban wastewater and the potential application of wastewater-based epidemiology.

Prevalence and Abundance of Beta-Lactam Resistance Genes in Hospital Wastewater and Enterobacterales Wastewater Isolates

Antimicrobial resistance may develop in nature including in hospital wastewater through horizontal genetic transfer. Few studies were conducted on the antimicrobial resistance genes in hospital wastewater and wastewater isolates in Indonesia. The prevalence and abundance of beta-lactam resistance genes in hospital wastewater and Enterobacterales wastewater isolates were investigated. Twelve wastewater samples were collected from an influent wastewater treatment plant. Escherichia coli and Klebsiella pneumoniae were isolated from the wastewater samples by culture-based methods. DNA was extracted from wastewater samples and the isolates. Nineteen beta-lactam resistance genes were tested by a high throughput qRT-PCR method. blaGES and blaTEM were the most abundant genes detected in hospital wastewater and Escherichia coli, respectively (p < 0.001). The relative abundance of blaCMY_2, blaCTX-M5, blaCTX-M8, blaGES, blaNDM, and blaSHV11 in Klebsiella pneumoniae was higher than in the wastewater and Escherichia coli (p < 0.001; p = 0.006; p = 0.012; p < 0.001; p = 0.005; p < 0.001). Klebsiella pneumoniae might be associated with resistance to piperacillin/tazobactam, ceftriaxone, and cefepime (p < 0.001; p = 0.001; p < 0.001). In conclusion, ESBL genes showed higher abundance than carbapenemase genes in hospital wastewater samples. The ESBL-producing bacteria that were predominantly found in hospital wastewater may originate from clinical specimens. The culture-independent antibiotic resistance monitoring system might be developed as an early warning system for the increasing beta-lactam resistance level in clinical settings.

The crisis of carbapenemase-mediated carbapenem resistance across the human-animal-environmental interface in India

Carbapenems are the decision-making antimicrobials used to combat severe Gram-negative bacterial infections in humans. Carbapenem resistance poses a potential public health emergency, especially in developing countries such as India, accounting for high morbidity, mortality, and healthcare cost. Emergence and transmission of plasmid-mediated "big five" carbapenemase genes including KPC, NDM, IMP, VIM and OXA-48-type among Gram-negative bacteria is spiralling the issue. Carbapenemase-producing carbapenem-resistant organisms (CP-CRO) cause multi- or pan-drug resistance by co-harboring several antibiotic resistance determinants. In addition of human origin, animals and even environmental sites are also the reservoir of CROs. Spillage in food-chains compromises food safety and security and increases the chance of cross-border transmission of these superbugs. Metallo-β-lactamases, mainly NDM-1 producing CROs, are commonly shared between human, animal and environmental interfaces worldwide, including in India. Antimicrobial resistance (AMR) surveillance using the One Health approach has been implemented in Europe, the United-Kingdom and the United-States to mitigate the crisis. This concept is still not implemented in most developing countries, including India, where the burden of antibiotic-resistant bacteria is high. Lack of AMR surveillance in animal and environmental sectors underestimates the cumulative burden of carbapenem resistance resulting in the silent spread of these superbugs. In-depth indiscriminate AMR surveillance focusing on carbapenem resistance is urgently required to develop and deploy effective national policies for preserving the efficacy of carbapenems as last-resort antibiotics in India. Tracking and mapping of international high-risk clones are pivotal for containing the global spread of CP-CRO.

Characterization of cephalosporin and fluoroquinolone resistant Enterobacterales from Irish farm waste by whole genome sequencing

Background

The Enterobacterales are a group of Gram-negative bacteria frequently exhibiting extended antimicrobial resistance (AMR) and involved in the transmission of resistance genes to other bacterial species present in the same environment. Due to their impact on human health and the paucity of new antibiotics, the World Health Organization (WHO) categorized carbapenem resistant and ESBL-producing as critical. Enterobacterales are ubiquitous and the role of the environment in the transmission of AMR organisms or antimicrobial resistance genes (ARGs) must be examined in tackling AMR in both humans and animals under the one health approach. Animal manure is recognized as an important source of AMR bacteria entering the environment, in which resistant genes can accumulate.

Methods

To gain a better understanding of the dissemination of third generation cephalosporin and fluoroquinolone resistance genes between isolates in the environment, we applied whole genome sequencing (WGS) to Enterobacterales (79 E. coli, 1 Enterobacter cloacae, 1 Klebsiella pneumoniae, and 1 Citrobacter gillenii) isolated from farm effluents in Ireland before (n = 72) and after (n = 10) treatment by integrated constructed wetlands (ICWs). DNA was extracted using the MagNA Pure 96 system (Roche Diagnostics, Rotkreuz, Switzerland) followed by WGS on a MiSeq platform (Illumina, Eindhoven, Netherlands) using v3 chemistry as 300-cycle paired-end runs. AMR genes and point mutations were identified and compared to the phenotypic results for better understanding of the mechanisms of resistance and resistance transmission.

Results

A wide variety of cephalosporin and fluoroquinolone resistance genes (mobile genetic elements (MGEs) and chromosomal mutations) were identified among isolates that mostly explained the phenotypic AMR patterns. A total of 31 plasmid replicon types were identified among the 82 isolates, with a subset of them (n = 24), identified in E. coli isolates. Five plasmid replicons were confined to the Enterobacter cloacae isolate and two were confined to the Klebsiella pneumoniae isolate. Virulence genes associated with functions including stress, survival, regulation, iron uptake secretion systems, invasion, adherence and toxin production were identified.

Conclusion

Our study showed that antimicrobial resistant organisms (AROs) can persist even following wastewater treatment and could transmit AMR of clinical relevance to the environment and ultimately pose a risk to human or animal health.

Critical review of technologies for the on-site treatment of hospital wastewater: From conventional to combined advanced processes

This review aims to assess different technologies for the on-site treatment of hospital wastewater (HWW) to remove pharmaceutical compounds (PhCs) as sustances of emerging concern at a bench, pilot, and full scales from 2014 to 2020. Moreover, a rough characterisation of hospital effluents is presented. The main detected PhCs are antibiotics and psychiatric drugs, with concentrations up to 1.1 mg/L. On the one hand, regarding the presented technologies, membrane bioreactors (MBRs) are a good alternative for treating HWW with PhCs removal values higher than 80% in removing analgesics, anti-inflammatories, cardiovascular drugs, and some antibiotics. Moreover, this system has been scaled up to the pilot plant scale. However, some target compounds are still present in the treated effluent, such as psychiatric and contrast media drugs and recalcitrant antibiotics (erythromycin and sulfamethoxazole). On the other hand, ozonation effectively removes antibiotics found in the HWW (>93%), and some studies are carried out at the pilot plant scale. Even though, some families, such as the X-ray contrast media, are recalcitrant to ozone. Other advanced oxidation processes (AOPs), such as Fenton-like or UV treatments, seem very effective for removing pharmaceuticals, Antibiotic Resistance Bacteria (ARBs) and Antibiotic Resistance Genes (ARGs). However, they are not implanted at pilot plant or full scale as they usually consider extra reactants such as ozone, iron, or UV-light, making the scale-up of the processes a challenging task to treat high-loading wastewater. Thus, several examples of biological wastewater treatment methods combined with AOPs have been proposed as the better strategy to treat HWW with high removal of PhCs (generally over 98%) and ARGs/ARBs (below the detection limit) and lower spending on reactants. However, it still requires further development and optimisation of the integrated processes.

