Bolan et al concluded that microbial population density in poultry excreta or waste can outstrip 1010 cells per g of litter and gram positive bacteria composed almost 90% of the microbial diversity (Bolan et al. 2010). Salmonella spp and Campylobacter spp are those poultry bacteria that mainly cause the human food-borne illnesses, according to the available research (Hafez 2005).
2.1 Campylobacter spp
Campylobacter spp also plays a role in food-borne diseases and is the leading cause of zoonotic enteric infections across the globe. Diseases caused by Campylobacter in humans are largely transmitted through the food chain. In the case of a known poultry house infection, there is no confirmation of horizontal or vertical transfer from one flock to another. Microorganisms, on the other hand, can be found in the guts of dead birds. As a result, environmental horizontal transmission appears to be the primary mode of Campylobacter infection chickens. Various slaughter techniques, like as shipping, de-feathering, and evisceration, increase the external Campylobacter load per bird (Hafez et al. 2014).
2.2 Salmonella spp.
Salmonella is found in a various diversified range of foods, however it is most commonly found in animal products, particularly pig and poultry (Hugas and Beloeil 2014). Salmonella typhimurium is spread by infected meat, eggs, and dung, among other things. These bacteria, particularly those with antibiotic resistance, when applied to croplands via animal manure poses a major environmental and human health hazard that should be closely and regularly monitored (Malik et al. 2021).
2.3 Enterococcus spp
Multi-resistant bacteria such as vancomycin-resistant enterococci (VRE) have enhanced nosocomial infections in humans (Simonetti et al. 2018). Enterococci are Gram-positive bacteria which are natural habitants of humans and animals’ gastrointestinal tracts with a broad range of species such as E. casseliflavus, E. faecalis, E. faecium, E. gallinarum, E. durans, E. munditi, E. avium and E. hirae (Zhou et al. 2020). Due to their frequent occurrence in both human and animal faeces and their prolonged survival in the environment, Enterococcus spp. have developed into a widespread indicator of faecal contamination in the environment (WHO 2018). Despite being regarded as a commensal in humans beings, several Enterococcus species have been found as high ranking (second only to staphylococci) agents responsible for nosocomial infections in humans (Haslam et al. 2018). Enterococci are faecal contamination markers. A comparative examination of genome sequences revealed that E. faecium was found in fertilized soil which is up to seven weeks older after manure application, as well as in exhaled dust. Previously, comparable enterococci retention in manure-fertilized soil has been described. Genome sequencing of bacterial species had not before been used to track down the source of any faecal contamination (Hodgson et al. 2016).
2.4 Escherichia coli
E. coli is a Gram-negative rod shaped bacteria that is not spore forming. It could be mobile i.e. through flagella or some other means, while others may be non-motile or also non flagellated. The bacterial species is a facultative anaerobe that can ferments simple carbohydrates like glucose to end products like produce lactic, acetic, and formic acids; the favorable pH for development is 6.0 to 8.0, but growth can be observed at pH 4.3 and as high as pH 9 to 10 (Mitscherlich and Marth 1984). E. coli is a big and diversified bacterial group. The majority of E. coli strains are innocuous; but, some strains of have developed features, such as the ability to produce toxins, that render them hazardous to humans (Garcia et al. 2010).
E. coli may survive in the environment for long periods of time and can multiply in vegetables and other foods. According to the pathogenic mechanism, pathogenic E. coli have been divided into six types.
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Enteropathogenic E. coli (EPEC)
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Enterohemorrhagic E. coli (EHEC)
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Enterotoxigenic E. coli (ETEC)
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Enteroaggregative E. coli (EAggEC)
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Enteroinvasive E. coli (EIEC)
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Attaching and Effacing E. coli (A/EEC) (Croxen et al. 2013; WHO 2015).
When litter was used as manure, E. coli that were resilient to carbapenems and extended range beta-lactams might have gotten into the ecosystem. The improper utilization antibiotics as growth boosters in chicken and poultry diet may be the cause of this (Sebastian et al. 2021).
2.5 Bacillus spp
Bacillus subtilis, B. pumilus, and B. megaterium are the bacteria found in fresh litter generally but can also be a part of reused or old litter. These are generally used as the prebiotic based cleaning products. The results of this study show that treatment with PB can accelerate the naturally occurring process of diminishing populations of Enterobacteriaceae, which mostly contained the genus Escherichia, hence improving animal health and preventing poultry diseases (De Cesare et al. 2019).
