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Gupta CL, Avidov R, Kattusamy K, Saadi I, Varma VS, Blum SE, Zhu YG, Zhou XY, Su JQ, Laor Y, Cytryn E. Spatial and temporal dynamics of microbiomes and resistomes in broiler litter stockpiles. Comput Struct Biotechnol J 2021; 19:6201-6211. [PMID: 34900133 PMCID: PMC8637134 DOI: 10.1016/j.csbj.2021.11.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 11/08/2022] Open
Abstract
Farmers apply broiler chicken litter to soils to enrich organic matter and provide crops with nutrients, following varying periods of stockpiling. However, litter frequently harbors fecal-derived microbial pathogens and associated antibiotic resistance genes (ARGs), and may be a source of microbial contamination of produce. We coupled a cutting-edge Loop Genomics long-read 16S rRNA amplicon-sequencing platform with high-throughput qPCR that targeted a suite of ARGs, to assess temporal (five time points over a 60-day period) and spatial (top, middle and bottom layers) microbiome and resistome dynamics in a broiler litter stockpile. We focused on potentially pathogenic species from the Enterobacteriaceae, Enterococcaceae and Staphylococcaceae families associated with food-borne disease. Bacterial diversity was significantly lower in the middle of the stockpile, where targeted pathogens were lowest and Bacillaceae were abundant. E. coli was the most abundant Enterobacteriaceae species, and high levels of the opportunistic pathogen Enterococcus faecium were detected. Correlation analyses revealed that the latter was significantly associated with aminoglycoside (aac(6′)-Ib(aka aacA4), aadA5), tetracycline (tetG), vancomycin (vanC), phenicol (floR) and MLSB (mphB) resistance genes. Staphylococcaceae were primarily non-pathogenic, but extremely low levels of the opportunistic pathogen S. aureus were detected, as was the opportunistic pathogen S. saprophyticus, which was linked to vancomycin (vanSA, vanC1), MLSB (vatE, ermB) and tetracycline (tetK) resistance genes. Collectively, we found that stockpile microbiomes and resistomes are strongly dictated by temporal fluctuations and spatial heterogeneity. Insights from this study can be exploited to improve stockpile management practice to support sustainable antimicrobial resistance mitigation policies in the future.
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Affiliation(s)
- Chhedi Lal Gupta
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
| | - Ran Avidov
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Karuppasamy Kattusamy
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
| | - Ibrahim Saadi
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Vempalli Sudharsan Varma
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Shlomo E Blum
- Department of Bacteriology, Kimron Veterinary Institute, 50250 Beit Dagan, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xin-Yuan Zhou
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jian-Qiang Su
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yael Laor
- Institute of Soil, Water and Environmental Sciences, Volcani Institute, Agricultural Research Organization, Newe Ya'ar Research Center, Ramat Yishai, 30095, Israel
| | - Eddie Cytryn
- Department of Soil Chemistry, Plant Nutrition and Microbiology, Institute of Soil, Water and Environmental Sciences, The Volcani Institute, Agriculture Research Organization, 7528809 Rishon Lezion, Israel
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Xu S, Harvey A, Barbieri R, Reuter T, Stanford K, Amoako KK, Selinger LB, McAllister TA. Inactivation of Bacillus anthracis Spores during Laboratory-Scale Composting of Feedlot Cattle Manure. Front Microbiol 2016; 7:806. [PMID: 27303388 PMCID: PMC4882334 DOI: 10.3389/fmicb.2016.00806] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 05/12/2016] [Indexed: 12/22/2022] Open
Abstract
Anthrax outbreaks in livestock have social, economic and health implications, altering farmer’s livelihoods, impacting trade and posing a zoonotic risk. Our study investigated the survival of Bacillus thuringiensis and B. anthracis spores sporulated at 15, 20, or 37°C, over 33 days of composting. Spores (∼7.5 log10 CFU g-1) were mixed with manure and composted in laboratory scale composters. After 15 days, the compost was mixed and returned to the composter for a second cycle. Temperatures peaked at 71°C on day 2 and remained ≥55°C for an average of 7 days in the first cycle, but did not exceed 55°C in the second. For B. thuringiensis, spores generated at 15 and 21°C exhibited reduced (P < 0.05) viability of 2.7 and 2.6 log10 CFU g-1 respectively, as compared to a 0.6 log10 CFU g-1 reduction for those generated at 37°C. For B. anthracis, sporulation temperature did not impact spore survival as there was a 2.5, 2.2, and 2.8 log10 CFU g-1 reduction after composting for spores generated at 15, 21, and 37°C, respectively. For both species, spore viability declined more rapidly (P < 0.05) in the first as compared to the second composting cycle. Our findings suggest that the duration of thermophilic exposure (≥55°C) is the main factor influencing survival of B. anthracis spores in compost. As sporulation temperature did not influence survival of B. anthracis, composting may lower the viability of spores associated with carcasses infected with B. anthracis over a range of sporulation temperatures.
