Challenges of pathogen inactivation in animal manure through anaerobic digestion: a short review

Figures & data

Table 1. The main disease-causing bacteria

Bacteria (Genus)	Disease-causing bacteria (Species)
Acinetobacter	A. baumannii, A. nosocomialis, A. pittii
Aeromonas	A. hydrophila, A. salmonicida, A. veronii, A. caviae
Anaplasma	A. centrale, A. marginale, A. phagocytophilum
Bacillus	B. anthracis, B. cereus
Bartonella	B. bacilliformis, B. quintana, B. henselae
Bordetella	B. pertussis, B. parapertussis, B. bronchiseptica
Brucella	B. melitensis, B. abortus, B. suis, B. canis.
Burkholderia	B. pseudomallei, B. mallei, B. cenocepacia, B cepacia
Campylobacter	C. jejuni
Chlamydia	C. trachomatis, C. pneumoniae
Clostridium	Cl. absonum, Cl. argentinense, Cl. barati, Cl. bifermentans, Cl. botulinum, Cl. butyricum, Cl. cadaveris, Cl. carnis, Cl. clostridioforme, Cl. chauvoei, Cl. difficile, Cl. fallax, Cl. glycolicum, Cl. haemolyticum, Cl. histolyticum, Cl. intestinalis, Cl. limosum, Cl. malenominatum, Cl. novyi, Cl. disporicum Cl. paraputrificum, Cl. perfringens, Cl. putrificum, Cl. septicum, Cl. sordellii, Cl. sporogenes, Cl. sunterminale, Cl. tertium, Cl. tetani
Corynebacterium	C. diphtheria, C. jeikeium
Coxiella	C. burnetii
Enterococcus	E. faecalis, E. faecium
Escherichia	Enterotoxigenic E. coli (ETEC), Enteroinvasive E. coli (EIEC), Enteropathogenic E. coli (EPEC), Enterohemorrhagic E. coli (EHEC), Enteroaggregative E. coli (EAEC), Diffusely adherent E. coli (DAEC)
Francisella	F. tularensis, F. novicida, F. philomiragia
Haemophilus	H. influenzae
Helicobacter	H. pylori
Klebsiella	K. pneumoniae
Legionella	L. longbeachae, L. pneumophila
Listeria	L. monocytogenes, L. ivanovii
Mycobacterium	M. tuberculosis, M. leprae, M. ulcerans
Neisseria	N. gonorrhoeae, N. meningitidis
Pseudomonas	P. aeruginosa
Rickettsia	R. rickettsii, R. conorii, R. prowazekii, R. typhi
Salmonella	S. typhimurium, S. typhi
Shigella	S. dysenteriae, S. flexneri, S. boydii, S. sonnei.
Staphylococcus	S. aureus, S. epidermidis
Streptococcus	S. pyogenes, S. agalactiae
Vibrio	V. cholerae, V. parahaemolyticus, V. vulnificus
Yersinia	Y. pestis, Y. pseudotuberculosis, Y. enterocolitica

Figure 1. Examples of pathogenic microorganisms in different animal manures.

Table 2. Literature data about the efficiency of AD process on pathogens inactivation in animal manure

