Skip to main content
SpringerLink
Log in

Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method

  • Research Article
  • Published:
Environmental Science and Pollution Research Aims and scope Submit manuscript

Abstract

Fishmeal is a fundamental ingredient of feedstuffs and is used globally in aquaculture. However, there are few data on the antibiotic resistance genes (ARGs) and human pathogenic bacteria in fishmeal and little understanding of the potential risks of fishmeal application in mariculture systems. Here, we investigated the high-throughput profiles of ARGs and human potential pathogenic bacteria (HPPB) in representative fishmeals (n = 5) and the potential impact of fishmeal on mariculture sediments. ARGs were quantified with microbial DNA quantitative PCR arrays and HPPB were analyzed with Illumina sequencing of 16S rRNA genes. The impact of the fishmeal on the aquaculture sediments was assessed in a microcosm study. Twenty-four unique ARGs (3–14 per sample) and 25 HPPB species were detected in the fishmeal samples. The most prevalent ARGs were fluoroquinolone resistance genes. The overall abundance of HPPB was 5.0–25.5%, and the HPPB species were dominated by Vibrio parahaemolyticus, Clostridium novyi, and Escherichia coli. In the mariculture microcosm sediment, fishmeal significantly increased the normalized abundance of the class I integrase gene (25.4-fold), which plays an important role in the dissemination of ARGs. Dosing with fishmeal also contributed to increases in a resident sulfanilamide resistance gene (sulI gene) and the emergence of a macrolide resistance gene (ermB gene) in the sediment. These findings demonstrated that fishmeal itself is an underestimated reservoir and source of ARGs and HPPBs, and that the application of fishmeal facilitates the dissemination of ARGs in aquaculture sediments. Our results extend our knowledge of the ARGs and HPPB within fishmeal and may provide a feasible and effective approach to the detection of ARGs and HPPB in fishmeal during food safety inspection.

ᅟ

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • (2002) Aerobic and anaerobic transformation in aquatic sediment systems. In Guidelines for testing of chemicals no. 308; Organisation for Economic Cooperation and Development: Paris

  • Baker-Austin C, Wright MS, Stepanauskas R, McArthur JV (2006) Co-selection of antibiotic and metal resistance. Trends Microbiol 14:176–182

    Article  CAS  Google Scholar 

  • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120

    Article  CAS  Google Scholar 

  • Bouwman L, Beusen A, Glibert PM, Overbeek C, Pawlowski M, Herrera J, Mulsow S, Yu RC, Zhou MJ (2013) Mariculture: significant and expanding cause of coastal nutrient enrichment. Environ Res Lett 8:4

    Article  Google Scholar 

  • Cai L, Zhang T (2013) Detecting human bacterial pathogens in wastewater treatment plants by a high-throughput shotgun sequencing technique. Environ Sci Technol 47:5433–5441

    Article  CAS  Google Scholar 

  • Cao L, Naylor R, Henriksson P, Leadbitter D, Metian M, Troell M, Zhang WB (2015) China's aquaculture and the world’s wild fisheries. Science 347:133–135

    Article  CAS  Google Scholar 

  • Caporaso JG, Kuczynski J, Stombaugh J, Bittinger K, Bushman FD, Costello EK, Fierer N, Peña AG, Goodrich JK, Gordon JI, Huttley GA, Kelley ST, Knights D, Koenig JE, Ley RE, Lozupone CA, McDonald D, Muegge BD, Pirrung M, Reeder J, Sevinsky JR, Turnbaugh PJ, Walters WA, Widmann J, Yatsunenko T, Zaneveld J, Knight R (2010) Qiime allows analysis of high-throughput community sequencing data. Nat Methods 7:335–336

    Article  CAS  Google Scholar 

  • Chen LH, Yang J, Yu J, Ya ZJ, Sun LL, Shen Y et al (2005) Vfdb: a reference database for bacterial virulence factors. Nucleic Acids Res 33:D325–D328

    Article  CAS  Google Scholar 

  • De Santis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie EL, Keller K et al (2006) Greengenes, a chimera-checked 16s rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 72:5069–5072

    Article  CAS  Google Scholar 

  • Edgar RC (2010) Search and clustering orders of magnitude faster than BLAST. Bioinformatics 26(19):2460–2461

