Occurrences of Pathogens and Antibiotic Resistance

Some microorganisms, including bacteria, viruses, and fungi, can cause human diseases. Although humans and animals are the primary reservoirs for these pathogens, some pathogens can survive and grow outside their host (e.g., soils, sediments). 

Traditionally, fecal indicator bacteria (FIB) such as E. coli have been used to predict pathogen occurrence, due to analytical obstacles to detecting and quantifying multiple pathogens in a timely manner. However, FIB of non-fecal origin are now widely recognized, and poor correlations have been reported between concentrations of FIB and pathogens. Thus, FIB may be an inadequate surrogate for predicting the occurrence of pathogens. A more reliable FIB-independent approach is needed to assess human health risks due to pathogens. 

My lab has developed a novel tool to address this issue. The tool is based on microfluidics technology and simultaneously quantifies multiple bacterial and viral pathogens. We have since applied it to monitor levels of pathogen contamination in irrigation water samples and to assess the risk of infection. Our results showed that direct multi-pathogen quantification is technically feasible for both bacterial and viral pathogens. The broader impact of these studies may be substantial: our FIB-independent direct multi-pathogen quantification approach could replace the standard, and globally ubiquitous, FIB-based approach. 

In addition, we are working to identify the sources of pathogens by sequencing the pathogen marker genes in a high throughput manner, and to clarify the ecology of pathogens, especially Arcobacter and Campylobacter, in the environments. 

Related projects:

  • Ishii, S. (PI) and Hamilton, K.W. (co-PI). 2020-2023. Collaborative Research: Comprehensive Microbiological Water Quality and Risk Assessment Tools for Timely Water Management. NSF-CBET 1916025.
  • Ishii, S. (PI), LaPara, T. (co-PI), Anderson, A. (co-PI), Rice, N. (co-PI). 2020-2021. Evaluation of Microbial and Chemical Contaminant Removals in Different Stormwater Reuse Systems. Minnesota Stormwater Research Council. 
  • Ishii, S. (PI), Anderson, A. (co-PI), Rice, N. (co-PI). 2019. Temporal dynamics of pathogens and antibiotic resistance in raw and treated stormwater. Minnesota Stormwater Research Council. 
  • Ishii, S. (PI), LaPara, T. (cp-PI), Anderson, A. (co-PI), Rice, N. (co-PI). 2017-2019. Assessment of water quality for reuse. Legislative-Citizen Commission on Minnesota Resources 
  • Ishii, S. (PI), Johnson, T. (co-PI), Knights, D. (co-PI). 2016-2018. Prevalence of Campylobacter and Salmonella in poultry: high-resolution, temporal dynamics of the pathogen populations. Healthy Foods Healthy Lives Initiative. 
  • Yan, T. (PI), Ishii, S. (co-PI). 2015-2020. Transform municipal wastewater treatment systems into community enteric disease information networks. NSF-CBET 1507979.

Select publications:

  • Ishii, S. 2020. Quantification of antibiotic resistance genes for environmental monitoring: Current methods and future directions. Curr. Op. Environ. Sci. Health 16, 47-53. Abstract
  • Ahmed, W., Zhang, Q., Lobos, A., Senkbeil, J., Sadowsky, M. J., Harwood, V. J., Saeidi, N., Marinoni, O, and Ishii, S. 2018. Precipitation influences pathogenic bacteria and antibiotic resistance gene abundance in storm drain outfalls in coastal sub-tropical waters. Environ. Int. 116, 308-318. Abstract
  • Zhang, Q., and Ishii, S. 2018. Improved simultaneous quantification of multiple waterborne pathogens and fecal indicator bacteria with the use of a sample process control. Water Res. 137, 193-200. Abstract
  • Zhang, Q., Al-Ghalith, G. A., Kobayashi, M., Segawa, T., Maeda, M., Okabe, S., Knights, D., Ishii, S. 2018. High-throughput flaA short variable region sequencing to assess Campylobacter diversity in fecal samples from birds. Front. Microbiol. 9, 2201. Abstract
  • Sandberg, K. D., Ishii, S., and LaPara, T. M. 2018. A microfluidic quantitative polymerase chain reaction method for the simultaneous analysis of dozens of antibiotic resistance and heavy metal resistance genes. Environ. Sci. Technol. Lett. 5, 20-25. Abstract
  • Zhang, Q., Eichmiller, J. J., Staley, C., Sadowsky, M. J., and Ishii, S. 2016. Correlations between pathogen concentration and fecal indicator marker genes in beach environments. Sci. Total Environ. 573, 826-830. Abstract
  • Byappanahalli, M. N., Nevers, M. B., Whitman, R. L., and S. Ishii. 2015. Application of a microfluidic quantitative polymerase chain reaction technique to monitor bacterial pathogens in beach water and complex environmental matrices. Environ. Sci. Technol. Lett. 2, 347–351. Abstract
  • Ishii, S., Kitamura, G., Segawa, T., Kobayashi, A., Miura, T., Sano, D., and Okabe, S. 2014. Microfluidic quantitative PCR for simultaneous quantification of multiple viruses in environmental water samples. Appl. Environ. Microbiol. 80, 7505-7511. Abstract (Microbe magazine)
  • Ishii, S., Nakamura, T., Ozawa, S., Kobayashi, A., Sano, D., and Okabe, S. 2014. Water quality monitoring and risk assessment by simultaneous multipathogen quantification. Environ. Sci. Technol. 48, 4744-4749. Abstract (Chemical and Engineering News)
  • Ishii, S., Segawa, T., and Okabe, S. 2013. Simultaneous quantification of multiple food and waterborne pathogens by use of microfluidic quantitative PCR. Appl. Environ. Microbiol. 79, 2891-2898. Abstract (AEM Spotlights)