The Experience of Implementing a National Antimicrobial Resistance Surveillance System in Brazil

Comparative genomics of IncQ1 plasmids carrying blaGES variants from clinical and environmental sources in Brazil

IncQ-type plasmids have become important vectors in the dissemination of blaGES among different bacterial genera and species from different environments around the world, and studies estimating the occurrence of Guiana extended-spectrum (GES)-type β-lactamases are gaining prominence. We analyzed the genetic aspects of two IncQ1 plasmids harboring different blaGES variants from human and environmental sources. The blaGES variants were identified using polymerase chain reaction (PCR) in Aeromonas veronii isolated from hospital effluent and Klebsiella variicola isolated from a rectal swab of a patient admitted to the cardiovascular intensive care unit in a different hospital. Antimicrobial-susceptibility testing and transformation experiments were performed for phenotypic analysis. Whole-genome sequencing was performed using Illumina and Oxford Nanopore platforms. The comparative analysis of plasmids was performed using BLASTn, and the IncQ1 plasmids showed a high identity and similar size. A. veronii harbored blaGES-7 in a class 1 integron (In2061), recently described by our group, and K. variicola carried blaGES-5 in the known class 1 integron. Both integrons showed a fused gene cassette that encodes resistance to aminoglycosides and fluoroquinolones, with an IS6100 truncating the 3'-conserved segment. The fused genes are transcribed together, although the attC site is disrupted. These gene cassettes can no longer be mobilized. This study revealed a mobilome that may contribute to the dissemination of GES-type β-lactamases in Brazil. Class 1 integrons are hot spots for bacterial evolution, and their insertion into small IncQ-like plasmids displayed successful recombination, allowing the spread of blaGES variants in various environments. Therefore, they can become prevalent across clinically relevant pathogens.

Biodiversity of carbapenem-resistant bacteria in clinical samples from the Southwest Amazon region (Rondônia/Brazil)

Brazil is recognized for its biodiversity and the genetic variability of its organisms. This genetic variability becomes even more valuable when it is properly documented and accessible. Understanding bacterial diversity through molecular characterization is necessary as it can improve patient treatment, reduce the length of hospital stays and the selection of resistant bacteria, and generate data for health and epidemiological surveillance. In this sense, in this study, we aimed to understand the biodiversity and molecular epidemiology of carbapenem-resistant bacteria in clinical samples recovered in the state of Rondônia, located in the Southwest Amazon region. Retrospective data from the Central Public Health Laboratories (LACEN/RO) between 2018 and 2021 were analysed using the Laboratory Environment Manager Platform (GAL). Seventy-two species with carbapenem resistance profiles were identified, of which 25 species carried at least one gene encoding carbapenemases of classes A (blaKPC-like), B (blaNDM-like, blaSPM-like or blaVIM-like) and D (blaOXA-23-like, blaOXA-24-like, blaOXA-48-like, blaOXA-58-like or blaOXA-143-like), among which we will highlight Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Serratia marcescens, and Providencia spp. With these results, we hope to contribute to the field by providing epidemiological molecular data for state surveillance on bacterial resistance and assisting in public policy decision-making.

How a laboratory-based antimicrobial resistance (AMR) regional surveillance system can address large-scale and local AMR epidemiology: the MICRO-BIO experience

Antimicrobial resistance is a significant threat to public health, with Italy experiencing substantial challenges in terms of AMR rate, surveillance system and activities to combat AMR. In response, the MICRO-BIO project was initiated as part of the National Plan to Combat Antibiotic Resistance by Region Lombardy health department. It was launched in 2018 with the aim of creating a surveillance tool by integrating data on bacterial isolates from microbiology laboratories. The participating laboratories were directly involved in reviewing and addressing discrepancies in the transmission data quality assessment. Despite the disruptions caused by COVID-19, 30 out of 33 laboratories in the Lombardy Region were successfully integrated by October 2023, with 1,201,000 microbiological data collected in the first nine months of 2023. In 2022 the analysis yielded 15,037 blood culture results from 20 labs passing validation. Data regarding the antimicrobial resistance profile of high-priority pathogens was analyzed at regional and single-hospital levels. The MICRO-BIO project represents a significant step toward strengthening AMR surveillance in a highly populated region. As a multi-disciplinary tool encompassing the fields of public health and IT (information technology), this tool has the potential to inform regional and local AMR epidemiology.

