Critically important antimicrobial resistant Enterobacteriaceae in Irish farm effluent and their removal in integrated constructed wetlands

An evaluation of conventional and nature-based technologies for controlling antibiotic-resistant bacteria and antibiotic-resistant genes in wastewater treatment plants

Antibiotic resistance is a globally recognized health concern which leads to longer hospital stays, increased morbidity, increased mortality, and higher medical costs. Understanding how antibiotic resistance persists and exchanges in environmental systems like soil, water, and wastewater are critically important for understanding the emergence of pathogens with new resistance profiles and the subsequent exposure of people who indirectly/directly come in contact with these pathogens. There are concerns about the widespread application of prophylactic antibiotics in the clinical and agriculture sectors, as well as chemicals/detergents used in food and manufacturing industries, especially the quaternary ammonium compounds which have been found responsible for the generation of resistant genes in water and soil. The rates of horizontal gene transfer increase where there is a lack of proper water/wastewater infrastructure, high antibiotic manufacturing industries, or endpoint users - such as hospitals and intensive agriculture. Conventional wastewater treatment technologies are often inefficient in the reduction of ARB/ARGs and provide the perfect combination of conditions for the development of antibiotic resistance. The wastewater discharged from municipal facilities may therefore be enriched with bacterial communities/pathogens and provide a suitable environment (due to the presence of nutrients and other pollutants) to enhance the transfer of antibiotic resistance. However, facilities with tertiary treatment (either traditional/emerging technologies) provide higher rates of reduction. This review provides a synthesis of the current understanding of wastewater treatment and antibiotic resistance, examining the drivers that may accelerate their possible transmission to a different environment, and highlighting the need for tertiary technologies used in treatment plants for the reduction of resistant bacteria/genes.

Multidrug antibiotic resistance in hospital wastewater as a reflection of antibiotic prescription and infection cases

Antimicrobial resistance (AMR) is an escalating issue that can render illnesses more difficult to treat if effective antibiotics become resistant. Many studies have explored antibiotic resistance in bacteria (ARB) in wastewater, comparing results with clinical data to ascertain the public health risk. However, few investigations have linked the prevalence of ARB in hospital wastewater (HWW) with these outcomes. This study aimed to bridge this gap by assessing the prevalence of ARB in HWW and its receiving waters. Among the 144 isolates examined, 24 were obtained from each of the six sites (untreated wastewater, aeration tank, sedimentation tank, effluent after disinfection, upstream canal, and downstream canal). A significant portion (87.5 %) belonged to the Enterobacteriaceae family, with Klebsiella pneumoniae as the predominant species (47.9 %). The antimicrobial sensitivity testing (AST) showed that 57.6 % of the isolates were resistant to amoxicillin/clavulanic acid (AMX), the most prevalent antibiotic used within the studied hospital. The total resistance rate before and after treatment was 27.7 % and 28.0 %, respectively, with an overall multi-drug resistance (MDR) rate of 33.3 %. The multiple antibiotic resistance index (MARI) range varied between 0.0 and 0.9. The outpatient ward's three-day mean bacterial infection cases showed a significant association (Spearman's rho = 0.98) with the MARI in the sedimentation tank. Moreover, a strong correlation (Spearman's rho = 0.88) was found between hospital effluent's MARI and the seven-day mean inpatient ward case. These findings indicate that applying wastewater-based epidemiology (WBE) to hospital wastewater could provide valuable insights into understanding ARB contamination across human domains and water cycles. Future studies, including more comprehensive collection data on symptomatic patients and asymptomatic carriers, will be crucial in fully unravelling the complexities between human health and environmental impacts related to AMR.

Antimicrobial resistance in southeast Asian water environments: A systematic review of current evidence and future research directions

Antimicrobial resistance has been a serious and complex issue for over a decade. Although research on antimicrobial resistance (AMR) has mainly focused on clinical and animal samples as essential for treatment, the AMR situation in aquatic environments may vary and have complicated patterns according to geographical area. Therefore, this study aimed to examine recent literature on the current situation and identify gaps in the AMR research on freshwater, seawater, and wastewater in Southeast Asia. The PubMed, Scopus, and ScienceDirect databases were searched for relevant publications published from January 2013 to June 2023 that focused on antimicrobial resistance bacteria (ARB) and antimicrobial resistance genes (ARGs) among water sources. Based on the inclusion criteria, the final screening included 41 studies, with acceptable agreement assessed using Cohen's inter-examiner kappa equal to 0.866. This review found that 23 out of 41 included studies investigated ARGs and ARB reservoirs in freshwater rather than in seawater and wastewater, and it frequently found that Escherichia coli was a predominant indicator in AMR detection conducted by both phenotypic and genotypic methods. Different ARGs, such as blaTEM, sul1, and tetA genes, were found to be at a high prevalence in wastewater, freshwater, and seawater. Existing evidence highlights the importance of wastewater management and constant water monitoring in preventing AMR dissemination and strengthening effective mitigation strategies. This review may be beneficial for updating current evidence and providing a framework for spreading ARB and ARGs, particularly region-specific water sources. Future AMR research should include samples from various water systems, such as drinking water or seawater, to generate contextually appropriate results. Robust evidence regarding standard detection methods is required for prospective-era work to raise practical policies and alerts for developing microbial source tracking and identifying sources of contamination-specific indicators in aquatic environment markers.