Antimicrobial Resistance Monitoring of Water Environments: A Framework for Standardized Methods and Quality Control

Antimicrobial resistance (AMR) is a grand societal challenge with important dimensions in the water environment that contribute to its evolution and spread. Environmental monitoring could provide vital information for mitigating the spread of AMR; this includes assessing antibiotic resistance genes (ARGs) circulating among human populations, identifying key hotspots for evolution and dissemination of resistance, informing epidemiological and human health risk assessment models, and quantifying removal efficiencies by domestic wastewater infrastructure. However, standardized methods for monitoring AMR in the water environment will be vital to producing the comparable data sets needed to address such questions. Here we sought to establish scientific consensus on a framework for such standardization, evaluating the state of the science and practice of AMR monitoring of wastewater, recycled water, and surface water, through a literature review, survey, and workshop leveraging the expertise of academic, governmental, consulting, and water utility professionals.

Carbapenemase producing Enterobacteriaceae: Environmental reservoirs as primary targets for control and prevention strategies

Carbapenemase-producing Enterobacteriaceae (CPE) have become one of the greatest public health challenges globally. In the past decade, antimicrobial resistance (AMR) was viewed as a clinical problem in many parts of the world; hence, the role and magnitude of the contribution of the environment were not well appreciated. This review article was done with online published articles extracted from different databases using search terms related to the work. Evidence has shown that there exists the presence of carbapenemase genes in the environment, consequently fuelling the dissemination with alarming consequences. CPE when acquired causes life-threatening infections in humans. The health and economic impact of these infections are numerous, including treatment failure due to limited therapeutic options which hamper the containment of infectious diseases, further contaminating the environment and worsening the public health challenge. It is a well-known fact that the rate of emergence of resistant genes has outpaced the production of new antimicrobial agents, so it is pertinent to institute effective environmental measures to combat the spread of AMR organisms before it will completely gain a foothold and take us back to 'the pre-antibiotic era'. Environmental sources and reservoirs of resistant genes should therefore be amongst the primary targets for the control and prevention of the spread of resistant genes in the environment. This calls for the effective implementation of the 'one health' strategy with stakeholders committed to the design and enforcement of environmental mitigation policies and guidelines.

Temporal Variation of Meropenem Resistance in E. coli Isolated from Sewage Water in Islamabad, Pakistan

The WHO has classified carbapenem-resistant Enterobacteriaceae in most critical priority pathogens that pose a threat to human health. The present study investigated the prevalence of meropenem-resistant Escherichia coli (E. coli) in relation to its temporal variation in different seasons along with its resistance markers in sewage water. E. coli was selected on MacConkey agar containing meropenem (3 µg/mL). There were 27% of sites/sewage samples carrying meropenem-resistant E. coli. All E. coli were confirmed through the amplification of the uidA gene. All isolated E. coli were multidrug-resistant (MDR), and among them, 51% were extensively drug-resistant (XDR). An antibiogram determined against 15 antibiotics showed the highest resistance to ampicillin and cefotaxime (98% each) and lowest resistance to fosfomycin (2%). Phylogenetic groups and resistance gene analysis through PCR showed a significant co-occurrence of carbapenemases with extended spectrum beta lactamases (ESBLs), plasmid encoded quinolone, and colistin resistance genes. The higher number of resistance genes in E. coli isolates in community sewage indirectly indicate that these isolates circulate abundantly in the community.

Genetic diversity and multidrug resistance of phylogenic groups B2 and D in InPEC and ExPEC isolated from chickens in Central China

BACKGROUND

Avian colibacillosis is an infectious bacterial disease caused by avian pathogenic Escherichia coli (APEC). APEC causes a wide variety of intestinal and extraintestinal infections, including InPEC and ExPEC, which result in enormous losses in the poultry industry. In this study, we investigated the prevalence of InPEC and ExPEC in Central China, and the isolates were characterized using molecular approaches and tested for virulence factors and antibiotic resistance.

RESULTS

A total of 200 chicken-derived E. coli isolates were collected for study from 2019 and 2020. The prevalence of B2 and D phylogenic groups in the 200 chicken-derived E. coli was verified by triplex PCR, which accounted for 50.53% (48/95) and 9.52% (10/105) in ExPEC and InPEC, respectively. Additionally, multilocus sequence typing method was used to examine the genetic diversity of these E. coli isolates, which showed that the dominant STs of ExPEC included ST117 (n = 10, 20.83%), ST297 (n = 5, 10.42%), ST93 (n = 4, 8.33%), ST1426 (n = 4, 8.33%) and ST10 (n = 3, 6.25%), while the dominant ST of InPEC was ST117 (n = 2, 20%). Furthermore, antimicrobial susceptibility tests of 16 antibiotics for those strains were conducted. The result showed that more than 60% of the ExPEC and InPEC were resistant to streptomycin and nalidixic acid. Among these streptomycin resistant isolates (n = 49), 99.76% harbored aminoglycoside resistance gene strA, and 63.27% harbored strB. Among these nalidixic acid resistant isolates (n = 38), 94.74% harbored a S83L mutation in gyrA, and 44.74% harbored a D87N mutation in gyrA. Moreover, the prevalence of multidrug-resistant (MDR) in the isolates of ExPEC and InPEC was 31.25% (15/48) and 20% (2/10), respectively. Alarmingly, 8.33% (4/48) of the ExPEC and 20% (2/10) of the InPEC were extensively drug-resistant (XDR). Finally, the presence of 13 virulence-associated genes was checked in these isolates, which over 95% of the ExPEC and InPEC strains harbored irp2, feoB, fimH, ompT, ompA. 10.42% of the ExPEC and 10% of the InPEC were positive for kpsM. Only ExPEC isolates carried ibeA gene, and the rate was 4.17%. All tested strains were negative to LT and cnf genes. The carrying rate of iss and iutA were significantly different between the InPEC and ExPEC isolates (P < 0.01).

CONCLUSIONS

To the best of our knowledge, this is the first report on the highly pathogenic groups of InPEC and ExPEC in Central China. We find that 50.53% (48/95) of the ExPEC belong to the D/B2 phylogenic group. The emergence of XDR and MDR strains and potential virulence genes may indicate the complicated treatment of the infections caused by APEC. This study will improve our understanding of the prevalence and pathogenicity of APEC.

High carriage of plasmid-mediated quinolone resistance (PMQR) genes by cefotaxime-resistant Escherichia coli recovered from surface-leaking sanitary sewers

There is a rapid rise in the incidence of quinolone resistant bacteria in Nigeria. Most studies in Nigeria have focused on isolates from the clinical settings, with few focusing on isolates of environmental origin. This study aimed to investigate the antibiogram and carriage of plasmid-mediated quinolone resistance (PMQR) genes by quinolone-resistant isolates obtained from a pool of cefotaxime-resistant Escherichia coli (E. coli) recovered from sewage leaking out of some surface-leaking sanitary sewers in a University community in Nigeria. Isolation of E. coli from the sewage samples was done on CHROMagar E. coli, after enrichment of the samples was done in Brain Heart Infusion broth amended with 6 µg/mL of cefotaxime. Identification of presumptive E. coli was done using molecular methods (detection of uidA gene), while susceptibility to antibiotics was carried out using the disc diffusion method. Detection of PMQR genes (qnrA, qnrB, qnrS, aac(6')-lb-cr, qepA and oqxAB) was carried out using primer-specific PCR. A total of 32 non-repetitive cefotaxime-resistant E. coli were obtained from the sewage, with 21 being quinolone-resistant. The quinolone-resistant isolates showed varying level of resistance to the tested antibiotics, with imipenem being the only exception with 0% resistance. The PMQR genes: aac(6')-lb-cr, qnrA, qnrB, qnrS and qepA and oqxAB were detected in 90.5%, 61.9%, 47.6%, 38.1%, 4.8% and 0% respectively of the isolates. The findings of this study showed a high level of resistance to antibiotics and carriage of PMQR genes by quinolone-resistant E. coli obtained from the leaking sanitary sewers, suggesting a potential environmental and public health concern.

