Extended spectrum beta-lactamase-producing Escherichia coli surveillance in the human, food chain, and environment sectors: Tricycle project (pilot) in Indonesia

Distribution of extended-spectrum β-lactamase producing Escherichia coli genes in an integrated poultry-fish farming system in Bogor, Indonesia

Background and Aim

The excessive use of antimicrobials in livestock farming leads to the emergence and dissemination of antimicrobial-resistant organisms. This study aimed to detect extended-spectrum β-lactamase (ESBL)-producing Escherichia coli genes in integrated poultry-fish farms in Bogor, Indonesia.

Materials and Methods

A total of 256 samples were collected from six poultry-fish farms. One hundred and seventy-five chicken cloaca swabs, 60 fish skin swabs, six pond water samples, and 15 farmer's hand swabs. ESBL-producing E. coli was confirmed through double-disk diffusion. The specific primers and probe genes for quantitative polymerase chain reaction detection of ESBL-producing E. coli targeted blaTEM, blaCTX-M, blaSHV, and blaOXA-48 genes.

Results

Among the 256 samples tested, 145 (56.6%) were positive for E. coli, and 67.6% (98/145) were identified as ESBL-producing E. coli. The most ESBL-producing E. coli isolates were obtained from chicken cloaca (78.3%, 72/92), followed by pond water (66.7%, 4/6), fish skin (47.6%, 20/42), and farmer's hand swabs (40%, 2/5). About 100% of the isolates carried the genes blaTEM and blaCTX-M, whereas 17.3% and 24.5% carried blaSHV and blaOXA-48, respectively.

Conclusion

ESBL-producing E. coli genes were investigated in chicken cloaca, fish, pond water, and farmers' hands within an interconnected poultry-fish farming operation. The ESBL-producing E. coli in chickens can transfer resistant genes to aquatic environments. The transfer could harm other aquatic species and food chains, potentially threatening human health.

The scope of the antimicrobial resistance challenge

Each year, an estimated 7·7 million deaths are attributed to bacterial infections, of which 4.95 million are associated with drug-resistant pathogens, and 1·27 million are caused by bacterial pathogens resistant to the antibiotics available. Access to effective antibiotics when indicated prolongs life, reduces disability, reduces health-care expenses, and enables access to other life-saving medical innovations. Antimicrobial resistance undoes these benefits and is a major barrier to attainment of the Sustainable Development Goals, including targets for newborn survival, progress on healthy ageing, and alleviation of poverty. Adverse consequences from antimicrobial resistance are seen across the human life course in both health-care-associated and community-associated infections, as well as in animals and the food chain. The small set of effective antibiotics has narrowed, especially in resource-poor settings, and people who are very young, very old, and severely ill are particularly susceptible to resistant infections. This paper, the first in a Series on the challenge of antimicrobial resistance, considers the global scope of the problem and how it should be measured. Robust and actionable data are needed to drive changes and inform effective interventions to contain resistance. Surveillance must cover all geographical regions, minimise biases towards hospital-derived data, and include non-human niches.

Occurrence, antibiotic resistance profiles and associated risk factors of Klebsiella pneumoniae in poultry farms in selected districts of Somalia Reginal State, Ethiopia

BACKGROUND

Klebsiella pneumoniae is an opportunistic infection that causes production losses and death in the chicken industry. A cross-sectional study was conducted on exotic chicken breeds reared at the Jigjiga poultry farm from November 2022 to May 2023 to estimate the occurrence, associated risk factors, and antimicrobial susceptibility profiles of Klebsiella pneumoniae. The chickens were selected using systematic random sampling techniques. A total of 384 cloacal swabs were collected aseptically and transported to the laboratory for analysis. For statistical analysis, STATA® version 14.0 statistical software was used.

RESULTS

From 384 examined faecal samples, 258 (67.2%) prevalences of Klebsiella pneumoniae were found. Furthermore, the association of the study's risk factors with the prevalence of Klebsiella pneumoniae was explored, and no statistically significant association was identified between sex and age. Nonetheless, relative prevalence at the age level was higher in chickens aged 12 months (67.6%) and Sasso breeds (90.0%). Similarly, male chickens and those raised for meat and egg production had a high prevalence rate of 72.5 and 75.8%, respectively. A total of 30 isolated Klebsiella pneumoniae colonies were tested in vitro for antibiotic sensitivity for six drugs, and it was shown that Klebsiella pneumoniae is moderately sensitive to Penicillin G (43.3%) while having higher resistance to Oxytetracycline (80.0%).