2.6 Comamonas spp
There are four major species of genus Comamonas named as, C. aquatica, C. kerstersii, C. terrigena and C. testosteroni found in poultry litter. These are the areas where the low-virulence diseases that occasionally affect humans and animals are caused by the cascade cage layers houses’ nipple drinking mechanism (Chen et al. 2021).
2.7 Proteus spp.
Proteus species comes under the family Enterobacteriaceae of Gram negative bacilli. According to reports, one of the major causes of human pneumonia (Lysy et al. 1985) and other infection conditions related to lungs (Wu et al. 2006) is the bacterium Proteus mirabilis. 90% of Proteus infections are caused by Proteus mirabilis, which is typically seen in individuals with weekened immune system (Cordoba et al. 2005). This infection has the potential to progress to endotoxin-induced sepsis, which causes systematic inflammatory response syndrome and has a 50% fatality risk. Additionally, it has been demonstrated that Proteus mirabilis can infect the CNS (Central Nervous System) (Kassim et al. 2003). The urea hydrolysis mediated by the enzyme urease produced by this bacterium is what leads to the development of urolithasis. Actually, the hydrolysis causes an increase in pH that results in the precipitation of crystals of Calcium Phosphate (apatite) and magnesium ammonium phosphate (struvite), which obstructs the urinary system (Mobley and Warren 1987). P. mirailis also contributes to the inability of some avian species to reproduce (Cabassi et al. 2004). Additionally, P. mirabilis has been linked to animal kidney and urinary tract infections in earlier studies (Greenberg et al. 2004).
Research on the biochemical responses of human P. mirabilis isolates and the degree of variation in their traits has been extensively published in the literature (Bergey 1993). Unfortunately, there is very scant information available about P. mirabilis that is of animal origin. Finding biochemical similarities between organisms causing illnesses in humans and animals is crucial, particularly when the biochemical trait is also a virulence factor, like the existence of the urease enzyme in P. mirabilis, which contributes to the development of kidney stones (Li et al. 2002).
2.8 Citrobacter spp
Citrobacter genus bacteria and Salmonella share several similarities in their cell surface antigens and biochemical characteristics because of their close kinship. By demonstrating that around one-third of Citrobacter and Salmonella genes are made up of core genes, Pillar et al. confirmed the close kinship of two organisms (Pilar et al. 2020). Their shared evolutionary history and genetic exchange can account for this unusually high genotypic resemblance. Citrobacter spp could be mistaken for Salmonella due to all of the above-mentioned characteristics. It is also crucial to note that it takes an additional day or two to confirm ambiguous identifications, delaying the results and driving up the cost of analysis (Retchless and Lawrence 2010). Citrobacter spp was the second most prevalent bacteria to be retrieved and recognized from chicken litter during a research, following E. coli, out of 149 isolates (Meshref et al. 2021).
2.9 Other bacterial species
Culture based bacterial identification indicated Enterococcus spp. and Coliforms, but culture independent approaches revealed additional bacteria such Globicatella sulfidofaciens, Corynebacterium ammoniagenes, Corynebacterium urealyticum, and Clostridium aminovalericum, Arthrobacter spp and Denitrobacter permanens. When chicken litter DNA samples were utilized as templates for microbial diversity evaluation, other harmful bacterial species such as Clostridia, Staphylococci, and Bordetella spp were also discovered (Meshref et al. 2021). Nocardiopsis spp, Anthrobacter spp, Brachybacterium spp, Brevibacterium avium, Cornibacterium ammoniagenes, and Clostridium lituseburense were among the microorganisms found by Enticknap et al. also Lactobacillus avarius, Jeotgaloccus pinnipedialis, Paraliobacillus ryukyuensis, Virgibacillus carmonensis and few other Bacillus species that are the incharge for the formation of biofertilizer from poultry litter. Bacterial strains such as Atopostipessuicloacalis, Aerococcus viridians, Corynebacterium ammoniagenes, Facklamia sourekii, Brevibacterium avium, Jeotgalicoccus spp, Salinicoccus halodurans, Virgibacillus marismortui, Staphylococcus arlettae, Staphylococcus cohnii and Bacilli hackensackii were found to be prominent in both wet and dry poultry litter samples, out of which Staphylococcus, Salinicoccus, Virgibacillus, Jeotgalicoccus, Facklamia, Brevibacterium and Bacilli were found to be dominant (Wadud et al. 2012).
The impact of fresh or used excrement on the maturation of broiler chicken’s immune systems has recently been described, in addition to the relationship between the kind of litter and gut microbiota, demonstrating the intricate relationship between the development of immune cells and the type of litter used for chicken growth (Lee et al. 2011; Torok et al. 2009).