Antimicrobial stewardship in the intensive care unit

High resistance rates to antimicrobials continue to be a global health threat. The incidence of multidrug-resistant (MDR) microorganisms in intensive care units (ICUs) is quite high compared to in the community and other units in the hospital because ICU patients are generally older, have higher numbers of co-morbidities and immune-suppressed; moreover, the typically high rates of invasive procedures performed in the ICU increase the risk of infection by MDR microorganisms. Antimicrobial stewardship (AMS) refers to the implementation of coordinated interventions to improve and track the appropriate use of antibiotics while offering the best possible antibiotic prescription (according to dose, duration, and route of administration). Broad-spectrum antibiotics are frequently preferred in ICUs because of greater infection severity and colonization and infection by MDR microorganisms. For this reason, a number of studies on AMS in ICUs have increased in recent years. Reducing the use of broad-spectrum antibiotics forms the basis of AMS. For this purpose, parameters such as establishing an AMS team, limiting the use of broad-spectrum antimicrobials, terminating treatments early, using early warning systems, pursuing infection control, and providing education and feedback are used. In this review, current AMS practices in ICUs are discussed.

Low performance of Policimbac® broth microdilution in determining polymyxin B MIC for Klebsiella pneumoniae

Klebsiella pneumoniae is a global threat to healthcare, and despite the availability of new drugs, polymyxins are still an important therapeutic option for this and other resistant gram-negative pathogens. Broth microdilution is the only method that is recommended for polymyxins. In this study, we evaluated the accuracy of a commercial Policimbac® plate in determining the polymyxin B MIC for K. pneumoniae clinical isolates. The results were compared with those of the broth microdilution method according to ISO 16782. The Policimbac® plate had an excellent 98.04% categorical agreement, but unacceptable 31.37% essential agreement rates. Almost 2% of major errors as observed. Additionally, 52.94% of the strains overestimated the MIC at 1 µg/mL. Three isolates were excluded from the analysis due to the drying of the Policimbac® plate. To avoid dryness, we included wet gauze for the test, obtaining a 100% of categorical agreement rate; however, a low essential agreement was maintained (25.49%). In conclusion, the Policimbac® plate was unable to correctly determine the polymyxin B MIC for K. pneumoniae isolates. This low performance may interfere with the clinical use of the drug and, thus, with the result of the patient's treatment.

[The evolution of Brazilian human health policies for the prevention and control of antimicrobial resistance: a scoping reviewEvolución de las políticas de prevención y control de la resistencia a los antimicrobianos desde la perspectiva de la salud humana en Brasil: revisión exploratoria]

Objective

To map the policies related to the prevention and control of antimicrobial resistance from a human health perspective in Brazil and systematize the historical course of these policies.

Method

A scoping review was performed following Joana Briggs Institute and PRISMA guidelines. A literature search was performed in December 2020 in the LILACS, PubMed and EMBASE databases. The terms "antimicrobial resistance" AND "Brazil" as well as their synonyms were used. Using the same keywords, Brazilian government websites were searched for documents published until December 2021. Studies of all designs were included, with no language or date restrictions. Clinical documents, reviews and epidemiological studies that did not focus on antimicrobial resistance management policies in Brazil were excluded. Categories based on World Health Organization documents were used for data systematization and analysis.

Results

In Brazil, policies related to antimicrobial resistance such as the National Immunization Program and hospital infection control programs can be traced back to before the creation of the Unified Health System. In the late 1990s and 2000s, the first specific policies on antimicrobial resistance (surveillance networks and programs) and education strategies were established; especially noteworthy is The National Action Plan for the Prevention and Control of Antimicrobial Resistance in the Single Health Scope (PAN-BR) of 2018.