CONCLUSIONS

The current findings revealed that the research area had the highest prevalence of Klebsiella pneumoniae, and the isolates were resistant to commonly used drugs in the study area. Thus, a long-term intervention plan, thorough research to determine a nationwide status, as well as further multi-drug resistance patterns and molecular characterization, were urged.

Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia

Antimicrobial agents are administered to humans and livestock, and bacterial antimicrobial resistance (AMR) and antimicrobial agents are released into the environment. In this study, to investigate the trend of AMR in humans, livestock, and the environment, we performed a metagenomic analysis of multidrug-resistant bacteria with CHROMagar ESBL in environmental river water samples, which were collected using syringe filter units from waters near hospitals, downtown areas, residential areas, and water treatment plants in Surabaya, Indonesia. Our results showed that Acinetobacter, Pseudomonas, Aeromonas, Enterobacter, Escherichia, and Klebsiella grew in CHROMagar ESBL; they were most frequently detected in water samples from rivers surrounding hospitals contaminated with various AMR genes (ARGs) in high levels. These results identified bacteria as ARG reservoirs and revealed that hospitals could be sources for various ARGs disseminated into the environment. In conclusion, this study details a novel metagenomic analysis of collected bacteria in environmental water samples using a syringe filter unit for an AMR epidemiological study based on the One Health approach.

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.

Response to antimicrobial resistance in South-East Asia Region

Antimicrobial resistance (AMR) inflicts significant mortality, morbidity and economic loss in the 11 countries in the WHO South-East Asia Region (SEAR). With technical assistance and advocacy from WHO, all countries have developed their respective National Action Plans on AMR that are aligned with the Global Action Plan. Historically, the WHO Regional Office has been proactive in advocacy at the highest political level. The past decade has seen an enhancement of the country's capacity to combat AMR through national efforts catalyzed and supported through several WHO initiatives at all levels-global, regional and country levels. Several countries including Bangladesh, India, Indonesia, Nepal, Sri Lanka and Thailand have observed a worrying trend of increasing drug resistance, despite heightened awareness and actions. Recent AMR data generated by the countries are indicative of fragmented progress. Lack of technical capacity, financial resources, weak regulatory apparatus, slow behavioural changes at all levels of the antimicrobial stewardship landscape and the COVID-19 pandemic have prevented the effective application of several interventions to minimize the impact of 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.

Lessons from a global antimicrobial resistance surveillance network

The World Health Organization developed the Tricycle surveillance programme to obtain a global picture of antimicrobial resistance, especially in countries with limited surveillance capacity. The programme was developed within a One Health perspective. Tricycle provides a framework for applying a standardized technical protocol to determining the prevalence of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in three sectors: the human, animal and environment sectors. Regular use of the protocol would enable information to be obtained on time trends and on inter- and intraregional variations, thereby generating dynamic data on antibacterial resistance for decision-makers. To date, 19 countries have begun implementing the Tricycle protocol, while other countries will start implementation in the coming years. The Network for Enhancing Tricycle ESBL Surveillance Efficiency (NETESE) was established to support countries implementing the Tricycle protocol. Currently, NETESE includes representatives from 15 institutions in eight low- or middle-income countries at different stages of Tricycle protocol implementation, and from four European countries involved in devising the protocol. This paper describes the Tricycle protocol, reports the initial experiences of NETESE participants with its implementation and discusses future challenges and opportunities.

Prevalence and characterization of ESBL-producing Escherichia coli in healthy pregnant women and hospital environments in Benin: an approach based on Tricycle

Introduction

Extended-Spectrum Beta-Lactamase (ESBL)-producing Enterobacterales are recognized as significant pathogens due to their resistance to multiple antibiotics. This study aimed to determine the prevalence of ESBL-producing Escherichia coli (E. coli) in different settings, including healthy pregnant women, the food chain, and the environment of tertiary hospitals in Benin.

Methods

Samples were collected from various sources, including fecal samples from healthy pregnant women, food samples from hospital canteens, and hospital effluents from four tertiary hospitals in southern Benin. Fecal samples were plated on MacConkey agar supplemented with cefotaxime (4 μg/mL), while food and water samples were plated on Tryptone Bile X agar supplemented with cefotaxime (4 μg/mL). Urea indole tests were used for preliminary identification of E. coli colonies, followed by confirmation of ESBL production using the double disk synergy technique. Antibiotic susceptibility testing of ESBL-producing E. coli strains was conducted using the disk diffusion method on MH agar. Polymerase Chain Reaction (PCR) was used to investigate the presence of ESBL-encoding genes.

