Whole-genome sequencing to investigate the prevalence and transmission multidrug-resistant organisms in intensive care units in Hanoi, Vietnam

Background
Increasing resistance to antibiotic drugs is one of the greatest threats to human health, and is estimated to cause 700,000 deaths annually. Bacteria that are resistant to many antibiotics are called multidrug-resistant organisms (MDRO). They are more commonly found in hospitals, where they may cause healthcare-associated infections (HCAI). Patients in intensive care units (ICU) are more vulnerable to HCAI. Several outbreaks of infection with MDRO have been reported in intensive care units, and are associated with high death rates. Methods to improve the early detection and prompt management of MDRO are urgently required.

Microbial whole-genome sequencing (WGS) is a new technology that is transforming the way that we identify and treat infections. Advances in technology mean that it now possible to work out the genetic code (DNA) of a bacterium in one day at a reasonable cost. This can give us lots of information including the name of the organism, what antibiotics it is resistant to, and what virulence factors are present that may cause harm to humans.

Vietnam has a high burden of infectious diseases with rising mortality rates. In 2010, 30% of deaths in state health facilities were estimated to be infectious diseases related. Vietnam also has high levels of resistance to antibiotics. As a result, current antibiotic guidelines are unlikely to be effective and may result in high death rates. There is currently no surveillance system for looking for antibiotic-resistant bacteria, and no national policy or guidelines on the best way to detect and manage these organisms.

Aims and objectives of the research
The aims of this project are four-fold:
1. To determine the prevalence and transmission of MDRO in intensive care units (ICU) in two hospitals in Hanoi, Vietnam, using bacterial whole-genome sequencing (WGS)
2. To use rapid WGS for the investigation of a putative outbreaks of infection in two intensive care units in Hanoi, Vietnam
3. To provide training in sequencing and bioinformatics to Vietnamese scientists and build clinical and laboratory capacity to tackle MDRO in Vietnam
4. To use the data from these studies to inform infection control practice and public health policy for the surveillance and management of MDRO in Vietnam.

Research studies
We will conduct two research studies in the ICUs at the National Hospital for Tropical Diseases (NHTD) and Bach Mai Hospital (BMH) in Hanoi, Vietnam:

1. Prospective observational cohort study
This study will include all patients admitted to the ICU during the study period. We will collect clinical and laboratory information and samples on admission to ICU, on discharge from ICU and weekly in patients who are admitted to ICU for 7 days or more. Samples will be processed in the laboratory at NHTD and DNA extracts will be shipped to the Wellcome Trust Sanger Institute (WTSI) in the UK for high throughput WGS. This study will give us information about how common MDRO are in this setting, how often these organisms are transmitted between patients, and provide genomic context for the second study.

2. Prospective surveillance and outbreak investigation
This study will perform prospective surveillance for outbreaks of MDRO by performing rapid WGS on samples collected from patients during a suspected outbreaks of infection in the ICUs. Clinical and laboratory information and samples will be collected from all patients in the suspected outbreak and from patients who we do not think are involved in the outbreak (control patients). Samples will be sequenced at NHTD and information will be fed back to clinicians / infection control staff to help them to manage the outbreak. This study will enable sequencing and bioinformatic analysis to be performed locally, thus facilitating translation of rapid microbial WGS into the clinical environment to inform clinical care and infection control practices in real-time.

Clinical studies will be based in the ICUs the National Hospital of Tropical Diseases (NHTD) and Bach Mai Hospital (BMH),Hanoi, Vietnam.

Study 1: A prospective observational cohort study of all patents admitted to ICU. All patients admitted to the ICU during the study period will be screened for MDRO. Samples will be collected on admission to ICU, on discharge from ICU, and weekly from patients whose duration of admission is 7 days or more. We will also collect environmental samples during the study period. Samples will be processed to identify target organisms e.g. methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), and carbapenem-resistant GNB. Samples will also undergo DNA extraction and quantification at NHTD and DNA extracts will be shipped to the Wellcome Trust Sanger Institute (WTSI) for high-throughput sequencing. Clinical and laboratory data will be collected and analysed using a standard statistical methods. Bacterial sequence data will be analysed using WTSI bioinformatic pipelines. This study will provide information about the prevalence and transmission rates of MDRO in this setting, and will provide genomic context for Study 2. It will also train Vietnamese scientists in sequencing and bioinformatics, and build clinical and laboratory capacity to tackle HCAIs using WGS.

Study 2: Investigation of a putative outbreak of MDRO on the ICUs
All patients admitted to the ICUs during the study period will be screened for MDRO using methods determined in Study 1. If a suspected outbreak of infection occurs (e.g. an increase in the number of patients colonised with a particular organism) intensified surveillance will be performed (e.g. twice weekly screening). Samples will also undergo DNA extraction, library preparation and WGS on a rapid sequencing platform in the microbiology laboratory at NHTD. Bacterial sequence data will be analysed using bioinformatics pipelines developed during study 1. This study

We will seek to actively identify and engage all of the relevant stakeholders at various stages of the research project i.e. during study preparation and set-up, during the course of the research studies, and when we present and disseminate the research findings.

This project will establish new collaborations between a multi-disciplinary group of researchers at leading UK and Vietnamese institutions. The investigators involved in the research will acquire new knowledge and expertise on the prevalence and transmission of MDRO in Vietnam.
The proposed studies will be the first comprehensive surveillance studies of MDRO in an ICU setting in Vietnam. They will not only establish the prevalence of these organisms but also enable us to accurately define transmission pathways. This research has the potential to benefit patients with MDRO in Vietnam, particularly those who are involved in an outbreak during the study period, as it will enable rapid diagnosis and implementation of appropriate infection control measures.

The research will result in capacity building through training of Vietnamese scientists, and enable the translation of cutting-edge technology into a developing country setting to enable local investigation and management of HCAIs. We will organize / provide training in sequencing and bioinformatic analysis to the study investigators, drawing in the existing expertise and infrastructure available in Cambridge and at the Wellcome Trust Sanger Institute. This will comprise attendance at training courses and personal supervision.

The results of these studies will be presented at national and international meetings and published in peer-reviewed journals. It will therefore benefit the scientific community both in Vietnam and beyond. We will also disseminate the findings via institutional press releases / websites, standard media outlets (websites, newspaper, television and radio interviews) and social media (e.g. Twitter).

The information gained from these studies will be used to develop local infection control procedures to control MDRO in the Vietnamese healthcare setting during the course of the project. We will engage with local clinicians and infection control practitioners to develop appropriate policies and procedures for use in the 2 hospitals.

These studies will also provide a framework for systematic surveillance of MDRO, which could be used to develop national public health policy for the surveillance and management of MDRO on a wider scale and in the longer term. We will engage with national stakeholders (e.g. the Ministry of Heath) to help develop appropriate strategy for the surveillance and management of MDRO in Vietnam. These may also be applicable to other countries that have similarly high rates of MDRO, and which lack infection control and public health policies and procedures.

In terms of beneficiaries within the commercial private sector these are likely to include companies that currently manufacture commercially available rapid sequencing platforms (e.g. Illumina Inc and Pacific Biosciences). The challenge will be for them to reduce the costs of consumables such that these platforms can be used in resource-constrained settings where the costs of sequencing are currently prohibitive for clinical use. Companies that manufacture rapid sequencing platforms that can sequence bacteria directly from clinical samples (e.g. Oxford Nanopore) are likely to benefit in the future. Finally, the research training, laboratory skills and bioinformatic analysis skills obtained during the project are potentially transferable to other sectors.