Background
Methods
Search strategy and selection criteria
Risk of bias in individual studies
Results
Bacteria genera | Species | Medical and/or veterinary importance | Geographical occurrence | Site of specimen collection | Host stage infected | Prevalence | Lab or field study | Site of isolation | References |
---|---|---|---|---|---|---|---|---|---|
Helicobacter
|
H. pylori
| Medical | Worldwide | Laboratory reared | Adult | – | Lab | External surfaces/internal organs | |
Campylobacter
|
C. jejuni
| Medical and veterinary | Worldwide | Poultry, piggery | Adult/larvae | 6.2% | Field/ Lab | External surfaces/internal organs | |
C. coli
| Medical and veterinary | Worldwide | Poultry, piggery | Adult | 90.1% | Field | External surfaces/internal organs | [74] | |
Others | Medical and veterinary | Worldwide | Restaurant, refuse dumps, barbecue shops, fruits and food vendors, markets, poultries (broiler farms) | Adult | – | Field | External surfaces/internal organs | ||
Salmonella
|
S. typhimurium
| Medical | Worldwide | Laboratory experiment | Adult | – | Lab | [37] | |
S. enterica serovar Enteritidis
| Medical | Worldwide | Poultry, dumpsters | Adult/larvae | 6–70% | Lab/field | External surfaces/internal organs | ||
Others | Medical | Worldwide | Restaurant, refuse dumps, barbecue shops, fruits and food vendors, markets, fish vendors, human habitation | Adult | 11.8–66.67% | Field | External surfaces/internal organs | ||
Escherichia
|
E. coli
| Medical | Worldwide | Human habitation, cafeteria and food centers, hospitals, open fields, poultry farms, slaughter houses, cattle farms, animal hospitals | Adult/larvae | 10.5–76.3% | Field/lab | External surfaces/internal organs | |
Bacillus
|
B. anthrax
| Medical and veterinary | Worldwide | Laboratory reared | Adult | – | Lab | External surfaces/Internal organs | [76] |
B. megatarium
| non | Worldwide | Cafeteria and food centers | Adult | 50% | Field | External surfaces/Internal organs | [7] | |
B. sphaericus
| Medical | Worldwide | Cafeteria and food centers | Adult | 50% | Field | External surfaces/Internal organs | [7] | |
B. cereus
| Medical | Worldwide | Fresh fish | Larvae | – | Field | External surfaces/Internal organs | ||
B. alvei
| Medical | Worldwide | Cafeteria and food centers | Adult | 50% | Field | External surfaces/Internal organs | [7] | |
B. pumilus
| Medical | Worldwide | Adult | – | Field | External surfaces/Internal organs | [46] | ||
B. thuringiensis
| non | Worldwide | Adult | – | Field | External surfaces/Internal organs | [46] | ||
Others | Medical | Worldwide | Dairy farms, hospitals, slaughter houses, fruit and food centers | Adult | 31.1% | Field | External surfaces | ||
Staphylococcus
|
S. aureus
| Medical | Worldwide | Human habitation, fresh fish | Adult/ larvae | 26.9% | Field | External surfaces/Internal organs | |
S. epidermidis
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces/Internal organs | [40] | |
S. sciuri
| Medical/veterinary | Worldwide | Dumpsters of restaurants | Adult | – | Field | External surfaces | [46] | |
S. saprophyticus
| Medical | Worldwide | Dumpsters of restaurants | Adult | – | Field | External surfaces | [46] | |
S. xylosus
| Medical | Worldwide | Dumpsters of restaurants | Adult | – | Field | External surfaces | [46] | |
Others | Medical/veterinary | Worldwide | Poutry, animal farms, garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals | Adult | 22.9–28.2% | Field | External surfaces/Internal organs | ||
Enterococcus
|
E. faecalis
| Medical | Worldwide | Restaurants, piggery farms | Adult | 55.5–88.2% | Field/lab | External surfaces/Internal organs | |
E. faecium
| Medical | Worldwide | Restaurants, piggery farms | Adult | 6.8–12.8% | Field/lab | External surfaces/Internal organs | ||
E. casseliflavus
| Medical | Worldwide | Restaurants, piggery farms | Adult | 4.9–6.7% | Field/lab | External surfaces/Internal organs | ||
E. hirae
| Medical/veterinary | Worldwide | piggery farms | Adult | 12.8% | Field/lab | External surfaces/Internal organs | [50] | |
Aeromonas
|
A. caviae
| Medical | Worldwide | Hospitals, streets, slaughter houses (abattoir) | Adult | 39–78% | Field | Internal organs | |
A hydrophila
| Medical | Worldwide | Open field | Adult | – | Field | Internal organs | [82] | |
Others | Medical | Worldwide | Poutry, animal farms, garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals | Adult | – | Field | Internal organs | [79] | |
Shigella
|
S. sonnei
| Medical | Worldwide | Hospitals, streets, slaughter houses | Adult | – | Field | Internal organs | [48] |
S. dysenteriae
| Medical | Worldwide | Dumpsters of restaurants | Adult | – | Field | Internal organs | [46] | |
Others | Medical | Worldwide | Poultry, animal farms, garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals | Adult | 4.8–66.67% | field | External surfaces/ internal organs | ||
Klebsiella
|
K. pneumoniae
| Medical | Worldwide | Hospitals, human habitation, slaughter houses | Adult | 11.3–82% | field | External surfaces/ internal organs | |
K. oxytoca
| Medical | Open field | Adult | – | Field | External surfaces | [83] | ||
Others | Medical | Poutry, animal farms,garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals, slaughter houses, open field | Adult | – | Field | External surfaces | |||
Pseudomonas
|
P. aeruginosa
| Medical | Worldwide | Dump sites, slaughter houses, open field, human habitation, fresh fish, hospitals | Adult/larvae | 37% | field | External surfaces/internal organs | |
Others | Medical | Worldwide | Hospitals, streets, slaughter houses, | Adult | 21.8% | Field | External surfaces/internal organs | ||
Proteus
|
P. mirabilis
| Medical | Worldwide | Slaughter houses, hospitals | Adult | 29.1% | field | External surfaces/internal organs | [15] |
P. vulgaris
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces/internal organs | [40] | |
Proteus sp.