Elucidating the resistance repertoire, biofilm production, and phylogenetic characteristics of multidrug-resistant Escherichia coli isolated from community ponds: A study from West Bengal, India

This study details about the phenotypic and molecular characteristics of multidrug-resistant (MDR) Escherichia coli in the fresh community pond water (n = 257) collected from three districts of West Bengal, India. In total, 57 isolates were MDR of which 38 emerged as extended spectrum and 7 as AmpC-type β-lactamase producers in phenotypic assay. Among β-lactamase genes, blaCTXM-1was predominant (87.71%) followed by blaAmpC (77.2%) and blaTEM-1 (22.8%). Six MDR strains carried metallo-β-lactamase (MBL, blaNDM-1) gene. Tissue culture plate assay confirmed strong biofilm (SP) production in four MDR and one non-MDR isolates. In PCR-based replicon typing (PBRT), multiple plasmids of diverse replicon types (Frep, FIB, I1, FIA, K/B, HI1, and Y) were identified. The enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR)-based phylogenetic analysis revealed a high degree of genetic divergence among the MDR isolates. Multiplex PCR-based phylogrouping categorized 11 isolates as virulent (B2/D/F), which carried blaCTXM-1 gene and three had blaNDM-1 gene. Relative transcriptional activity of AcrAB efflux pump was significantly elevated among the SP and MBL producers. The presence of MDR E. coli isolates, particularly those resistant to carbapenem, in pond water used for daily domestic and household work, is a cause of concern as these pathogens may sneak into human food chain causing life-threatening infections. PRACTITIONER POINTS: Multidrug-resistant biofilm producing E. coli isolated from community pond water. A few of them were carbapenem-resistant and belonged to virulent (B2/D) types. Expression of AcrAB efflux pumps was found significantly elevated among biofilm producers and carbapenem-resistant population.

Prevalence of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in wastewater: a systematic review and meta-analysis

Wastewater is considered a hotspot niche of multi-drug and pathogenic bacteria such as Enterobacteriaceae-producing extended-spectrum beta-lactamases (ESBL-E). Thus, the aim of this meta-analysis was to evaluate the prevalence of ESBL-E in different wastewater sources. Different databases (Medline, EMBASE, and Cochrane Library) were searched from inception to March 2021. Data were analyzed using random-effects modeling, and subgroup and meta-regression analyses were used to ascertain heterogeneity among the subgroups. Fifty-seven observational studies were selected, and the pooled prevalence of ESBL-E in wastewater was 24.81% (95% CI, 19.28-30.77). Escherichia coli had the highest ESBL prevalence. The blaCTX-M genes were the most prevalent in the selected studies (66.56%). The pooled prevalence of ESBL was significantly higher in reports from America (39.91%, 95% CI, 21.82-59.51) and reports studying hospital and untreated wastewaters (33.98%, 95% CI, 23.82-44.91 and 27.36%, 95% CI, 19.12-36.42). Overall, this meta-analysis showed that the prevalence of ESBL-E in wastewater is increasing over time and that hospital wastewater is the most important repository of ESBL-E. Therefore, there is a need for developing new sewage treatment systems that decrease the introduction of resistant bacteria and antibiotic residues.

Prevalence and Absolute Quantification of NDM-1: a β-Lactam Resistance Gene in Water Compartment of Lakes Surrounding Hyderabad, India

NDM-1(New Delhi Metallo-beta-lactamase-1) is considered an emerging environmental contaminant, which causes severe hazards for public health. The abuse of antimicrobials for public health and veterinary use could favor the proliferation of resistance in bacteria. In this study, screening and absolute quantification of the NDM-1 in 17 water samples collected from a different sampling location surrounding Hyderabad, India performed using a real-time quantitative polymerase chain reaction (qPCR). Absolute quantification achieved by running the isolated DNA (Deoxy-ribonucleic acid) samples from different water bodies in triplicate with the known standards of the NDM-1 and results reported as gene copy number/ng(nanogram) of template DNA. All collected samples had shown a positive signal for the NDM-1 during qPCR analysis. Among the tested samples, the highest gene copy number/ng of template DNA was observed in the Mir Alam tank (985.74).  Further, based on pollution sources and observed data, a hierarchical clustering analysis was performed to categorize the different sampling locations and results presented in the form of a dendrogram.

Carbapenemase-producing Gram-negative bacteria in aquatic environments: a review

Antibiotic resistance is one of the greatest public-health challenges worldwide, especially with regard to Gram-negative bacteria (GNB). Carbapenems are the β-lactam antibiotics of choice with the broadest spectrum of activity and, in many cases, are the last-resort treatment for several bacterial infections. Carbapenemase-encoding genes, mainly carried by mobile genetic elements, are the main mechanism of resistance against carbapenems in GNB. These enzymes exhibit a versatile hydrolytic capacity and confer resistance to most β-lactam antibiotics. After being considered a clinical issue, increasing attention is being giving to the dissemination of such resistance mechanisms in the environment and especially through water. Aquatic environments are among the most significant microbial habitats on our planet, known as a favourable medium for antibiotic gene transfer, and they play a crucial role in the huge spread of drug resistance in the environment and the community. In this review, we present current knowledge regarding the spread of carbapenemase-producing isolates in different aquatic environments, which may help the implementation of control and prevention strategies against the spread of such dangerous resistant agents in the environment.

Investigating the impact of hospital antibiotic usage on aquatic environment and aquaculture systems: A molecular study of quinolone resistance in Escherichia coli

Quinolones are one of the most important classes of antibacterials available for the treatment of infectious diseases in humans. However, there is a growing concern about bacterial resistance to antimicrobials including quinolones. The spread of antibiotic-resistant bacteria in the aquatic environment has been recognized as a growing threat to public health and hospitals appear to be a major contributor to this. The objective of this study was to investigate the prevalence of quinolone resistance in Escherichia coli from selected water bodies receiving direct hospital effluents in Kerala, India. Standard disc diffusion and E-test were used for antibiotic susceptibility testing. As antibiotic resistance can develop in bacterial isolates by different means, EtBr Agar Cartwheel method was used to detect the efflux pump activity and presence of resistant genes was detected by PCR. The mechanism of transfer of plasmid mediated resistance was confirmed by conjugation experiments. A total of 209 multidrug-resistant Escherichia coli were isolated from different hospital effluent discharge sites and aquaculture farms located in their vicinity. Among them, qnrB was found to be most prevalent followed by qnrS, OqxAB, qnrA and aac (6')-Ib-cr. The results suggested that the antibiotics present at sub-inhibitory concentrations in direct hospital effluents increases the selection pressure impacting the cell function of even normal microorganisms in the aquatic environment to change the genetic expression of virulence factors or acquire resistance genes by different transfer mechanisms, posing a serious threat to public health.