Conclusions

Despite the long history of policies related to antimicrobial resistance in Brazil, gaps were identified, particularly in monitoring the use of antimicrobials and surveillance of antimicrobial resistance. The PAN-BR, the first government document prepared from a One Health perspective, represents an important milestone.

Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil

Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.

Country data on AMR in Brazil in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome

BACKGROUND

Antimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.

OBJECTIVES

To review the situation with respect to AMR in Brazil and initiatives addressing it. Identifying areas where more information is required will provide a call to action to minimize any further rises in AMR within Brazil and to improve patient outcomes.

METHODS

National initiatives to address AMR, antibiotic use and prescribing in Brazil, and availability of susceptibility data, particularly for the key community-acquired respiratory tract infections (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines for CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) commonly used locally were also reviewed, along with local antibiotic availability.

CONCLUSIONS

In Brazil there have been some initiatives addressing AMR such as the National Action Plan for AMR, established in 2018. Antibiotic consumption in Brazil is high but a ban on over-the-counter sales of antibiotics has led to a decrease in consumption. Local antibiotic susceptibility testing needs to be increased and the Survey of Antibiotic Resistance (SOAR) study in Brazil will provide useful data for pathogens causing CA-RTIs. A more standardized inclusive approach in developing local guidelines, using up-to-date surveillance data of isolates from community-acquired infections in Brazil, could make guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve clinical outcomes for patients.

Current status of NDM-producing Enterobacterales in Brazil: a narrative review

New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales was first detected in Brazil in 2014, in a Providencia rettgeri isolate recovered from surveillance swabs in the Southern region. Since then, an increasing number of NDM enzymes have been reported in different species. Nevertheless, comprehensive data on the current epidemiology of NDM-producing Enterobacterales in Brazil are lacking. Therefore, this study reviewed the available information on the status of NDM-producing bacteria in Brazil. The main finding was the diversity of bacteria producing NDM, including Klebsiella, Enterobacter, Morganella, Proteus, Escherichia, and Providencia. Limited data on clonality are available, but a few studies report different clonal backgrounds in NDM-producing K. pneumoniae, likely indicating local outbreaks. Over the years, a rise in the number of reported strains in different locations has been verified; however, different biases may have contributed to this finding. Therefore, a national surveillance study is warranted to identify the actual prevalence and incidence of NDM-producing Enterobacterales in Brazil and their role in patient management and outcome.

COVID-19 and zoonoses in Brazil: Environmental scan of one health preparedness and response

The emergence of the COVID-19 pandemic reinforced the central role of the One Health (OH) approach, as a multisectoral and multidisciplinary perspective, to tackle health threats at the human-animal-environment interface. This study assessed Brazilian preparedness and response to COVID-19 and zoonoses with a focus on the OH approach and equity dimensions. We conducted an environmental scan using a protocol developed as part of a multi-country study. The article selection process resulted in 45 documents: 79 files and 112 references on OH; 41 files and 81 references on equity. The OH and equity aspects are poorly represented in the official documents regarding the COVID-19 response, either at the federal and state levels. Brazil has a governance infrastructure that allows for the response to infectious diseases, including zoonoses, as well as the fight against antimicrobial resistance through the OH approach. However, the response to the pandemic did not fully utilize the resources of the Brazilian state, due to the lack of central coordination and articulation among the sectors involved. Brazil is considered an area of high risk for emergence of zoonoses mainly due to climate change, large-scale deforestation and urbanization, high wildlife biodiversity, wide dry frontier, and poor control of wild animals' traffic. Therefore, encouraging existing mechanisms for collaboration across sectors and disciplines, with the inclusion of vulnerable populations, is required for making a multisectoral OH approach successful in the country.