    Article  CAS  Google Scholar 

  • FAO. (Food and Agriculture Organization of the United Unions) (2014) Global aquaculture production 1950-2014. Available: http://www.Fao.Org/fishery/statistics/global-aquaculture-production/query/en[accessed 4 Mar 2016]

  • Fischbach MA, Walsh CT (2009) Antibiotics for emerging pathogens. Science 325:1089–1093

    Article  CAS  Google Scholar 

  • Gao P, Mao D, Luo Y, Wang L, Xu B, Xu L (2012) Occurrence of sulfonamide and tetracycline-resistant bacteria and resistance genes in aquaculture environment. Water Res 46:2355–2364

    Article  CAS  Google Scholar 

  • Han Y, Wang J, Zhao Z, Chen J, Lu H, Liu G (2017) Fishmeal application induces antibiotic resistance gene propagation in mariculture sediment. Environ Sci Technol 51(18):10850–10860

    Article  CAS  Google Scholar 

  • Hofacre CL, White DG, Maurer JJ, Morales C, Lobsinger C, Hudson C (2001) Characterization of antibiotic-resistant bacteria in rendered animal products. Avian Dis 45:953–961

    Article  CAS  Google Scholar 

  • Hsieh YC, Poole TL, Runyon M, Hume M, Herrman TJ (2016) Prevalence of nontyphoidal salmonella and salmonella strains with conjugative antimicrobial-resistant serovars contaminating animal feed in Texas. J Food Prot 79:194–204

    Article  CAS  Google Scholar 

  • Huang Y, Zhang L, Tiu L, Wang HH (2015) Characterization of antibiotic resistance in commensal bacteria from an aquaculture ecosystem. Front Microbiol 6:7

    Google Scholar 

  • International fish meal and fish oil organization (IFFO) (2015) IFFO response to the recent paper on China’s aquaculture and the world’s wild fisheries. Available: http://www.iffo.net/node/720. Accessed Dec 2017

  • Kang Y, Gu X, Hao Y, Hu J (2016) Autoclave treatment of pig manure does not reduce the risk of transmission and transfer of tetracycline resistance genes in soil: successive determinations with soil column experiments. Environ Sci Pollut Res 23:4551–4560

    Article  CAS  Google Scholar 

  • Klappenbach JA, Saxman PR, Cole JR, Schmidt TM (2001) rrndb: the ribosomal RNA operon copy number database. Nucleic Acids Res 29:181–184

    Article  CAS  Google Scholar 

  • Knapp CW, Dolfing J, Ehlert PAI, Graham DW (2010) Evidence of increasing antibiotic resistance gene abundances in archived soils since 1940. Environ Sci Technol 44:580–587

    Article  CAS  Google Scholar 

  • Kumaraswamy R, Amha YM, Anwar MZ, Henschel A, Rodriguez J, Ahmad F (2014) Molecular analysis for screening human bacterial pathogens in municipal wastewater treatment and reuse. Environ Sci Technol 48:11610–11619

    Article  CAS  Google Scholar 

  • Laxminarayan R, Duse A, Wattal C, Zaidi AKM, Wertheim HFL, Sumpradit N, Vlieghe E, Hara GL, Gould IM, Goossens H, Greko C, So AD, Bigdeli M, Tomson G, Woodhouse W, Ombaka E, Peralta AQ, Qamar FN, Mir F, Kariuki S, Bhutta ZA, Coates A, Bergstrom R, Wright GD, Brown ED, Cars O (2013) Antibiotic resistance-the need for global solutions. Lancet Infect Dis 13:1057–1098

    Article  Google Scholar 

  • Levy SB, Marshall B (2004) Antibacterial resistance worldwide: causes, challenges and responses. Nat Med 10:S122–S129

    Article  CAS  Google Scholar 

  • Looft T, Johnson TA, Allen HK, Bayles DO, Alt DP, Stedtfeld RD, Sul WJ, Stedtfeld TM, Chai B, Cole JR, Hashsham SA, Tiedje JM, Stanton TB (2012) In-feed antibiotic effects on the swine intestinal microbiome. Proc Natl Acad Sci U S A 109:1691–1696