Monitoring of Water Quality, Antibiotic Residues, and Antibiotic-Resistant Escherichia coli in the Kshipra River in India over a 3-Year Period

The emergence of antibiotic resistance is a major global and environmental health issue, yet the presence of antibiotic residues and resistance in the water and sediment of a river subjected to excessive anthropogenic activities and their relationship with water quality of the river are not well studied. The objectives of the present study were a) to investigate the occurrence of antibiotic residues and antibiotic-resistant Escherichia coli (E. coli) in the water and sediment of the Kshipra river in India at seven selected sites during different seasons of the years 2014, 2015, and 2016 and b) to investigate the association between antibiotic residues and antibiotic-resistant E. coli in water and sediment and measured water quality parameters of the river. Antibiotic residues and resistant E. coli were present in the water and sediment and were associated with the measured water quality parameters. Sulfamethoxazole was the most frequently detected antibiotic in water at the highest concentration of 4.66 µg/L and was positively correlated with the water quality parameters. Significant (p < 0.05) seasonal and spatial variations of antibiotic-resistant E. coli in water and sediment were found. The resistance of E. coli to antibiotics (e.g., sulfamethiazole, norfloxacin, ciprofloxacine, cefotaxime, co-trimoxazole, ceftazidime, meropenem, ampicillin, amikacin, metronidazole, tetracycline, and tigecycline) had varying associations with the measured water and sediment quality parameters. Based on the results of this study, it is suggested that regular monitoring and surveillance of water quality, including antibiotic residues and antibiotic resistance, of all rivers should be taken up as a key priority, in national and Global Action Plans as these can have implications for the buildup of antibiotic resistance.

Determination of carbapenems in water samples by UHPLC-MS/MS

A rapid and reliable method for the detection of five carbapenems (biapenem, imipenem, doripenem, meropenem, and faropenem) in water was developed and validated. After acidification of water samples with acetic acid, carbapenems were isolated using a Bond Elut PPL cartridge. The target compounds were separated using ultra high performance liquid chromatography with a chromatographic run time of 5 min and detected on a triple quadrupole mass spectrometer operated in positive electrospray ionization and multiple reaction monitoring mode. Mean recoveries were in the range of 76.6-106.5%, with satisfactory intraday and interday relative standard deviations lower than 10.0 and 10.8%, respectively. The limits of detection and quantification were in the ranges of 0.05-0.2 µg/L and 0.1-0.5 µg/L, respectively, depending on the analyte. The proposed method was applied to the analysis of river samples and wastewater samples from swine farms, and no carbapenems were detected in the collected samples.

Antibiotic resistant Klebsiella spp. from a hospital, hospital effluents and wastewater treatment plants in the uMgungundlovu District, KwaZulu-Natal, South Africa

Hospital effluents are crucial hotspots for the dissemination of antibiotic resistant microorganisms. This study analysed hospital effluent and proximate wastewater treatment plants for the presence of antibiotic resistant Klebsiella spp. Water samples were obtained twice over a three-month period from an urban and rural hospital at three effluent points each, and from two proximate wastewater treatment plants (WWTPs) comprising influent and effluent and river water samples up/downstream the WWTPs. Presumptive Klebsiella spp. were enumerated, isolated, and phenotypically confirmed using a well-established commercial test system for Enterobacteriaceae (API20E). Clinical Klebsiella pneumoniae isolates were provided by a hospital for comparison. The antibiotic resistance profiles of Klebsiella spp. isolates to 16 selected antibiotics were established according to EUCAST (European Committee on Antimicrobial Susceptibility Testing). In addition, extended spectrum β-lactamase (ESBL) and carbapenemase production was analysed. A total of 93 confirmed Klebsiella spp. isolates from hospital effluents and 37 from WWTPs were obtained, comprising K. pneumoniae and K. oxytoca. The viable counts for confirmed Klebsiella spp. for hospital effluents ranged from 1.38 × 10² to 1.03 × 10⁴, while those for WWTP influent were in a range of 1.76 × 10³ to 5.10 × 10³ CFU/ml. A higher proportion of Klebsiella spp. from urban hospital effluent was categorized as multidrug-resistant (MDR) (23%) compared to rural hospital effluent (9%). Resistance was observed to all antibiotic classes tested. Several clinical isolates presented resistance to four carbapenem antibiotics, while certain isolates from hospital effluent and WWTPs exhibited ertapenem and doripenem resistance. Fifteen Klebsiella spp. isolates (clinical and from urban hospital effluent) produced carbapenemases. Hospital effluents in South Africa contain antibiotic resistant Klebsiella spp. and may pose a risk to proximate informal communities if inadequately treated. Moreover, common phenotypic resistance profiles among isolates from the clinical-hospital effluent-wastewater works continuum suggest a need for further treatment of such effluent.

Detection of New Delhi metallo-beta-lactamase enzyme gene bla NDM-1 associated with the Int-1 gene in Gram-negative bacteria collected from the effluent treatment plant of a tuberculosis care hospital in Delhi, India

Background

Organisms possessing the bla_NDM-1 gene (responsible for carbapenem resistance) with a class-1 integron can acquire many other antibiotic resistance genes from the community sewage pool and become multidrug-resistant superbugs. In this regard, hospital sewage, which contains a large quantity of residual antibiotics, metals and disinfectants, is being recognized as a significant cause of antimicrobial resistance (AMR) origination and spread across the major centres of the world and is thus routinely investigated as a marker for tracing the origin of drug resistance. Therefore, in this study, an attempt has been made to identify and characterize the carbapenem-resistant microbes associated with integron genes amongst the organisms isolated from the effluent treatment plant (ETP) installed in a tertiary respiratory care hospital in Delhi, India.

Methods

One hundred and thirty-eight organisms belonging to Escherichia, Klebsiella, Pseudomonas and Acinetobacter spp. were collected from the incoming and outgoing sewage lines of the ETP. Carbapenem sensitivity and characterization was performed by the imipenem and imipenem-EDTA disc diffusion method. Later DNA extraction and PCR steps were performed for the Int-1 and bla_NDM-1 genes.

Results

Of the 138 organisms, 86 (62.3 %) were imipenem-resistant (P<0.05). One hundred and twenty-four (89.9 %) organisms had one or both of the genes. Overall, the bla_NDM-1 gene (genotypic resistance) was present in 71 % (98/138) of organisms. 53.6 % (74/138) organisms were double gene-positive (bla_NDM-1 + Int-1), of which 40 were producing the metallo-beta-lactamase enzyme, making up almost 28.9 % (40/138) of the collected organisms.

Conclusion

The current study strengthens the hypothesis that Carbapenem resistant organisms are in a high-circulation burden through the human gut and hospital ETPs are providing an environment for resistance origination and amplification.

Hospital wastewater treatment reduces NDM-positive bacteria being discharged into water bodies

New Delhi metallo-β-lactamase-1 (NDM-1) is a novel type of metallo-β-lactamase (MBL) associated with Enterobacteriaceae constitutes an important growing public health threat. The present study aims to characterize the NDM-1 producing Gram-negative bacteria (GNB) from the effluents of two tertiary care hospitals in Mangalore, South India and to profile their antibiotic resistance pattern. A total of 134 GNB were isolated from 30 hospital wastewater samples (treated and untreated) and analyzed. High-level resistance among untreated effluent sample was found toward nalidixic acid (74.52%), followed by cefotaxime (72.64%) and ampicillin (66.03%). Among the treated effluent isolates, the high resistance was found toward ampicillin (85.71%) followed by cefotaxime (85.71%) and piperacillin-tazobactam (53.57%). From untreated effluent isolates, 9 were NDM-1 positive by PCR; no isolates from treated effluent samples harbored bla_NDM-1 . Untreated hospital wastewater is found to be important reservoirs of antibiotic-resistant bacteria carrying bla_NDM-1 , and the presence of such bacteria in the effluents is a matter of great concern because they can contribute the antibiotic resistance to the natural environment. However, the absence of NDM in treated effluents emphasizes the importance of effluent treatment in reducing the dissemination of antibiotic-resistant bacteria. PRACTITIONER POINTS: Hospital wastewater is the important reservoir of antibiotic-resistant bacteria especially metallo-β-lactamase producers (NDM-1). Wastewater treatment procedures in hospitals reduce the NDM isolates in the treated effluent. Thereby reduces the risk of resistance spread in the environment.