Minas Artisanal Cheese As Potential Source of Multidrug-Resistant Escherichia coli

Bacteria develop resistance to antibiotics naturally, but the inappropriate and widespread use of antibiotics in humans and animals has made antimicrobial resistance one of the biggest threats to modern medicine. Raw milk cheese can represent an important source of antimicrobial resistance. Thus, the objective of this study was to evaluate the prevalence and sensitivity of Escherichia coli isolated from artisanal cheese made from raw milk produced in Minas Gerais, Brazil. E. coli counts were determined using the most probable number method. An antibiogram was performed using the disk diffusion method, following the protocol described by the Brazilian Committee on Antimicrobial Susceptibility Testing (BrCAST) for 14 antibiotics of nine classes. E. coli was detected in 35 (71.4%) of the samples, with populations between 0.56 to 4.87 log (NMP/g) of cheese. The presence of E. coli resistant to multiple antimicrobials was more frequent in cheeses, with an E. coli population below the levels established by regulatory limits. Only four samples (11.4%) had all E. coli isolates susceptible to the 14 antimicrobials evaluated. The results showed the heterogeneity of antimicrobial resistance in E. coli between the producing regions of Minas artisanal cheese. Multidrug resistance was detected in 29% of the E. coli isolates and in almost 40% (38.8%) of the cheese samples. The frequency of multidrug-resistant (MDR) isolates was different between the production regions (p < 0.05). The presence of MDR E. coli in cheese from region D was 14, 4, and 20 times more likely than in cheese from regions A, B, and C, respectively. A multiple antibiotic resistance index of 0.200 predicted the presence of MDR E. coli in raw milk artisanal cheese with 99% probability. In conclusion, artisanal cheese can act as sources of MDR E. coli to colonize the human gastrointestinal tract.

Electronic information systems for One Health surveillance of antimicrobial resistance: a systematic scoping review

INTRODUCTION

Electronic information systems (EIS) that implement a 'One Health' approach by integrating antimicrobial resistance (AMR) data across the human, animal and environmental health sectors, have been identified as a global priority. However, evidence on the availability, technical capacities and effectiveness of such EIS is scarce.

METHODS

Through a qualitative synthesis of evidence, this systematic scoping review aims to: identify EIS for AMR surveillance that operate across human, animal and environmental health sectors; describe their technical characteristics and capabilities; and assess whether there is evidence for the effectiveness of the various EIS for AMR surveillance. Studies and reports between 1 January 2000 and 21 July 2021 from peer-reviewed and grey literature in the English language were included.

RESULTS

26 studies and reports were included in the final review, of which 27 EIS were described. None of the EIS integrated AMR data in a One Health approach across all three sectors. While there was a lack of evidence of thorough evaluations of the effectiveness of the identified EIS, several surveillance system effectiveness indicators were reported for most EIS. Standardised reporting of the effectiveness of EIS is recommended for future publications. The capabilities of the EIS varied in their technical design features, in terms of usability, data display tools and desired outputs. EIS that included interactive features, and geospatial maps are increasingly relevant for future trends in AMR data analytics.

CONCLUSION

No EIS for AMR surveillance was identified that was designed to integrate a broad range of AMR data from humans, animals and the environment, representing a major gap in global efforts to implement One Health approaches to address AMR.

Quality Assessment of an Antimicrobial Resistance Surveillance System in a Province of Nepal

Antimicrobial resistance (AMR) is a global problem, and Nepal is no exception. Countries are expected to report annually to the World Health Organization on their AMR surveillance progress through a Global Antimicrobial Resistance Surveillance System, in which Nepal enrolled in 2017. We assessed the quality of AMR surveillance data during 2019-2020 at nine surveillance sites in Province 3 of Nepal for completeness, consistency, and timeliness and examined barriers for non-reporting sites. Here, we present the results of this cross-sectional descriptive study of secondary AMR data from five reporting sites and barriers identified through a structured questionnaire completed by representatives at the five reporting and four non-reporting sites. Among the 1584 records from the reporting sites assessed for consistency and completeness, 77-92% were consistent and 88-100% were complete, with inter-site variation. Data from two sites were received by the 15th day of the following month, whereas receipt was delayed by a mean of 175 days at three other sites. All four non-reporting sites lacked dedicated data personnel, and two lacked computers. The AMR surveillance data collection process needs improvement in completeness, consistency, and timeliness. Non-reporting sites need support to meet the specific requirements for data compilation and sharing.