Analyzing Resistance to Last Line Antibiotics in the Post-COVID-19 Era in Argentina
In the wake of COVID-19, antimicrobial resistance (AMR) has surged, posing a grave threat to healthcare systems worldwide. In Argentina, scientists are racing to understand and counter the AMR threats in their region, particularly against carbapenem-resistant bacteria, known as the 'last line' of defense in treating severe infections.
Background
Due to stressors on the healthcare system, such as overcrowding and increased use of antibiotics, AMR has worsened in the post-pandemic era. To better understand resistance to carbapenems, last line antibiotics reserved for serious, highly-resistant infections, Argentina's Antimicrobial Division, the National Reference Laboratory for Antimicrobial Resistance (NRL), located in the National Institute of Infectious Diseases (INEI) ANLIS "Dr. Carlos G. Malbrán", collaborated with U.S. CDC, IANPHI-US, and Emory University to conduct a study to better understand this clinically-important resistance in Argentina.
Initial Study
This work built on prior research conducted by the Antimicrobial Division in 2023. This research included a national prevalence survey that was conducted across Argentina to understand the epidemiology of carbapenem-resistant Enterobacterales and collected clinical samples from 183 hospitals across the 24 jurisdictions of Argentina. Eight hundred and twenty-two carbapenem-resistant Enterobacterales isolates were identified.
That study also identified a new and concerning AMR landscape in Argentina, with mobile genetic elements (i.e., plasmids) carrying genes that code for a specific type of carbapenem resistance, called carbapenemases[1], that bacteria can easily trade and acquire. This makes it easy for carbapenemase-producing Enterobacterales (CPE) to spread rapidly in hospitals and beyond. The study identified two major types of CPE, Klebsiella pneumoniae-Carbapenemase (KPC) and New Delhi-Metalloenzyme (NDM), circulating in the clinical isolates, as well as clinical isolates with multiple combinations of carbapenemases (e.g., NDM+KPC).
CPE are challenging to treat with the antibiotics currently available in Argentina and are associated with increased illness and death and healthcare costs. However, further characterization of these AMR concerning CPE via molecular methods, including long-read whole genome sequencing (WGS)[2], was not possible at the time the study was conducted, due to budget restraints and limited infrastructure to conduct advanced molecular sequencing testing.
Enhancing Research Capacity: Genomic and Epidemiologic Analysis of CPE in RECAPT-AR-II
Given the concerning resistance identified, a follow-on study was funded by U.S. CDC. From September 2023 through July 2024, U.S. CDC aimed to strengthen the Antimicrobial Division's capacity for long-read WGS by supporting further characterization of the CPE isolates.
This project was structured into three main modules. The first module focused on upgrading and expanding the capacity of the Antimicrobial Division's laboratory with second and third-generation WGS supplies and equipment. The second module concentrated on training Antimicrobial Division scientists in the use of third-generation WGS and bioinformatics. The aim was to support laboratory capacity in this area and to standardize bioinformatics protocols and genomic analytic skills. In June of 2024, two young-career scientists traveled to U.S. CDC for training in both laboratory and bioinformatics techniques. This training was crucial for improving the Antimicrobial Division's competency to perform a comprehensive study of the molecular epidemiology of CPE isolates.
Malbrán's scientist setting up for third generation DNA sequencing technology in the Antimicrobial Division the first time.
The training at U.S. CDC provided an opportunity for the Antimicrobial Division to advance its capacity to conduct and analyze long-read WGS using modern techniques and efficient workflows. The 21-day program included one week of bench work and two weeks of bioinformatics training for the two Argentine scientists, ensuring that the acquired knowledge was effectively transferred back to the NRL.
Utilizing the knowledge from the training at U.S. CDC headquarters to characterize the isolates will allow the Antimicrobial Division to offer more informed guidance to the public health system on emerging and potentially novel genetic mechanisms of resistance circulating in Argentina. In addition, this capacitation is crucial for developing evidence-based infection control measures, outbreak responses, and providing ongoing reference laboratory services for Argentina and the region.
Knowledge Exchange and Networking
Finally, the third module of this study aimed to communicate the scientific work of the Antimicrobial Division. Through this collaboration, the Antimicrobial Divison's senior researcher was able to attend the European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) in Barcelona in April 2024. The Division's extensive research on Gram-negative pathogens was showcased through seven poster presentations, each contributing valuable insights into the field. The work presented explored new therapeutic options for challenging infections, including the efficacy of novel β-lactam combinations. The work done also evaluated advanced diagnostic tools for detecting various carbapenemase variants, which are crucial for timely and accurate identification of resistant strains in the post COVID-19 epidemiological context. Other Antimicrobial Division posters presented at ECCMID focused on demonstrating the impact of implementing rapid and economic methods to detect resistant Gram-negative bacteria in the general wards, highlighting the practical benefits of their work in infection control.
The project also supported the two scientists that received training at CDC to attend the ASM Microbe conference that took place in Atlanta, Georgia in June 2024. ASM Microbe is one of the largest microbial science meetings in the world, where scientists can meet, exchange knowledge and views. Attendance at the congress allowed them to attend the poster presentation of work in which they collaborated, the keynote sessions, the Meet the Expert symposia and attend mini conferences focusing on specific topic areas in the microbial sciegion.
Overcoming Challenges
Among the various activities, the Argentinean team is most proud of its handling of budget execution challenges amidst local regulatory complications, supply cost fluctuations, delivery constraints, and price changes. Overcoming these challenges required proactive communication with IANPHI and Emory, as well as with suppliers and strategic budget adjustments. The team's ability to adapt to changing circumstances and optimize resource allocation reflects its commitment to project sustainability and responsibility, highlighting its capacity to overcome obstacles and ensure the project's progression.
Conclusion
The success of this project mainly resides in the relationships built among the working groups at CDC, IANPHI, Emory and Malbrán's institute through continuous interaction and communication. In particular, the role and commitment of CDC staff in Buenos Aires was crucial, articulating logistical and academic activities related to the development of the project.
This pioneering collaboration between Malbrán's Antimicrobial Division, CDC, IANPHI, and Emory University has strengthened Argentina's ability to monitor, study, and respond to antimicrobial resistance at a critical time. The training, technical upgrades, and networking opportunities have laid a solid foundation for the Division to continue advancing AMR research and develop targeted infection control measures. By building the capacity for long-read whole genome sequencing and bioinformatics analysis, the Antimicrobial Division is now better equipped to detect emerging resistance patterns and inform timely interventions.
The experience and resilience gained through this project will support Argentina's broader public health goals and serve as a model for similar efforts in other countries and in NPHI Regional Labs. As the team looks forward, they remain committed to leveraging these skills and partnerships to ensure that insights gained from their research can inform policies and clinical practices, protecting communities from the escalating threat of antimicrobial resisegion.
[1] Carbapenemases are enzymes produced by bacteria that break down many types of antibiotics, including carbapenems, penicillins, cephalosporins, and monobactams.
[2] Long-read sequencing is a form of next-generation sequencing (NGS) that has technical advantages over short-read sequencing for the detection of specific types of genetic variation.