Prevalence of Colistin-Resistant, Carbapenem-Hydrolyzing Proteobacteria in Hospital Water Bodies and Out-Falls of West Bengal, India

Indiscriminate use of antibiotics has resulted in a catastrophic increase in the levels of antibiotic resistance in India. Hospitals treat critical bacterial infections and thus can serve as reservoirs of multidrug resistant (MDR) bacteria. Hence, this study was conducted to gauge the prevalence patterns of MDR bacteria in hospital wastewater. Water samples collected from 11 hospitals and 4 environmental sources belonging to 5 most-densely populated districts of West Bengal, India were grown on MacConkey and Eosin Methylene Blue agar. A total of 84 (hospital-associated = 70, environmental water sources = 14) isolates were characterized. The predominant species found in water from hospital-associated areas (HAA) were Acinetobacter baumannii (22.9%), Escherichia coli (28.6 %), and Klebsiella pneumoniae (25.7%). Greater than 75% of the HAA isolates were found to be mcr-1 gene negative and colistinresistant. Meropenem non-susceptibility was also high among the HAA isolates at 58.6%, with the presence of the carbapenemase gene and bla_NDM in 67.1% of the non-susceptible isolates. Among the three predominant species, significantly higher numbers of E. coli isolates were found to be non-susceptible to meropenem ((80%), p-value = 0.00432) and amikacin (AK (90%), p-value = 0.00037). This study provides evidence for the presence of high numbers of colistin-resistant and carbapenem-hydrolyzing Proteobacteriain hospital wastewater.

Environmental Prevalence of Carbapenem Resistance Enterobacteriaceae (CRE) in a Tropical Ecosystem in India: Human Health Perspectives and Future Directives

In the past few decades, infectious diseases have become increasingly challenging to treat, which is explained by the growing number of antibiotic-resistant bacteria. Notably, carbapenem-resistant Enterobacteriaceae (CRE) infections at global level attribute a vast, dangerous clinical threat. In most cases, there are enormous difficulties for CRE infection except a few last resort toxic drugs such as tigecycline and colistin (polymyxin E). Due to this, CRE has now been categorized as one among the three most dangerous multidrug resistance (MDR) pathogens by the US Centres for Disease Control and Prevention (CDC). Considering this, the study of the frequency of CRE infections and the characterization of CRE is an important area of research in clinical settings. However, MDR bacteria are not only present in hospitals but are spreading more and more into the environment, thereby increasing the risk of infection with resistant bacteria outside the hospital. In this context, developing countries are a global concern where environmental regulations are often insufficient. It seems likely that overcrowding, poor sanitation, socioeconomic status, and limited infrastructures contribute to the rapid spread of MDR bacteria, becoming their reservoirs in the environment. Thus, in this review, we present the occurrence of CRE and their resistance determinants in different environmental compartments in India.

Human, animal and environmental contributors to antibiotic resistance in low-resource settings: integrating behavioural, epidemiological and One Health approaches

Antibiotic resistance (ABR) is recognized as a One Health challenge because of the rapid emergence and dissemination of resistant bacteria and genes among humans, animals and the environment on a global scale. However, there is a paucity of research assessing ABR contemporaneously in humans, animals and the environment in low-resource settings. This critical review seeks to identify the extent of One Health research on ABR in low- and middle-income countries (LMICs). Existing research has highlighted hotspots for environmental contamination; food-animal production systems that are likely to harbour reservoirs or promote transmission of ABR as well as high and increasing human rates of colonization with ABR commensal bacteria such as Escherichia coli However, very few studies have integrated all three components of the One Health spectrum to understand the dynamics of transmission and the prevalence of community-acquired resistance in humans and animals. Microbiological, epidemiological and social science research is needed at community and population levels across the One Health spectrum in order to fill the large gaps in knowledge of ABR in low-resource settings.

The nature and epidemiology of OqxAB, a multidrug efflux pump

Background

OqxAB efflux pump has been found to mediate multidrug resistance (MDR) in various bacteria over the past decades. The updates on the nature and epidemiology of OqxAB efflux pump need to be fully reviewed to broaden our understanding of this MDR determinant.

Methods

A literature search using the keyword of "oqxAB" was conducted in the online databases of Pubmed and ISI Web of Science with no restriction on the date of publication. The 87 publications were included into this review as references due to their close relevance to the nature and/or epidemiology of OqxAB efflux pump.

Results

The oqxAB gene generally locates on chromosome and/or plasmids flanked by IS26-like elements in clinical isolates of Enterobacteriaceae and Klebsiella pneumoniae, conferring low to intermediated resistance to quinoxalines, quinolones tigecycline, nitrofurantoin, several detergents and disinfectants (benzalkonium chloride, triclosan and SDS). It could co-spread with other antimicrobial resistance genes (bla _CTX-M, rmtB and aac(6')-Ib etc.), virulence genes and heavy metal resistance genes (pco and sil operons). Both RarA (activator) and OqxR (repressor) play important roles on regulation of the expression of OqxAB.

Conclusions

The dissemination of oqxAB gene may pose a great risk on food safety and public health. Further investigation and understanding of the natural functions, horizontal transfer, and regulation mechanism of the OqxAB efflux pump will aid in future strategies of antimicrobial usage.

The role of wildlife (wild birds) in the global transmission of antimicrobial resistance genes

Antimicrobial resistance is an urgent global health challenge in human and veterinary medicine. Wild animals are not directly exposed to clinically relevant antibiotics; however, antibacterial resistance in wild animals has been increasingly reported worldwide in parallel to the situation in human and veterinary medicine. This underlies the complexity of bacterial resistance in wild animals and the possible interspecies transmission between humans, domestic animals, the environment, and wildlife. This review summarizes the current data on expanded-spectrum β-lactamase (ESBL), AmpC β-lactamase, carbapenemase, and colistin resistance genes in Enterobacteriaceae isolates of wildlife origin. The aim of this review is to better understand the important role of wild animals as reservoirs and vectors in the global dissemination of crucial clinical antibacterial resistance. In this regard, continued surveillance is urgently needed worldwide.

Seasonal Variations in Water-Quality, Antibiotic Residues, Resistant Bacteria and Antibiotic Resistance Genes of Escherichia coli Isolates from Water and Sediments of the Kshipra River in Central India

OBJECTIVES

To characterize the seasonal variation, over one year, in water-quality, antibiotic residue levels, antibiotic resistance genes and antibiotic resistance in Escherichia coli isolates from water and sediment of the Kshipra River in Central India.

