Characterization of Clostridium Perfringens Isolates Collected from Three Agricultural Biogas Plants over a One-Year Period.

Lorine Derongs,Christine Ziebal,Anne-Marie Pourcher,Céline Druilhe,Caroline Le Maréchal

doi:10.3390/ijerph17155450

Abstract

Digestate produced by agricultural biogas plants (BGPs) may contain pathogenic bacteria. Among them, Clostridium perfringens deserves particular attention due to its ability to grow under anaerobic conditions and persist in amended soil. The aim of this study was to examine the potential pathogenicity and the antimicrobial resistance of C. perfringens in manure and digestate collected from three agricultural biogas plants (BGPs). A total of 157 isolates (92 from manure, 65 from digestate) were screened for genes encoding seven toxins (cpa, cpb, etx, iap cpe, netB, and cpb2). The 138 cpa positive isolates were then screened for tetA(P), tetB(P), tet(M), and erm(Q) genes and tested for antimicrobial susceptibility. The toxinotypes identified in both manure and digestate were type A (78.3% of the isolates), type G (16.7%), type C (3.6%), and type D (1.4%), whereas none of the isolates were type F. Moreover, half of the isolates carried the cpb2 gene. The overall prevalence of tetA(P) gene alone, tetA(P)-tetB(P) genes, and erm(Q) gene was 31.9, 34.8, and 6.5%, respectively. None of the isolates harbored the tet(M) gene. Multiple antimicrobial resistant isolates were found in samples that were collected from all the manure and digestates. Among them, 12.3% were highly resistant to some of the antibiotics tested, especially to clindamycin (MIC ≥ 16 µg/mL) and tilmicosin (MIC > 64 µg/mL). Some isolates were highly resistant to antibiotics used in human medicine, including vancomycin (MIC > 8 µg/mL) and imipenem (MIC > 64 µg/mL). These results suggest that digestate may be a carrier of the virulent and multidrug resistant C. perfringens.

Highlights

The number of biogas plants has increased considerably in Europe in the last decade [1], most of them operating with agricultural substrates.On-farm anaerobic digestion converts livestock manure into biogas and digestate, and the latter is commonly applied to agricultural soils
These results suggest that digestate may be a carrier of the virulent and multidrug resistant C. perfringens
The aims of this study were (i) to identify the toxinotype and the antimicrobial resistance profiles of C. perfringens isolates in digestates originating from three agricultural biogas plants and (ii) to compare the profiles with C. perfringens isolates in manure that was collected in the same biogas plants

Summary

Introduction

On-farm anaerobic digestion converts livestock manure into biogas and digestate, and the latter is commonly applied to agricultural soils. The spread of zoonotic pathogens and antibiotic resistant bacteria that are potentially present in digestate raises serious concerns. Among these bacteria, Clostridium perfringens, which causes food poisoning in humans and enteric diseases in domestic animals [2], deserves particular attention due to its persistence in soil amended with manure, digestate, or manure compost [3,4,5]. Clostridia are suspected of playing a role in the dissemination of antibiotic resistance genes in manure-amended soil [4,5,6]. C. perfringens has been suggested to be a reservoir for conjugative antimicrobial resistance genes [7,8]

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