Antimicrobial Resistance Is Prevalent in E. coli and Other Enterobacterales Isolated from Public and Private Drinking Water Supplies in the Republic of Ireland

High levels of bacterial antimicrobial resistance (AMR) have been reported in many environmental studies conducted in Ireland and elsewhere. The inappropriate use of antibiotics in both human and animal healthcare as well as concentrations of residual antibiotics being released into the environment from wastewaters are thought to be contributing factors. Few reports of AMR in drinking water-associated microbes are available for Ireland or internationally. We analysed 201 enterobacterales from group water schemes and public and private water supplies, only the latter having been surveyed in Ireland previously. The organisms were identified using conventional or molecular techniques. Antimicrobial susceptibility testing for a range of antibiotics was performed using the ARIS 2X interpreted in accordance with EUCAST guidelines. A total of 53 Escherichia coli isolates, 37 Serratia species, 32 Enterobacter species and enterobacterales from seven other genera were identified. A total of 55% of isolates were amoxicillin resistant, and 22% were amoxicillin-clavulanic acid resistant. A lower level of resistance (<10%) was observed to aztreonam, chloramphenicol, ciprofloxacin, gentamicin, ceftriaxone and trimethoprim-sulfamethoxazole. No resistance to amikacin, piperacillin/tazobactam, ertapenem or meropenem was detected. The level of AMR detected in this study was low but not insignificant and justifies ongoing surveillance of drinking water as a potential source of antimicrobial resistance.

Building an International One Health Strain Level Database to Characterise the Epidemiology of AMR Threats: ESBL—AmpC Producing E. coli as An Example—Challenges and Perspectives

Antimicrobial resistance (AMR) is one of the top public health threats nowadays. Among the most important AMR pathogens, Escherichia coli resistant to extended spectrum cephalosporins (ESC-EC) is a perfect example of the One Health problem due to its global distribution in animal, human, and environmental sources and its resistant phenotype, derived from the carriage of plasmid-borne extended-spectrum and AmpC β-lactamases, which limits the choice of effective antimicrobial therapies. The epidemiology of ESC-EC infection is complex as a result of the multiple possible sources involved in its transmission, and its study would require databases ideally comprising information from animal (livestock, companion, wildlife), human, and environmental sources. Here, we present the steps taken to assemble a database with phenotypic and genetic information on 10,763 ESC-EC isolates retrieved from multiple sources provided by 13 partners located in eight European countries, in the frame of the DiSCoVeR Joint Research project funded by the One Health European Joint Programme (OH-EJP), along with its strengths and limitations. This database represents a first step to help in the assessment of different geographical and temporal trends and transmission dynamics in animals and humans. The work performed highlights aspects that should be considered in future international efforts, such as the one presented here.

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.

Whole Genome Sequencing (WGS) Analysis of Virulence and AMR Genes in Extended-Spectrum β-Lactamase (ESBL)-Producing Escherichia coli from Animal and Environmental Samples in Four Italian Swine Farms

Whole genome sequencing (WGS) is a powerful tool to analyze bacterial genomes rapidly, and can be useful to study and detect AMR genes. We carried out WGS on a group of Escherichia coli (n = 30), sampled from healthy animals and farm environment in four pigsties in northern Italy. Two × 250bp paired end sequencing strategy on Illumina MiSeq™ was used. We performed in silico characterization of E. coli isolates through the web tools provided by the Center for Genomic Epidemiology (cge.cbs.dtu.dk/services/) to study AMR and virulence genes. Bacterial strains were further analyzed to detect phenotypic antimicrobial susceptibility against several antimicrobials. Data obtained from WGS were compared to phenotypic results. All 30 strains were MDR, and they were positive for the genes bla_CTX-M and bla_TEM as verified by PCR. We observed a good concordance between phenotypic and genomic results. Different AMR determinants were identified (e.g., qnrS, sul, tet). Potential pathogenicity of these strains was also assessed, and virulence genes were detected (e.g., etsC, gad, hlyF, iroN, iss), mostly related to extraintestinal E. coli pathotypes (UPEC/APEC). However, enterotoxin genes, such as astA, ltcA and stb were also identified, indicating a possible hybrid pathogenic nature. Various replicons associated to plasmids, previously recovered in pathogenic bacteria, were identified (e.g., IncN and IncR plasmid), supporting the hypothesis that our strains were pathogenic. Eventually, through WGS it was possible to confirm the phenotypic antibiotic resistance results and to appreciate the virulence side of our ESBL-producing E. coli. These findings highlight the need to monitor commensal E. coli sampled from healthy pigs considering a One Health perspective.

Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates That Cause Diarrhea in Sheep in Northwest China

Development of extended-spectrum-β-lactamase (ESBL)-producing Escherichia coli is one the greatest threats faced by mankind. Among animals, chickens, pigs, and cattle are reservoirs of these pathogens worldwide. Nevertheless, there is a knowledge gap on ESBL-producing E. coli from small ruminants (i.e., sheep and goats) in China. The aim of this study was to identify and characterize the resistance profiles, resistomes, and sequence features of 67 ESBL-producing E. coli isolates from sheep in northwest China. The findings showed that blaCTX-M and blaTEM were the most prevalent. Interestingly, we found that the resistance gene mcr-1 was widespread in sheep merely from Shaanxi areas, accounting for 19.2% (5/26). The highly prevalent serotypes and FumC-FimH (CH) typing isolates were O8 and C4H32, respectively. High-risk E. coli clones, such as sequence type 10 (ST10), ST23, ST44, and ST58, were also found in China's sheep population. A total of 67 ESBL-producing isolates were divided into five phylogenetic groups, namely, B1 (n = 47, 70.1%), B2 (n = 1, 1.5%), C (n = 14, 20.9%), E (n = 1, 1.5%), and F (n = 1, 1.5%), with the phylogenetic groups for 3 isolates (4.5%) remaining unknown. Moreover, ESBL-producing E. coli isolates were also characterized by the abundance and diversity of biocide/metal resistance genes and insert sequences. We found that in ESBL-producing E. coli isolates, there were two different types of isolates, those containing ESBL genes or not, which led to large discrepancies between resistance phenotypes and resistomes. In summary, our study provides a comprehensive overview of resistance profiles and genome sequence features in ESBL-producing E. coli and highlights the possible role of sheep as antibiotic resistance gene disseminators into humans. IMPORTANCE Antimicrobial resistance (AMR), especially the simultaneous resistance to several antibiotics (multidrug resistance [MDR]), is one of the greatest threats to global public health in the 21st century. Among animals, chickens, pigs, and cattle are reservoirs of these pathogens worldwide. Nevertheless, there is a knowledge gap on ESBL-producing E. coli from small ruminants in China. This study is the largest and most comprehensive analysis of ESBL-producing E. coli isolates from sheep, including antibiotic resistance profiles, phylogenetic groups, serotypes, multilocus sequence types (MLST), insert sequences (IS), antibiotic resistance genes, disinfectant resistance genes, and heavy metal resistance genes. We recommend extending the surveillance of AMR of sheep-origin E. coli to prevent future public health risks.

Prevalence and Characterization of Extended-Spectrum β-Lactamase- and Carbapenemase-Producing Enterobacterales from Tunisian Seafood

Aquaculture is a rapidly expanding sector in which it is important to monitor the occurrence of multi-drug resistant (MDR) bacteria. The presence of extended-spectrum β-lactamase (ESBL-) or carbapenemase-producing Enterobacterales is a commonly used indicator of the resistance burden in a given sector. In this study, 641 pieces of farmed fish (sea bream and sea bass), as well as 1075 Mediterranean clams, were analyzed. All ESBL- and carbapenemase-producing Enterobacterales collected were whole-genome sequenced. The proportion of ESBL-producing Enterobacterales was 1.4% in fish and 1.6% in clams, carried by Escherichia coli (n = 23) and Klebsiella pneumoniae (n = 4). The ESBL phenotype was exclusively due to the presence of bla_CTX-M genes, the most frequent one being bla_CTX-M-15. The bla_CTX-M-1 gene was also identified in six E. coli, among which four were carried by IncI1/pST3 plasmids, possibly betraying an animal origin. Carbapenemases were absent in fish but identified in two K. pneumoniae isolates from clams (bla_NDM-1 and bla_OXA-48). Several sequence types (STs) identified were associated with human MDR clones such as E. coli ST131 and ST617, or K. pneumoniae ST307 and ST147. Our results might indicate that bacteria from hospital or farm effluents can reach the open sea and contaminate seafood and fish that are living or raised nearby. Therefore, monitoring the quality of water discharged to the sea and the presence of MDR bacteria in seafood is mandatory to ensure the quality of fishery products.