METHODS

Water and sediment samples were collected from seven selected points from the Kshipra River in the Indian city of Ujjain in the summer, rainy season, autumn and winter seasons in 2014. Water quality parameters (physical, chemical and microbiological) were analyzed using standard methods. High-performance liquid chromatography⁻tandem mass spectrometry was used to determine the concentrations of antibiotic residues. In river water and sediment samples, antibiotic resistance and multidrug resistance patterns of isolated E. coli to 17 antibiotics were tested and genes coding for resistance and phylogenetic groups were detected using multiplex polymerase chain reaction. One-way analysis of variance (ANOVA) and Fisher tests were applied to determine seasonal variation.

RESULTS

In river water, seasonal variation was significantly associated with various water quality parameters, presence of sulfamethoxazole residues, bacteria resistant to ampicillin, cefepime, meropenem, amikacin, gentamicin, tigecycline, multidrug resistance and CTX-M-1 gene. The majority of the Extended Spectrum Beta-Lactamase (ESBL)-producing E. coli isolates from river water and sediment in all different seasons belonged to phylogenetic group A or B1.

CONCLUSIONS

Antibiotic pollution, resistance and resistance genes in the Kshipra River showed significant seasonal variation. Guidelines and regulatory standards are needed to control environmental dissemination of these “pollutants” in this holy river.

Genomic Analysis of Hospital Plumbing Reveals Diverse Reservoir of Bacterial Plasmids Conferring Carbapenem Resistance

The hospital environment is a potential reservoir of bacteria with plasmids conferring carbapenem resistance. Our Hospital Epidemiology Service routinely performs extensive sampling of high-touch surfaces, sinks, and other locations in the hospital. Over a 2-year period, additional sampling was conducted at a broader range of locations, including housekeeping closets, wastewater from hospital internal pipes, and external manholes. We compared these data with previously collected information from 5 years of patient clinical and surveillance isolates. Whole-genome sequencing and analysis of 108 isolates provided comprehensive characterization of bla_KPC/bla_NDM-positive isolates, enabling an in-depth genetic comparison. Strikingly, despite a very low prevalence of patient infections with bla_KPC-positive organisms, all samples from the intensive care unit pipe wastewater and external manholes contained carbapenemase-producing organisms (CPOs), suggesting a vast, resilient reservoir. We observed a diverse set of species and plasmids, and we noted species and susceptibility profile differences between environmental and patient populations of CPOs. However, there were plasmid backbones common to both populations, highlighting a potential environmental reservoir of mobile elements that may contribute to the spread of resistance genes. Clear associations between patient and environmental isolates were uncommon based on sequence analysis and epidemiology, suggesting reasonable infection control compliance at our institution. Nonetheless, a probable nosocomial transmission of Leclercia sp. from the housekeeping environment to a patient was detected by this extensive surveillance. These data and analyses further our understanding of CPOs in the hospital environment and are broadly relevant to the design of infection control strategies in many infrastructure settings.

Carbapenemase-producing organisms (CPOs) are a global concern because of the morbidity and mortality associated with these resistant Gram-negative bacteria. Horizontal plasmid transfer spreads the resistance mechanism to new bacteria, and understanding the plasmid ecology of the hospital environment can assist in the design of control strategies to prevent nosocomial infections. A 5-year genomic and epidemiological survey was undertaken to study the CPOs in the patient-accessible environment, as well as in the plumbing system removed from the patient. This comprehensive survey revealed a vast, unappreciated reservoir of CPOs in wastewater, which was in contrast to the low positivity rate in both the patient population and the patient-accessible environment. While there were few patient-environmental isolate associations, there were plasmid backbones common to both populations. These results are relevant to all hospitals for which CPO colonization may not yet be defined through extensive surveillance.

The fate of carbapenem-resistant bacteria in a wastewater treatment plant

Wastewater treatment plants have been considered potential sources of antibiotic resistance gene exchange and release into the environment. The aim of our study was to quantify environmental and human-associated carbapenem-resistant bacterial populations (CRBPs) across wastewater treatment stages and correlate bacterial counts to physicochemical and other bacteriological parameters in order to see their behaviour in wastewater and sludge and their potential dissemination in the environment. Samples were taken from five sites (treatment stages) of the largest Croatian wastewater treatment plant (20 per site) over 10 months of monitoring. CRBPs were found at all wastewater treatment stages save for the lime-treated, stabilised sludge, which underlines the importance of effluent and digested sludge disinfection. Secondary sludge settling removed 99% of CRBP from the effluent, but the relative proportion of CRBP in the total bacterial count significantly increased in the effluent (0.0020%) and digested sludge (0.0019%) compared to the influent (0.0006%), indicating selection for resistant bacteria in these settings. CRBP counts did not correlate with measured carbapenem concentrations in wastewater, which suggests that antibiotic concentrations were not the reason for CRBP selection. Negative correlation between activated sludge retention time and CRBP indicated that their number could be reduced by increasing the retention time during secondary treatment. Despite the indications that WWTPs select for antibiotic-resistant bacteria, wastewater treatment is very efficient in reducing their absolute numbers, and proper effluent and sludge disinfection can significantly reduce dissemination of antibiotic-resistant bacteria into the environment.

Biomedical waste management guidelines 2016: What's done and what needs to be done

The latest biomedical waste (BMW) management guidelines which have been introduced in 2016 are simplified and made easier so that they can be easily followed by various health agencies. The categories of BMW have been reduced from ten (in 1998) to four in the latest (2016) guidelines. Many changes have been made in these latest guidelines, which have been summarised in the article below. The segregation of hospital waste plays a very important role, so the waste has to be sorted out at the source of generation according to the category to which it belongs as given in the newer guidelines. Newer waste treatment facilities such as plasma pyrolysis, encapsulation, inertisation have been introduced, and we have to do away with older facilities such as incineration as toxic fumes (dioxins and furans) are produced which are harmful to both health and environment. We can even think of using these wastewater treatment plants to remove the antimicrobial resistance genes during the processing of the waste, which is being generated from the hospitals.

Antibiotic Resistance and Antibiotic Resistance Genes in Escherichia coli Isolates from Hospital Wastewater in Vietnam

The environmental spread of antibiotic-resistant bacteria has been recognised as a growing public health threat for which hospitals play a significant role. The aims of this study were to investigate the prevalence of antibiotic resistance and antibiotic resistance genes (ARGs) in Escherichia coli isolates from hospital wastewater in Vietnam. Wastewater samples before and after treatment were collected using continuous sampling every month over a year. Standard disk diffusion and E-test were used for antibiotic susceptibility testing. Extended-spectrum beta-lactamase (ESBL) production was tested using combined disk diffusion. ARGs were detected by polymerase chain reactions. Resistance to at least one antibiotic was detected in 83% of isolates; multidrug resistance was found in 32%. The highest resistance prevalence was found for co-trimoxazole (70%) and the lowest for imipenem (1%). Forty-three percent of isolates were ESBL-producing, with the blaTEM gene being more common than blaCTX-M. Co-harbouring of the blaCTX-M, blaTEM and qepA genes was found in 46% of isolates resistant to ciprofloxacin. The large presence of antibiotic-resistant E. coli isolates combined with ARGs in hospital wastewater, even post-treatment, poses a threat to public health. It highlights the need to develop effective processes for hospital wastewater treatment plants to eliminate antibiotic resistant bacteria and ARGs.

A Three-Year Follow-Up Study of Antibiotic and Metal Residues, Antibiotic Resistance and Resistance Genes, Focusing on Kshipra-A River Associated with Holy Religious Mass-Bathing in India: Protocol Paper

BACKGROUND

Antibiotic resistance (ABR) is one of the major health emergencies for global society. Little is known about the ABR of environmental bacteria and therefore it is important to understand ABR reservoirs in the environment and their potential impact on health.