Pathogen	Substrate	T (°C)	Operation mode	Initial count (CFU/g or mL)	Finial count (CFU/g or mL)	Log10 reduction	Tr^a/HRT (d)	Reference
E. coli	Dairy manure	25	Batch	6.5 × 10^7	<10^2	>6	60	[19]
E. coli	Dairy manure	35	Batch	3.6 × 10^5	Below LOD^b	3.6	62	[12]
E. coli	Cow manure	37	Batch	1.85 × 10^7	<10^3	4	41	[19]
E. coli	Cow manure	37	Batch	6 × 10^4	Below LOD	4.94	6	[31]
E. coli	Chicken manure	37	Batch	2.3 × 10^7	35	5.8	35	[20]
E. coli	Chicken manure	42	Batch	1.7 × 10^7	27–34	5.7	9	[20]
E. coli	Dairy manure	52.5	Batch	2.5 × 10^7	Below LOD	>7	3.5	[19]
E. coli	Chicken manure	55	Batch	10^6	2–4	5.5	2 h	[16]
E. coli	Cow manure	55	Batch	6 × 10^4	Below LOD	4.37	40 min	[31]
E. coli	Cow manure	70	Batch	6 × 10^4	Below LOD	2.6	2 min	[31]
E. coli	Swine manure	24	Continuous	4.0 × 10^2–5.8 × 10^5		0.9–2.9	7,14	[17]
E. coli	Cow manure	33	Continuous	1 × 10^3	3 × 10^2	~0.5	55	[21]
E. coli	Cattle manure	45	Continuous		Below LOD	3	55	[21]
Coliforms	Swine manure	22	Batch	10^5–10^6	~10^3	2–3	25	[22]
Coliforms	Cattle slurry	22	Batch	10^4–10^5	~10^2	2–3	28	[22]
Coliforms	Swine manure	38	Batch	10^5–10^6	Below LOD	3–4	3	[22]
Coliforms	Cattle slurry	38	Batch	10^4–10^5	Below LOD	2–3	14	[22]
Coliforms	Swine manure	55	Batch	10^5–10^6	Below LOD	3–4	1	[22]
Coliforms	Cattle slurry	55	Batch	10^4–10^5	Below LOD	2–3	1	[22]
Coliforms	Cattle manure	33	Continuous	10^3	10^2	1	55	[21]
Coliforms	Cattle manure	45	Continuous	10^3	10^2	1	55	[21]
Total coliforms	Swine manure	24	Continuous	6.0 × 10^2–1.5 × 10^6		1.0–2.9	7,14	[17]
Fecal coliforms	Swine manure	24	Continuous	5.0 × 10^2–1.6 × 10^6		0.9–3	7,14	[17]
Fecal coliforms	Pig slurry/manure	39	Continuous	1.8 × 10^4	2.0 × 10^3	1.1–4.1	28	[33]
Salmonella	Swine manure	16	Batch	10^6–10^7	10–10^2	5	60	[23]
Salmonella	Swine manure	22	Batch	10^6–10^7	10–10^2	5	60	[23]
Salmonella	Dairy manure	35	Batch	7.4 × 10^3	Below LOD	1.9	133	[24]
Salmonella	Swine manure	37	Batch	10^6–10^7	10–10^2	5	3	[23]
Salmonella	Swine manure	24	Continuous	<10^2-5.0 × 10^3		0.9–1.4	7,14	[17]
Enterococcus/Enterococci	Cow manure	37	Batch	6.6 × 10^5		3.13	15	[31]
Enterococcus/Enterococci	Cow manure	55	Batch	6.6 × 10^5		1.7	2	[31]
Enterococcus/Enterococci	Cow manure	70	Batch	6.6 × 10^5		1.77	1	[31]
Enterococcus/Enterococci	Pig manure	24	Continuous	1.8 × 10^4–1.7 × 10^6		0.6–1	7,14	[17]
Enterococcus/Enterococci	Cow manure	33	Continuous	10^6–10^7	10^4	2–3	55	[21]
Clostridium perfringens	Cow manure	37	Batch	10^3–10^4		1.35	15	[31]
Clostridium perfringens	Cow manure	55	Batch	10^3–10^4		<1	2	[31]
Clostridium perfringens	Cow manure	70	Batch	10^3–10^4		<1	1	[31]
Clostridium perfringens	Swine manure	24	Continuous	<1 × 10^3–3.7 × 10^6		0–0.2	7,14	[17]
Clostridium perfringens	Pig slurry/manure	39	Continuous	5 × 10^4	4.2 × 10^3	1.08	28	[33]
Clostridium perfringens	Pig slurry	37–43	Continuous	8.9 × 10^4	5 × 10^4	0.25	40–56	[34]
Clostridium perfringens	Cattle manure	48	Continuous	1.9 × 10^5	1 × 10^6	−0.74	90	[34]

A, Tr, residence time of batch experiment; b, LOD, limit of detection.

Figure 2. Common indicator bacteria.

Figure 3. Threshold levels of pathogens in anaerobic residues.

a, FM, fresh matter; b, PFU, plaque-forming unit; *, in ambient AD and MAD; **, in TAD.

Table 3. The characteristics of Clostridium botulinum, Clostridium perfringens, and Clostridium difficile.

