CarbaPhOrGe: Carbapenem resistance monitoring in hospital wastewaters

Network-wide hospital wastewater monitoring of carbapenem resistance through mining of bacteriophages, carbapenem-resistant organisms, and carbapenemase genes in urbanized areas of the Philippines toward applications in therapeutics, epidemiology, and diagnostics.

Mark Carascal, Registered Microbiologist and Senior Science Research Specialist of the Clinical and Translational Research Institute, The Medical City Philippines

Carbapenem-resistant organisms (CROs) remain the most urgent antimicrobial resistance (AMR) threat in low-to-middle-income countries (LMICs) like the Philippines. The latest nationwide surveillance report revealed carbapenem resistance rates between 10-52% among local Gram-negative isolates [1], with reports of superbug persistence in wastewaters [2]. Carbapenem resistance is expected to result in significant mortality and enormous economic toll in the next decade, with Southeast Asia at its epicenter [3]. Despite the impact, microbiological and molecular data in locally circulating CROs are unknown. This limits the progress on innovations in diagnostics, therapeutics, and infection control in LMICs.

Hospital wastewater antimicrobial resistance surveillance (HARS) is an emerging but understudied framework adaptable in LMICs [4]. The data could reflect the epidemiology of carbapenem resistance within the surrounding localities, providing insights into the spread and evolution of this AMR in areas being studied. 

The CarbaPhOrGe aims to monitor the microbiological and genetic drivers of carbapenem resistance in hospital wastewater through a network-wide HARS implementation, and ultimately provide scientific resources that could be used in developing innovations against CROs. The CarbaPhOrGe hopes to contribute to solving important One Health issues including the spread of antibiotic resistance and monitoring environmental contamination of resistant pathogens.

The CarbaPhOrGe envisions serving multiple stakeholders in healthcare, public health, and health regulations, with the lack of accurate and high coverage AMR-related data and resources as their common need.

In terms of healthcare stakeholders, scientists and clinicians are direct beneficiaries of CarbaPhOrGe since all the information and tangible resources produced from the solution (i.e., phage and superbug biobanks, genomic sequences) can be used for innovating alternative therapeutics and molecular diagnostics against carbapenem-resistant infections. These innovations, in turn, can also directly benefit the actual patient population and could lead to more funding opportunities for other antibiotic resistance surveillance research.

In terms of the public health aspect, communities and epidemiologists are also direct beneficiaries as the data generated (i.e., superbug clonality, core resistome) could be used as a reference in developing more effective infection/ pathogen/ AMR spillover control measures and antibiotic stewardship programs for the hospitals and the communities.

Finally, health policymakers and clinical guidelines developers are also direct beneficiaries as this preliminary surveillance data can serve as a basis for revamped national antibiotic usage policies.

Engagement among the stakeholders will be done through our established hospital network connections to local government units and collaborations with research and medical institutions.

The CarbaPhOrGe will provide public good through the publication of seminal information on carbapenem resistance epidemiology and evolution in the Philippines as reflected in the microbiological and genomic characteristics of hospital wastewaters within highly urbanized communities. The resulting information could be used by the various stakeholders identified (i.e., scientists, clinicians, patients, communities, epidemiologists, health policy makers/ regulators) through the development of new products (i.e., alternative therapeutics from phages, molecular testing kits for carbapenemase genes from the core resistome) or through adaptive policies on antibiotic usage and infection control. The tangible resources produced (PHageBank, TMC Microbial Culture Collection of reference antibiotic-resistant isolates) will also be available for use by local and international researchers for further development of products or services against AMR for the benefit of LMICs.

The CarbaPhOrGe will create a significant impact on the identified stakeholders (i.e., scientists, clinicians, communities, epidemiologists, and health policy makers/ regulators) by providing much-needed surveillance data to eventually develop products, policies, and additional research for combating the spread of carbapenem resistance within the local (and ultimately, regional and global) communities. Through the information generated from the project, alternative therapeutics and molecular diagnostic products could be innovated, thereby impacting patients and reducing the potential economic tolls brought about by AMR-related hospitalization and mortality. Finally, through hospital wastewater surveillance, early detection of potential AMR outbreaks or the discovery of new resistance drivers within the locality could be established, as successfully shown in the recent monitoring of poliovirus and SARS-CoV-2 from wastewater [12].

The CarbaPhOrGe will be a continuous surveillance initiative that can be scaled up to involve other public hospitals and rural communities. As such, the first three years of the pilot implementation will focus on optimizing adaptability and centralizing laboratory processes and data generation within the implementing institutions.

Year 1: Onsite implementation

The pilot implementation for year one will define the appropriate sampling workflows at the main hospital site (TMC Pasig). Scalability of the sampling process will be ensured by developing standard sampling kits that require minimal training. High-level laboratory workflows will be established at TMC Pasig.