Results

Among the 296 fecal samples collected from four tertiary hospitals, ESBL-producing E. coli was isolated from 22.30% (66) of the samples. All E. coli isolates from hospital effluents exhibited ESBL production, while ESBL-producing E. coli was not detected in food and drinking water samples. The analysis of variable associations showed no significant associations (p > 0.05) for the studied factors. Antibiotic susceptibility testing revealed high resistance rates among the ESBL-Ec isolates against several tested antibiotics, including amoxicillin, aztreonam, ceftriaxone, ciprofloxacin, and trimethoprim-sulfamethoxazole. However, most isolates remained susceptible to ertapenem, amoxicillin-clavulanate, and imipenem. The most prevalent ESBL-encoding genes were blaTEM (37.50%), blaOXA-1 (19.44%), and blaSHV (11.11%), while a smaller proportion of isolates carried blaCTXM-1/blaCTXM-15 (5.55%) and blaCTXM-9.

Discussion

This study provides insights into the prevalence of ESBL-producing E. coli carriage in the feces of healthy pregnant women in southern Benin. Additionally, it highlights hospital wastewater as a potential reservoir of ESBL-producing bacteria in the environment. The detection of ESBL-producing E. coli in hospital effluents raises concerns about the dissemination of antibiotic resistance genes into the environment. The high resistance rates observed among ESBL-Ec isolates against commonly used antibiotics emphasize the urgent need for antimicrobial stewardship and infection control measures. The identification of prevalent ESBL-encoding genes contributes to understanding the genetic basis of ESBL resistance in the studied population. Further research is warranted to explore the mechanisms of transmission and potential interventions to mitigate the spread of ESBL-producing Enterobacterales.

Faecal carriage of extended-spectrum β-lactamase-producing Escherichia coli in a remote region of Niger

OBJECTIVE

Whole genome sequencing (WGS) of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger.

METHODS

Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads.

RESULTS

Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome.

CONCLUSIONS

Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.

Screening for extended-spectrum beta-lactamase Escherichia coli in recreational beach waters in Singapore

Aims: As part of Singapore's One Health antimicrobial resistance (AMR) management, this work was designed to understand the AMR burden in recreational beach waters using extended-spectrum beta-lactamase Escherichia coli (ESBL-EC) as an indicator. Materials & methods: A total of 90 water samples were collected from six different recreational beaches over three different time periods. Only 28/90 (31.3%) water samples yielded E. coli colonies ranging from 1 to 80 colony-forming units/100 ml. Results & conclusion: Screening of all colonies using CHROMID® ESBL agar and Luria-Bertani broth supplemented with ceftriaxone showed that none was ESBL-EC. Further monitoring is required to understand the prevalence of ESBL-EC spatiotemporally, contributing to the national AMR surveillance program and providing timely risk assessment for exposure to ESBL-EC.

Extended spectrum beta lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae in Indonesia and South East Asian countries: GLASS Data 2018

Antimicrobial resistance is the rising global health issue that should not be ignored. This problem needs to be addressed and professionally handled since it is starting to threaten global health, which eventually could lead to disaster. Extended spectrum beta lactamase (ESBL)-producing bacteria were found threatening lives, since most antibiotics were found to not be effective in treating patients with infections caused by those bacteria. ESBL-producing Escherichia coli and Klebsiella pneumoniae are the two most reported bacteria in causing the bacteremia and nosocomial infections worldwide. In this article, the prevalence of ESBL-producing E. coli and K. pneumoniae in causing blood stream and urinary tract infections in Indonesia were compared to the neighboring countries based on the global antimicrobial resistance surveillance system performed worldwide by World Health Organization (WHO). In this article, the prevalence of ESBL-producing E. coli and K. pneumoniae in Indonesia and its neighboring countries were assayed and compared in order to evaluate the antimicrobial resistances. By comparing the prevalence data to the neighboring countries, some insightful evidence and information was served to support improved health in Indonesia. Some hurdles and strategies in combating the antimicrobial resistances were further discussed. Eventually, an alternate solution to overcome the antimicrobial drug resistance should be well-provided, studied and implemented globally.