Abstract
A large portion of annual deaths worldwide are due to infections caused by disease-causing pathogens. These pathogens contain virulence genes, which encode mechanisms that facilitate infection and microbial survival in hosts. More recently, antimicrobial resistance (AMR) genes, also found in these pathogens, have become an increasingly large issue. While the National Center for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser (NPDIB) database has been compiling genes involved in microbial virulence and antimicrobial resistance through isolate samples, few studies have identified the genes primarily responsible for virulence and compared them to those responsible for AMR. This study performed the first multivariate statistical analysis of the multidimensional NPDIB data to identify the major virulence genes from historical pathogen isolates for Australia, China, South Africa, UK, and US—the largely populated countries from five of the six major continents. The important virulence genes were then compared with the AMR genes to study whether there is correlation between their occurrences. Among the significant genes and pathogens associated with virulence, it was found that the genes fdeC, iha, iss, iutA, lpfA, sslE, ybtP, and ybtQ are shared amongst all five countries. The pathogens E. coli and Shigella, Salmonella enterica, and Klebsiella pneumoniae mostly contained these genes and were common among four of the five studied countries. Additionally, the trend of virulence was investigated by plotting historical occurrences of gene and pathogen frequency in the annual samples. These plots showed that the trends of E. coli and Shigella and Salmonella enterica were similar to the trends of certain virulence genes, confirming the two pathogens do indeed carry important virulence genes. While the virulence genes in the five countries are not significantly different, the US and the UK share the largest amount of important virulence genes. The plots from principal component analysis and hierarchical clustering show that the important virulence and AMR genes were not significantly correlated, with only few genes from both types of genes clustered into the same groups.
Highlights
Introduction25% of total deaths worldwide are attributed to microbial pathogens [1]. The emergence of a relatively new threat called antimicrobial resistance, or “AMR”, is largely responsible for this high percentage in recent decades
Every year, 25% of total deaths worldwide are attributed to microbial pathogens [1]
The trend of virulence was investigated by plotting historical occurrences of gene and pathogen frequency in the annual samples. These plots showed that the trends of E. coli and Shigella and Salmonella enterica were similar to the trends of certain virulence genes, confirming the two pathogens do carry important virulence genes
Summary
25% of total deaths worldwide are attributed to microbial pathogens [1]. The emergence of a relatively new threat called antimicrobial resistance, or “AMR”, is largely responsible for this high percentage in recent decades. Despite the initial success of antibiotics, overuse and misuse of the drugs have led to targeted bacteria developing resistance and mutations, and the emergence of superbugs. The rate of global antibiotic consumption increased by 39% from 2000 to Processes 2020, 8, 1589; doi:10.3390/pr8121589 www.mdpi.com/journal/processes. The high rate of consumption is due to misconceptions about when the drugs are necessary [3], and is centered mainly in developing countries, such as China and South Africa [2]. As a result of the overuse of antibiotics, super bugs (the bacteria resistant to most known antibiotics) have been a challenging threat to public health [4]. The World Health Organization declared AMR a global public health concern in 2014 [5]. Clinicians are currently seeking additional treatments to combat the growing AMR problem, and identifying the virulence genes from the historical pathogen samples may provide directions for establishing vital strategies to combat pathogen-causing diseases
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