METHOD/DESIGN

Quantitative and qualitative data will be collected during a 3-year follow-up study of a river associated with religious mass-bathing in Central India. Surface-water and sediment samples will be collected from seven locations at regular intervals for 3 years during religious mass-bathing and in absence of it to monitor water-quality, antibiotic residues, resistant bacteria, antibiotic resistance genes and metals. Approval has been obtained from the Ethics Committee of R.D. Gardi Medical College, Ujjain, India (No. 2013/07/17-311).

RESULTS

The results will address the issue of antibiotic residues and antibiotic resistance with a focus on a river environment in India within a typical socio-behavioural context of religious mass-bathing. It will enhance our understanding about the relationship between antibiotic residue levels, water-quality, heavy metals and antibiotic resistance patterns in Escherichia coli isolated from river-water and sediment, and seasonal differences that are associated with religious mass-bathing. We will also document, identify and clarify the genetic differences/similarities relating to phenotypic antibiotic resistance in bacteria in rivers during religious mass-bathing or during periods when there is no mass-bathing.

Environmental pollution with antimicrobial agents from bulk drug manufacturing industries in Hyderabad, South India, is associated with dissemination of extended-spectrum beta-lactamase and carbapenemase-producing pathogens

PURPOSE

High antibiotic and antifungal concentrations in wastewater from anti-infective drug production may exert selection pressure for multidrug-resistant (MDR) pathogens. We investigated the environmental presence of active pharmaceutical ingredients and their association with MDR Gram-negative bacteria in Hyderabad, South India, a major production area for the global bulk drug market.

METHODS

From Nov 19 to 28, 2016, water samples were collected from the direct environment of bulk drug manufacturing facilities, the vicinity of two sewage treatment plants, the Musi River, and habitats in Hyderabad and nearby villages. Samples were analyzed for 25 anti-infective pharmaceuticals with liquid chromatography-tandem mass spectrometry and for MDR Gram-negative bacteria using chromogenic culture media. In addition, specimens were screened with PCR for bla _VIM, bla _KPC, bla _NDM, bla _IMP-1, and bla _OXA-48 resistance genes.

RESULTS

All environmental specimens from 28 different sampling sites were contaminated with antimicrobials. High concentrations of moxifloxacin, voriconazole, and fluconazole (up to 694.1, 2500, and 236,950 µg/L, respectively) as well as increased concentrations of eight other antibiotics were found in sewers in the Patancheru-Bollaram industrial area. Corresponding microbiological analyses revealed an extensive presence of extended-spectrum beta-lactamase and carbapenemase-producing Enterobacteriaceae and non-fermenters (carrying mainly bla _OXA-48, bla _NDM, and bla _KPC) in more than 95% of the samples.

CONCLUSIONS

Insufficient wastewater management by bulk drug manufacturing facilities leads to unprecedented contamination of water resources with antimicrobial pharmaceuticals, which seems to be associated with the selection and dissemination of carbapenemase-producing pathogens. The development and global spread of antimicrobial resistance present a major challenge for pharmaceutical producers and regulatory agencies.

Antibiotic Resistance in an Indian Rural Community: A 'One-Health' Observational Study on Commensal Coliform from Humans, Animals, and Water

Antibiotic-resistant bacteria are an escalating grim menace to global public health. Our aim is to phenotype and genotype antibiotic-resistant commensal Escherichia coli (E. coli) from humans, animals, and water from the same community with a ‘one-health’ approach. The samples were collected from a village belonging to demographic surveillance site of Ruxmaniben Deepchand (R.D.) Gardi Medical College Ujjain, Central India. Commensal coliforms from stool samples from children aged 1–3 years and their environment (animals, drinking water from children's households, common source- and waste-water) were studied for antibiotic susceptibility and plasmid-encoded resistance genes. E. coli isolates from human (n = 127), animal (n = 21), waste- (n = 12), source- (n = 10), and household drinking water (n = 122) carried 70%, 29%, 41%, 30%, and 30% multi-drug resistance, respectively. Extended spectrum beta-lactamase (ESBL) producers were 57% in human and 23% in environmental isolates. Co-resistance was frequent in penicillin, cephalosporin, and quinolone. Antibiotic-resistance genes bla_CTX-M-9 and qnrS were most frequent. Group D-type isolates with resistance genes were mainly from humans and wastewater. Colistin resistance, or the mcr-1 gene, was not detected. The frequency of resistance, co-resistance, and resistant genes are high and similar in coliforms from humans and their environment. This emphasizes the need to mitigate antibiotic resistance with a ‘one-health’ approach.

High Prevalence of Plasmid-Mediated Quinolone Resistance and IncQ Plasmids Carrying qnrS2 Gene in Bacteria from Rivers near Hospitals and Aquaculture in China

Effluents from hospital and aquaculture are considered important sources of quinolone resistance. However, little information is available on the impact of this effluent on nearby rivers. In this study, 188 ciprofloxacin-resistant bacterial isolates obtained from rivers near hospitals and aquaculture were screened for plasmid-mediated quinolone resistance (PMQR) genes. Species identification, antibiotic susceptibility testing, and PMQR gene transferability assessment were conducted for PMQR-positive bacteria. Representative qnrS2-encoding plasmids were subsequently sequenced using a primer-walking approach. In total, 44 isolates (23.4%) were positive for qnr genes (16 qnrB2, 3 qnrS1, and 25 qnrS2) and 32 isolates (17.0%) were positive for aac(6')-Ib-cr. Other PMQR genes were not detected. The qnrB2 and aac(6')-Ib-cr genes had a higher prevalence in aquaculture samples than in hospital samples, and were significantly associated with Enterobacteriaceae (p < 0.05). In contrast, the prevalence of qnrS2 was not site-related, but was significantly associated with Aeromonas spp. (p < 0.05). All PMQR isolates were resistant to three or more classes of antibiotics. Eleven qnrS2-harboring plasmids from Aeromonas spp., including a novel conjugative plasmid pHP18, were selected for sequencing. These plasmids were small in size (6,388-16,197 bp) and belonged to the IncQ or IncU plasmid family, with qnrS2 being part of a mobile insertion cassette. Taken together, our findings suggest that aquaculture is a possible source for aac(6')-Ib-cr and qnrB2 dissemination, and demonstrate the ubiquity of qnrS2 in aquatic environments. Finally, Aeromonas spp. served as vectors for qnrS2 with the help of IncQ-type plasmids.

Distribution and Relationships of Antimicrobial Resistance Determinants among Extended-Spectrum-Cephalosporin-Resistant or Carbapenem-Resistant Escherichia coli Isolates from Rivers and Sewage Treatment Plants in India

To determine the distribution and relationship of antimicrobial resistance determinants among extended-spectrum-cephalosporin (ESC)-resistant or carbapenem-resistant Escherichia coli isolates from the aquatic environment in India, water samples were collected from rivers or sewage treatment plants in five Indian states. A total of 446 E. coli isolates were randomly obtained. Resistance to ESC and/or carbapenem was observed in 169 (37.9%) E. coli isolates, which were further analyzed. These isolates showed resistance to numerous antimicrobials; more than half of the isolates exhibited resistance to eight or more antimicrobials. The blaNDM gene was detected in 14/21 carbapenem-resistant E. coli isolates: blaNDM-1 in 2 isolates, blaNDM-5 in 7 isolates, and blaNDM-7 in 5 isolates. The blaCTX-M gene was detected in 112 isolates (66.3%): blaCTX-M-15 in 108 isolates and blaCTX-M-55 in 4 isolates. We extracted 49 plasmids from selected isolates, and their whole-genome sequences were determined. Fifty resistance genes were detected, and 11 different combinations of replicon types were observed among the 49 plasmids. The network analysis results suggested that the plasmids sharing replicon types tended to form a community, which is based on the predicted gene similarity among the plasmids. Four communities each containing from 4 to 17 plasmids were observed. Three of the four communities contained plasmids detected in different Indian states, suggesting that the interstate dissemination of ancestor plasmids has already occurred. Comparison of the DNA sequences of the blaNDM-positive plasmids detected in this study with known sequences of related plasmids suggested that various mutation events facilitated the evolution of the plasmids and that plasmids with similar genetic backgrounds have widely disseminated in India.