Types	Characteristics
Clostridium botulinum	Toxin types: A, B, C, D, E, F, G. Human botulism (A, B, E, F); Botulism in animals (C, D). Food poisoning: botulism. Incubation period: 8 hours to 8 days. Dose: 0.005–0.1 µg (proteolytic); 0.1–0.5 µg (non-proteolytic) for lethal. Symptoms: generalized muscular weakness; headache; dizziness; visual disturbances; nausea; vomiting; respiratory failure. Unique characteristic: strict anaerobic bacteria; heat labile toxin; produce neurotoxin. Inhibitory pH: 4.6 (A, B, F); 5.0 (B, E, F). Temperature range: 10–48°C (A, B, F); 3.3–45°C (B, E, F). D of spores: D100: 25 min (A, B, F); <0.1 min (B, E, F).
Clostridium perfringens	Toxin types: A. Food poisoning: Foodborne toxic infection. Incubation period: 8–22 hours. Dose: >10^5 cells/g for infective. Symptoms: diarrhea, severe abdominal pain, nausea (occasionally). Unique characteristic: strict anaerobic bacterium; produce toxins (Enterotoxin; Toxin production in the digestive tract is associated with sporulation). Inhibitory pH: 5.0. Temperature range: 15–50°C (optimum 43–45°C). D of spores: D95: 1.3–6.4 min.
Clostridium difficile	High prevalence of C. difficile in animals. C. difficile in foods: further research is needed. C. difficile is a major cause of illness. Initially recognized as a hospital pathogen; Now recognized as an important cause of severe community-acquired infections. The source of community-acquired C. difficile is yet to be established. Foodborne is one route considered.

D of spores, decimal reduction time of spores; D₁₀₀, D at 100°C; D₉₅, D at 95°C.

Figure 4. The relationship between normal pathogens and VBNC pathogens.

Pandey PK, Soupir ML. Escherichia coli inactivation kinetics in anaerobic digestion of dairy manure under moderate, mesophilic and thermophilic temperatures. Amb Express. 2011;1(1):18.

 PubMedGoogle Scholar

Manyi-Loh CE, Mamphweli SN, Meyer EL, et al. Inactivation of selected bacterial pathogens in dairy cattle manure by mesophilic anaerobic digestion (Balloon type digester). Int J Environ Res Public Health. 2014;11(7):7184–7194.

 PubMed Web of Science ®Google Scholar

Watcharasukarn M, Kaparaju P, Steyer JP, et al. Screening Escherichia coli, enterococcus faecalis, and Clostridium perfringens as indicator organisms in evaluating pathogen-reducing capacity in biogas plants. Microb Ecol. 2009;58(2):221–230.

 PubMed Web of Science ®Google Scholar

Smith SR, Lang NL, Cheung KHM, et al. Factors controlling pathogen destruction during anaerobic digestion of biowastes. Waste Manag. 2005;25(4):417–425.

 PubMed Web of Science ®Google Scholar

Thomas C, Idler C, Ammon C, et al. Inactivation of ESBL-/AmpC-producing Escherichia coli during mesophilic and thermophilic anaerobic digestion of chicken manure. Waste Manag. 2019;84:74–82.

 PubMed Web of Science ®Google Scholar

Massé D, Gilbert Y, Topp E. Pathogen removal in farm-scale psychrophilic anaerobic digesters processing swine manure. Bioresour Technol. 2011;102(2):641–646.

 PubMed Web of Science ®Google Scholar

Popova TP, Zaharinov B, Kaleva MD, et al. Reduction of microorganisms in thermophilic process of anaerobic digestion of cattle manure. Int J Curr Microbiol Appl Sci. 2013;2:653–660.

 Google Scholar

Varel VH, Wells JE, Shelver WL, et al. Effect of anaerobic digestion temperature on odour, coliforms and chlortetracycline in swine manure or monensin in cattle manure*. J Appl Microbiol. 2012;112(4):705–715.

 PubMed Web of Science ®Google Scholar

Orzi V, Scaglia B, Lonati S, et al. The role of biological processes in reducing both odor impact and pathogen content during mesophilic anaerobic digestion. Sci Total Environ. 2015;526:116–126.

 PubMed Web of Science ®Google Scholar

Fongaro G, Kunz A, Magri ME, et al. Evaluation of the effective inactivation of enteric bacteria and viruses from swine effluent and sludge at tropical temperatures. Water Air Soil Pollut. 2018;229(7). DOI:10.1007/s11270-018-3878-y.

 Web of Science ®Google Scholar

McCarthy G, Lawlor PG, Gutierrez M, et al. Assessing the biosafety risks of pig manure for use as a feedstock for composting. Sci Total Environ. 2013;463:712–719.

 PubMed Web of Science ®Google Scholar

Costa A, Gusmara C, Gardoni D, et al. The effect of anaerobic digestion and storage on indicator microorganisms in swine and dairy manure. Environ Sci Pollut Res. 2017;24(31):24135–24146.

 PubMed Web of Science ®Google Scholar