    Article  Google Scholar 

  • Luo Y, Mao DQ, Rysz M, Zhou DX, Zhang HJ, Xu L et al (2010) Trends in antibiotic resistance genes occurrence in the Haihe river, China. Environ Sci Technol 44:7220–7225

    Article  CAS  Google Scholar 

  • Magoc T, Salzberg SL (2011) Flash: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27:2957–2963

    Article  CAS  Google Scholar 

  • Malorny B, Huehn S, Dieckmann R, Kramer N, Helmuth R (2009) Polymerase chain reaction for the rapid detection and serovar identification of salmonella in food and feeding stuff. Food Anal Methods 2:81–95

    Article  Google Scholar 

  • Meeker DL (2009) North American rendering - processing high quality protein and fats for feed. Rev Bras Zootecn 38:432–U443

    Article  Google Scholar 

  • Muziasari WI, Managaki S, Parnanen K, Karkman A, Lyra C, Tamminen M et al (2014) Sulphonamide and trimethoprim resistance genes persist in sediments at Baltic Sea aquaculture farms but are not detected in the surrounding environment. PLoS One 9:e92702

    Article  CAS  Google Scholar 

  • Naylor RL, Goldburg RJ, Primavera JH, Kautsky N, Beveridge MCM, Clay J, Folke C, Lubchenco J, Mooney H, Troell M (2000) Effect of aquaculture on world fish supplies. Nature 405:1017–1024

    Article  CAS  Google Scholar 

  • Nygaard H, Hostmark O (2008) Microbial inactivation during superheated steam drying of fish meal. Dry Technol 26:222–230

    Article  CAS  Google Scholar 

  • Pruden A, Pei R, Storteboom H, Carlson KH (2006) Antibiotic resistance genes as emerging contaminants: studies in northern Colorado. Environ Sci Technol 40:7445–7450

    Article  CAS  Google Scholar 

  • Pruden A, Arabi M, Storteboom HN (2012) Correlation between upstream human activities and riverine antibiotic resistance genes. Environ Sci Technol 46:11541–11549

    Article  CAS  Google Scholar 

  • Sapkota AR, Lefferts LY, McKenzie S, Walker P (2007) What do we feed to food-production animals? A review of animal feed ingredients and their potential impacts on human health. Environ Health Perspect 115:663–670

    Article  CAS  Google Scholar 

  • Segata N et al (2012) Metagenomic microbial community profiling using unique clade-specific marker genes. Nat Methods 9(8):811–814

    Article  CAS  Google Scholar 

  • Shah SQA, Colquhoun DJ, Nikuli HL, Sorum H (2012) Prevalence of antibiotic resistance genes in the bacterial flora of integrated fish farming environments of Pakistan and Tanzania. Environ Sci Technol 46:8672–8679

    Article  CAS  Google Scholar 

  • Suzuki MT, Taylor LT, DeLong EF (2000) Quantitative analysis of small-subunit rRNA genes in mixed microbial populations via 5′-nuclease assays. Appl Environ Microbiol 66:4605–4614

    Article  CAS  Google Scholar 

  • Tamminen M, Karkman A, Lohmus A, Muziasari WI, Takasu H, Wada S et al (2011) Tetracycline resistance genes persist at aquaculture farms in the absence of selection pressure. Environ. Sci. Technol. 45:386–391

    Article  CAS  Google Scholar 

  • Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) Mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    Article  CAS  Google Scholar 

  • Tomova A, Ivanova L, Buschmann AH, Rioseco ML, Kalsi RK, Godfrey HP, Cabello FC (2015) Antimicrobial resistance genes in marine bacteria and human uropathogenic Escherichia coli from a region of intensive aquaculture. Environ Microbiol Rep 7:803–809

    Article  CAS  Google Scholar 

  • Udikovic-Kolic N, Wichmann F, Broderick NA, Handelsman J (2014) Bloom of resident antibiotic-resistant bacteria in soil following manure fertilization. Proc Natl Acad Sci U S A 111:15202–15207

    Article  CAS  Google Scholar 

  • Uyaguari MI, Scott GI, Norman RS (2013) Abundance of class 1-3 integrons in South Carolina estuarine ecosystems under high and low levels of anthropogenic influence. Mar Pollut Bull 76:77–84