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Affiliation(s)
- Shanwei Xu
- Lethbridge Research and Develeopment Centre, Agriculture and Agri-Food Canada, Lethbridge AB, Canada
| | - Amanda Harvey
- Lethbridge Research and Develeopment Centre, Agriculture and Agri-Food Canada, LethbridgeAB, Canada; Department of Biological Sciences, University of Lethbridge, LethbridgeAB, Canada
| | - Ruth Barbieri
- Lethbridge Research and Develeopment Centre, Agriculture and Agri-Food Canada, Lethbridge AB, Canada
| | - Tim Reuter
- Alberta Agriculture and Forestry, Lethbridge AB, Canada
| | - Kim Stanford
- Alberta Agriculture and Forestry, Lethbridge AB, Canada
| | - Kingsley K Amoako
- Lethbridge Laboratory, Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge AB, Canada
| | - Leonard B Selinger
- Department of Biological Sciences, University of Lethbridge, Lethbridge AB, Canada
| | - Tim A McAllister
- Lethbridge Research and Develeopment Centre, Agriculture and Agri-Food Canada, Lethbridge AB, Canada
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Stanford K, Harvey A, Barbieri R, Xu S, Reuter T, Amoako KK, Selinger LB, McAllister TA. Heat and desiccation are the predominant factors affecting inactivation of Bacillus licheniformis and Bacillus thuringiensis spores during simulated composting. J Appl Microbiol 2015; 120:90-8. [PMID: 26513540 DOI: 10.1111/jam.12991] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 10/06/2015] [Accepted: 10/23/2015] [Indexed: 01/12/2023]
Abstract
AIMS The suitability of composting for disposal of livestock mortalities due to Bacillus anthracis was assessed by measuring viability of surrogate spores from two strains each of Bacillus licheniformis and Bacillus thuringiensis after a heating cycle modelled on a cattle composting study. METHODS AND RESULTS Sporulation was attempted from 10 to 37°C, but poor yields at lower temperatures resulted in 25, 30 and 37°C being selected to generate sufficient spores (8 log10 CFU ml(-1) ) for experiments. Spores were inoculated into 3 g autoclaved dried-ground compost rehydrated with 6 ml water or silica beads in a factorial design for each strain, sporulation temperature, matrix and sampling day (0, 25, 50, 100, 150). Maximum incubation temperature was 62°C, but spores were maintained at ≥55°C for 78 of 150 days. Although significant differences existed among Bacillus strains and sporulation temperatures, numbers of viable spores after 150 days averaged 1·3 log10 CFU g(-1) , a 5·2 log10 reduction from day 0. CONCLUSIONS Spore inactivation was likely due to heat and desiccation as matrices were autoclaved prior to incubation, negating impacts of microflora. SIGNIFICANCE AND IMPACT OF STUDY Results support composting for disposal of anthrax mortalities, provided long-term thermophillic heating is achieved. Due to limited sporulation at 10°C, livestock mortalities from anthrax at this or lower ambient temperatures would likely be of lower risk for disease transmission.
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Affiliation(s)
- K Stanford
- Alberta Agriculture and Forestry, Lethbridge, AB, Canada
| | - A Harvey
- University of Lethbridge, Lethbridge, AB, Canada
| | - R Barbieri
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - S Xu
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| | - T Reuter
- Alberta Agriculture and Forestry, Lethbridge, AB, Canada
| | - K K Amoako
- Canadian Food Inspection Agency, Lethbridge, AB, Canada
| | - L B Selinger
- University of Lethbridge, Lethbridge, AB, Canada
| | - T A McAllister
- Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
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