Investigation of LA-MRSA in China and the UK

Both in China and the UK methicillin resistant Staphylococcus aureus (MRSA) remain an important problem that can lead to life threatening infections. A type of MRSA called livestock-associated MRSA (LA-MRSA) has been found both in China and the UK. While many strains of S. aureus seem to be restricted to particular host species, LA-MRSA are characterised by the fact that they freely jump between farm animals and people. The reservoir of LA-MRSA found on farms represents a considerable threat to human health and accounts for a large proportion of human MRSA infections in countries such as Denmark and the Netherlands. Recent reports from China show that the dominant LA-MRSA strains in China are different to those in Europe and North America. This research will determine the prevalence of LA-MRSA in China. Using whole genome sequencing, LA-MRSA found in people and animals will be compared to determine if these bacteria are transmitted from farms to people and also to look for genes that may be associated with the ability of LA-MRSA to colonise both people and animals. Farms where LA-MRSA are found will be compared to farms free of LA-MRSA to investigate any risk factors that may be associated with the presence of LA-MRSA. Further investigations of the host specificity of LA-MRSA will be performed using a technique called transposon mutagenesis. A library of many thousands of mutants will be made in LA-MRSA strains and used to identify individual genes that may play a role in enabling LA-MRSA avoid the immune defences of host animals and people.

The aim of the proposed research is to investigate livestock-associated MRSA (LA-MRSA) in China and the UK. LA-MRSA is an increasing problem in both China and the UK. The ST398 lineage is responsible for the majority of LA-MRSA carriage in European and North American farm animals, while in Asia the ST9 lineage is the dominant LA-MRSA type. This study will determine the prevalence and population structure of LA-MRSA in the two counties, and use functional genomics to investigate the genetic basis of the broad host species specificity demonstrated by LA-MRSA.

The proposed research is divided into 4 work packages:

WP 1: Measurement of the prevalence of LA-MRSA in pig farms in China in a cross-sectional survey. Isolates from the survey will be sequenced to determine the population structure and molecular epidemiology of LA-MRSA in China. This WP also includes a survey of human MRSA isolates from hospitals in the same region.

WP2: A case control study, to compare pig farms where LA-MRSA is present with those where it is absent, will be performed with a greater depth of sampling and further sequencing of MRSA and S. aureus (MSSA) in order to identify potentially out-competing methicillin susceptible (MSSA) lineages, and husbandry and management factors that may be associated with the presence of LA-MRSA.

WP3: Generation of transposon (Tn) mutant libraries of representative strains from the major lineages of LA-MRSA (ST398 MRSA in the UK and ST9 in China), and host (1 human and 1 porcine) specific lineages, and use these Tn mutant libraries in conjunction with Tn-seq to identify genes that may be associated with host colonisation, using in vitro assays as a proxy for infection/carriage.

WP4: In addition to conventional next generation sequencing chromosome conformation metagenomics (Hi-C and meta3c) will be used to look at the diversity in the staphylococcal flora both in pigs carrying LA-MRSA and those free from LA-MRSA from the same farms.

China has a flourishing and economically important pig industry. Food security and public confidence are particularly important to ensure adequate domestic supply and to reduce demand for foreign imports. Livestock-associated MRSA represent just one of the antimicrobial resistance issues facing the industry, but it provides a useful sentinel that has a clearly defined human health impact. The development of successful measures to control this reservoir of antimicrobial resistance, quite apart from the direct benefits, will show how the problem may be tackled more widely. This project has narrowly defined, achievable objectives which go beyond merely measuring the extent of the problem. This research aims to build upon existing Chinese research excellence with a collaboration that will generate improved and increased research capacity to provide solutions to antimicrobial resistance problems.

Informed decision-making concerning antimicrobial resistance can only be achieved in the light of reliable scientific data. This study will initially answer two important questions. Firstly how much livestock-associated MRSA is present in China? and secondly, is it the source of human MRSA infections? The answers to these questions will clearly help inform decisions on the actions and priories needed in an integrated animal and public health programme.

The first part of this study involves an evaluation of the reservoir of LA-MRSA in three provinces of Central China surrounding Wuhan (Hubei, Henan, Hunan) in order to establish a farm-level prevalence. The financial limitations imposed by the call restricts the geographical scope of the research, although additional studies are planned involving this consortium to expand this research to cover more areas of China. Nonetheless accurately establishing a baseline value for LA-MRSA in one region provides a valuable reference that can be used to look at changes over time. The impact of policies designed to reduce antimicrobial resistance levels in farm animals can only be measured if there is reliable data available prior to the implementation of such policies for comparison.

The farm level case control study will identify any obvious management and disease control factors that may affect the likelihood of LA-MRSA becoming established on pig farms (such as particular antibiotic regimens). This information will be of direct use to farmers and agricultural advisors.

The fundamental research into the host specificity of S. aureus will potentially lead to the development of therapeutic interventions that prevent or reduce the carriage of MRSA in both people and animals. This could be as simple as identifying strains of S. aureus that out compete MRSA on hosts so that these might be incorporated into a probiotic-like treatment. The functional genomics may reveal genes that play an important role in determining the host specificity that may then become targets for non-antibiotic pharmaceuticals. Any approach that reduces the need for antibiotics will contribute to a reduction in the selective pressure that generates antimicrobial resistance and help preserve the efficacy of antibiotics used in human and veterinary medicine.

The proposal includes 2 PhD studentships and 8 Masters studentships in China which will contribute to the research capacity and expertise in antimicrobial resistance research in China.