Year 2: Nearby site implementation

The optimized sampling workflow will be replicated in nearby hospital sites (TMC South Luzon, TMC Pangasinan, and TMC Clark). Sample collection will be done remotely, with minimal sample processing before sending out to the central laboratory in TMC Pasig.

Year 3: Long-distance implementation

The optimized sampling workflow will be replicated in a farther hospital site (TMC Iloilo) and selected community-based clinics within TMC network (located in different parts of the Philippines). Microbiological and molecular isolation processes will be done remotely, with the stable samples (transport cultures, DNA extracts) to be sent out to the central laboratory in TMC Pasig.

The following measurable indicators will be used to monitor the success of CarbaPhOrGe in each of its target aspects:

• Bacteriophage aspect- number of fully characterized bacteriophages in the established PHageBank, number of novel bacteriophages, depth of phagogram against carbapenem-resistant pathogens

• Carbapenem-resistant organisms aspect- number of fully characterized bacteria in the established TMC Microbial Culture Collection, occurrence of carbapenemase genes, depth of pathogen clonality and resistance gene mapping

• Carbapebemase genes aspect- occurrence of transferrable carbapenemase genes or mobile genetic elements, depth of core resistome

The impact of CarbaPhOrGe will be measured through the following outputs and outcomes:

• Publication- number of publications directly arising from the solution, and indirectly from the new research projects derived from the solution

• Products- number of intellectual properties and tangible innovations directly arising from the use of the generated surveillance data

• Policies- number of drafted and implemented community policies and clinical guidelines relating to carbapenem usage and carbapenem-resistant infection control

• People- number of trained hospital and community workers on the basic aspects of hospital wastewater antibiotic resistance surveillance

• Partnerships- number of new hospitals and communities outside the current network adapting the surveillance system for other antibiotic resistance monitoring efforts

The current barriers in the network-wide implementation of CarbaPhOrGe include limitations in finances, direct access to the core facilities and sequencing technologies, and involvement of community/ regulatory stakeholders in routine surveillance efforts. 

• Financial barriers- currently, the in-house implementation in the main site is achievable given our ongoing centralized research funding. However, given that the other network sites do not have access to these grants, smaller-scale intramural grants could be adapted for nearby site implementation, or bigger coverage grants (government- or industry-sponsored) could be pursued to complete the network-wide implementation.

• Access barriers- while the main implementation site has a dedicated research laboratory facility, the other network sites will only rely on their existing clinical microbiology laboratories for sample processing before analysis. A simple sample processing workflow using a defined kit with minimal training requirements will be adapted to address this challenge. Meanwhile, none of the network sites have in-house sequencing technologies. Hence, send-out sequencing services from local suppliers could be done, with in-house bioinformatic analysis.

• Stakeholder involvement barriers- parallel to the implementation of the surveillance system, regulatory and community involvement will be ensured through our established connections with the local government units for each hospital network.

As an emerging center of excellence for innovations in clinical microbiology, our hospital network, through our collaborative research programs, aims to be at the forefront of cutting-edge yet adaptable solutions in solving urgent threats to global health such as antibiotic resistance. The Trinity Challenge provides an avenue for us to realize this objective by allowing us to leverage the strengths of our network to implement a more scalable microbiological and molecular surveillance of carbapenem resistance that is more representative of the locality compared to just a single-site implementation. The Trinity Challenge also addresses all the barriers identified for the project as it will: (1) provide financial grant to pursue high-level scientific investigation towards attaining the project objectives, (2) help establish a core sequencing and bioinformatics facility that could be used for the continuous surveillance of carbapenem and other antibiotic resistance, and (3) provide a mechanism for producing seminal data that could be used as a starting point for stakeholder discussions. Finally, the Trinity Challenge can help us pivot towards a more holistic approach in studying antimicrobial resistance in the Philippines, with aspects not only covering the hospital setting but also the environment and the communities (aligning with One Health approach).

Through the CarbaPhOrGe, we wish to collaborate with member organizations that could help us further expand our surveillance and resource generation efforts on regional (i.e., Southeast Asia) and global scales. In this aspect, Wellcome could potentially provide extended grant support and network that are beneficial for sustainable solution implementation. Meanwhile, in terms of the technical aspect of implementing CarbaPhOrGe, collaborating with the University of Cambridge, Northeastern University, and Imperial College London would prove to be beneficial as all of these institutions have already established wastewater surveillance research programs. Finally, in terms of developing expanded solutions out of the surveillance data from CarbaPhOrGe, collaborating with GSK, the Global Virome Project, and Google could lead to more innovative products and services relating to alternative therapeutics, molecular diagnostics, or core resistome dashboards that impact our most important stakeholders: the patients and the community.

The Global Health Network announcement