    Article  CAS  Google Scholar 

  • Wang Q, Garrity GM, Tiedje JM, Cole JR (2007) Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl Environ Microbiol 73:5261–5267

    Article  CAS  Google Scholar 

  • Welch TJ, Fricke WF, McDermott PF, White DG, Rosso ML, Rasko DA, Mammel MK, Eppinger M, Rosovitz MJ, Wagner D, Rahalison L, LeClerc JE, Hinshaw JM, Lindler LE, Cebula TA, Carniel E, Ravel J (2007) Multiple antimicrobial resistance in plague: an emerging public health risk. PLoS One 2:e309

    Article  Google Scholar 

  • Wu B, Song JM, Li XG (2014) Evaluation of potential relationships between benthic community structure and toxic metals in Laizhou bay. Mar Pollut Bull 87:247–256

    Article  CAS  Google Scholar 

  • Yang J, Wang C, Shu C, Liu L, Geng J, Hu S, Feng J (2013) Marine sediment bacteria harbor antibiotic resistance genes highly similar to those found in human pathogens. Microb Ecol 65(4):975–981

    Article  CAS  Google Scholar 

  • Yang J, Wang C, Wu J, Liu L, Zhang G, Feng J (2014) Characterization of a multiresistant mosaic plasmid from a fish farm Sediment Exiguobacterium sp isolate reveals aggregation of functional clinic-associated antibiotic resistance genes. Appl Environ Microbiol 80:1482–1488

    Article  CAS  Google Scholar 

  • Ye L, Zhang L, Li X, Shi L, Huang Y, Wang HH (2013) Antibiotic-resistant bacteria associated with retail aquaculture products from Guangzhou, China. J Food Prot 76:295–301

    Article  Google Scholar 

  • Zhang T, Fang HHP (2006) Applications of real-time polymerase chain reaction for quantification of microorganisms in environmental samples. Appl Microbiol Biotechnol 70:281–289

    Article  CAS  Google Scholar 

  • Zhang XX, Zhang T, Zhang M, Fang HHP, Cheng SP (2009) Characterization and quantification of class 1 integrons and associated gene cassettes in sewage treatment plants. Appl Microbiol Biotechnol 82:1169–1177

    Article  CAS  Google Scholar 

  • Zhao Z, Wang J, Han Y, Chen J, Liu G, Lu H, Yan B, Chen S (2017) Nutrients, heavy metals and microbial communities co-driven distribution of antibiotic resistance genes in adjacent environment of mariculture. Environ Pollut 220:909–918

    Article  CAS  Google Scholar 

Download references

Acknowledgements

The authors would like to thank Professor Lin Cai at the Hong Kong University of Science and Technology, China, for providing the human pathogenic bacteria 16S rRNA gene database.

Funding

This work has been supported by the National Basic Research Program of China (2013CB430403).

Author information

Authors and Affiliations

  1. Key Laboratory of Industrial Ecology and Environmental Engineering, Ministry of Education, School of Environmental Science and Technology, Dalian University of Technology, 2#Linggong Road, Ganjingzi District, Dalian, Liaoning, 116024, People’s Republic of China

    Ying Han, Jing Wang, Zelong Zhao, Jingwen Chen, Hong Lu & Guangfei Liu

Authors
  1. Ying Han
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jing Wang
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Zelong Zhao
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Jingwen Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hong Lu
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Guangfei Liu
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Jing Wang.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Responsible editor: Diane Purchase

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Capsule: Broad spectrums of ARGs and HPPB in fishmeal

Highlights

● The study provides a feasible and effective method for detecting antibiotic resistance genes (ARGs) and human potential pathogenic bacteria (HPPB) in fishmeal during food safety inspections.

● Fishmeal is shown to be a reservoir and source of ARGs and HPPB.

● Our findings potentially provide strategies for mitigating ARGs in fishmeal-treated environments.

Electronic supplementary material

ESM 1

(DOCX 130 kb)

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Han, Y., Wang, J., Zhao, Z. et al. Detecting antibiotic resistance genes and human potential pathogenic Bacteria in fishmeal by culture-independent method. Environ Sci Pollut Res 26, 8665–8674 (2019). https://doi.org/10.1007/s11356-019-04303-1

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s11356-019-04303-1

Keywords

Search

Navigation