Quinolone co-resistance in ESBL- or AmpC-producing Escherichia coli from an Indian urban aquatic environment and their public health implications

Quinolone and β-lactam antibiotics constitute major mainstay of treatment against infections caused by pathogenic Escherichia coli. Presence of E. coli strains expressing co-resistance to both these antibiotic classes in urban aquatic environments which are consistently being used for various anthropogenic activities represents a serious public health concern. From a heterogeneous collection of 61 E. coli strains isolated from the river Yamuna traversing through the National Capital Territory of Delhi (India), those harboring blaCTX-M-15 (n = 10) or blaCMY-42 (n = 2) were investigated for co-resistance to quinolones and the molecular mechanisms thereof. Resistance was primarily attributed to amino acid substitutions in the quinolone resistance-determining regions (QRDRs) of GyrA (S83L ± D87N) and ParC (S80I ± E84K). One of the E. coli strains, viz., IPE, also carried substitutions in GyrB and ParE at positions Ser492→Asn and Ser458→Ala, respectively. The phenotypically susceptible strains nevertheless carried plasmid-mediated quinolone resistance (PMQR) gene, viz., qnrS, which showed co-transfer to the recipient quinolone-sensitive E. coli J53 along with the genes encoding β-lactamases and led to increase in minimal inhibitory concentrations of quinolone antibiotics. To the best of our knowledge, this represents first report of molecular characterization of quinolone co-resistance in E. coli harboring genes for ESBLs or AmpC β-lactamases from a natural aquatic environment of India. The study warrants true appreciation of the potential of urban aquatic environments in the emergence and spread of multi-drug resistance and underscores the need to characterize resistance genetic elements vis-à-vis their public health implications, irrespective of apparent phenotypic resistance.

Protocol: a 'One health' two year follow-up, mixed methods study on antibiotic resistance, focusing children under 5 and their environment in rural India

Background

Antibiotic resistance has been referred to as ‘the greatest malice of the 21^st century’ and a global action plan was adopted by the World Health Assembly in 2015. There is a wealth of independent studies regarding antibiotics and resistant bacteria in humans, animals and their environment, however, integrated studies are lacking, particularly ones that simultaneously also take into consideration the health related behaviour of participants and healthcare providers. Such, ‘One health’ studies are difficult to implement, because of the complex teamwork that they entail. This paper describes the protocol of a study that investigates ‘One health’ issues regarding antibiotic use and antibiotic resistance in children and their environment in Indian villages.

Methods/Design

Both quantitative and qualitative studies are planned for a cohort of children, from 6 villages, and their surrounding environment. Repeated or continues data collection is planned over 2 years for quantitative studies. Qualitative studies will be conducted once. Studies include parents’ health seeking behavior for their children (1–3 years of age at the onset), prescribing pattern of formal and informal healthcare providers, analysis of phenotypic antibiotic resistance of Escherichia coli from samples of stool from children and village animals, household drinking water, village source water and waste water, and investigation on molecular mechanisms governing resistance. Analysis of interrelationship of these with each other will also be done as basis for future interventions. Ethics approval has been obtained from the Institutional Ethics Committee R.D. Gardi Medical College, Ujjain, India (No: 2013/07/17-311).

Discussion

The findings of the study presented in this protocol will add to our knowledge about the multi-factorial nature of causes governing antibiotic use and antibiotic resistance from a ‘One health’ perspective. Our study will be the first of its kind addressing antibiotic use and resistance issues related to children in a One-health approach, particularly for rural India.

Multidrug Resistance in Quinolone-Resistant Gram-Negative Bacteria Isolated from Hospital Effluent and the Municipal Wastewater Treatment Plant

This study is aimed to assess if hospital effluents represent an important supplier of multidrug-resistant (MDR) Gram-negative bacteria that, being discharged in the municipal collector, may be disseminated in the environment and bypassed in water quality control systems. From a set of 101 non-Escherichia coli Gram-negative bacteria with reduced susceptibility to quinolones, was selected a group of isolates comprised by those with the highest indices of MDR (defined as nonsusceptibility to at least one agent in six or more antimicrobial categories, MDR ≥6) or resistance to meropenem or ceftazidime (n = 25). The isolates were identified and characterized for antibiotic resistance phenotype, plasmid-mediated quinolone resistance (PMQR) genes, and other genetic elements and conjugative capacity. The isolates with highest MDR indices were mainly from hospital effluent and comprised ubiquitous bacterial groups of the class Gammaproteobacteria, of the genera Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Klebsiella, and Pseudomonas, and of the class Flavobacteriia, of the genera Chryseobacterium and Myroides. In this group of 25 strains, 19 identified as Gammaproteobacteria harbored at least one PMQR gene (aac(6')-Ib-cr, qnrB, qnrS, or oqxAB) or a class 1 integron gene cassette encoding aminoglycoside, sulfonamide, or carbapenem resistance. Most of the E. coli J53 transconjugants with acquired antibiotic resistance resulted from conjugation with Enterobacteriaceae. These transconjugants demonstrated acquired resistance to a maximum of five classes of antibiotics, one or more PMQR genes and/or a class 1 integron gene cassette. This study shows that ubiquitous bacteria, other than those monitored in water quality controls, are important vectors of antibiotic resistance and can be disseminated from hospital effluent to aquatic environments. This information is relevant to support management options aiming at the control of this public health problem.

The challenge of efflux-mediated antibiotic resistance in Gram-negative bacteria

The global emergence of multidrug-resistant Gram-negative bacteria is a growing threat to antibiotic therapy. The chromosomally encoded drug efflux mechanisms that are ubiquitous in these bacteria greatly contribute to antibiotic resistance and present a major challenge for antibiotic development. Multidrug pumps, particularly those represented by the clinically relevant AcrAB-TolC and Mex pumps of the resistance-nodulation-division (RND) superfamily, not only mediate intrinsic and acquired multidrug resistance (MDR) but also are involved in other functions, including the bacterial stress response and pathogenicity. Additionally, efflux pumps interact synergistically with other resistance mechanisms (e.g., with the outer membrane permeability barrier) to increase resistance levels. Since the discovery of RND pumps in the early 1990s, remarkable scientific and technological advances have allowed for an in-depth understanding of the structural and biochemical basis, substrate profiles, molecular regulation, and inhibition of MDR pumps. However, the development of clinically useful efflux pump inhibitors and/or new antibiotics that can bypass pump effects continues to be a challenge. Plasmid-borne efflux pump genes (including those for RND pumps) have increasingly been identified. This article highlights the recent progress obtained for organisms of clinical significance, together with methodological considerations for the characterization of MDR pumps.