| Medical | Worldwide | Slaughter houses, dump sites, open fields, human habitations | Adult | 14.8% | Field | External surfaces/internal organs | ||
Citrobacter
|
C. freundi
| Medical | Worldwide | Cafeteria and food centers, Slaughter houses, hospitals | Adult | 28.4% | field | External surfaces/internal organs | |
Chronobacter
|
C. turicensis,
| Medical | Worldwide | Poultry, dumpsters | Adult/larvae | 14% | Field/lab | External surfaces/internal organs | |
C. universalis
| Medical | Worldwide | Poultry, dumpsters | Adult/larvae | – | Field/lab | External surfaces/internal organs | ||
C. sakazakii
| Medical | Worldwide | Poultry, dumpsters | Adult/larvae | – | Field/lab | External surfaces/internal organs | ||
Listeria
|
L. monocytogenes
| Medical | Worldwide | Poultry, dumpsters | Adult/larvae | 3–49.4% | Field/lab | External surfaces/internal organs | |
Others | Medical/veterinary | Worldwide | Animal farms | Adult | – | Field | External surfaces/internal organs | [78] | |
Streptococcus
|
S. pyogenes
| medical | Worldwide | Fresh fish, human habitation | Adult/larvae | – | Field | External surfaces/internal organs | |
S. faecalis
| Medical | Worldwide | Fresh fish | Larvae | – | Field | External surfaces/internal organs | [53] | |
Others | Medical | Worldwide | Hospitals, slaughter houses, streets, dump sites, open fields, human habitation | Adult | 66.67% | Field | External surfaces/internal organs | ||
Alternaria
|
Alternaria spp.
| Medical | Worldwide | Fresh fish, Human habitation | Larvae | 1.4–6% | Field | ||
Serratia
|
Serratia spp.
| Medical | worldwide | Human habitation | Adult | – | Field | Internal organs | [40] |
Enterobacter
|
Enterobacter spp.
| Medical | Worldwide | Human habitation | Adult | – | Field | Internal organs | |
Edwardsiella
|
Edwardsiella spp.
| Medical | Worldwide | Poultry | Adult | – | field | External surfaces/internal organs | [43] |
Providencia
|
Providencia spp.
| Medical | Worldwide | Poultry, animal farms, garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals, slaughter houses, open field | Adult | – | Field | External surfaces/ internal organs | |
Vibrio
| Vibrio cholera non O1 | Medical | Worldwide | Human habitation | Adult | 45.7% | Field | Internal organs | [29] |
Others | Medical / veterinary | Worldwide | Animal farms | Adult | – | Field | External surfaces/ internal organs | [78] | |
Morganella
|
M. morgana
| Medical | Worldwide | Poutry, animal farms,garden, garbage/dump areas, restaurants/cafeteria, markets, human habitation, hospitals, slaughter houses, open field | Adult | 16.67% | Field | External surfaces/Internal organs | |
Clostridium
|
Clostridium spp.
| Medical | Worldwide | Dairy farms | Adult | – | Field | Internal organs | [10] |
Corynebacterium
|
Corynebacterium spp.
| Medical | Worldwide | Dairy farms | Adult | – | Field | Internal organs | [10] |
Lactobacillus
|
Lactobacillus spp.
| Medical | Worldwide | Dairy farms | Adult | – | Field | Internal organs | [10] |
Yersinia
|
Y. enterocolitica
| Medical | Worldwide | Hospitals, streets, slaughter houses | Adult | – | Field | Internal organs | [48] |
Burkholderia
|
B. pseudomallei
| Medical | Worldwide | Open field | Adult | – | Field | Internal organs | [83] |
Acinetobacter
|
A. baumanni
| Medical | worldwide | Poultry, dumpsters | Adult | – | Field | Internal organs | |
Methylobacterium
|
M. persicinum
| Medical | Worldwide | Poultry, dumpsters | Adult | – | Field | Internal organs | [46] |
Micrococcus
|
Micrococcus sp.
| Medical | Worldwide | Garbage/dump areas, poultry, restaurants | Adult | – | Field | External surfaces/Internal organs | [89] |
Fungi genera | Species | Medical, veterinary or agricultural importance | Geographical occurrence | Site of specimen collection | Host stage infected | Prevalence | Lab or field study | Site of isolation | References |
---|---|---|---|---|---|---|---|---|---|
Cladosporum
|
C. cladosporoides
| Medical | Worldwide | Cattles diagnosed with bovine ringworm, animal pens, dump sites | Adult/larvae | 4.7–85% | Field/lab | External surfaces | |
Others
| Medical | Worldwide | Human habitation | Larvae | 0.2 | Field | External surfaces | ||
Penicillium
|
P. axalicum
| Medical | Worldwide | Fresh fish | Larvae | – | Field | External surfaces | [53] |
P. corylophilum
| Medical | Worldwide | Animal pens, dump sites | Larvae | – | Field | External surfaces | [57] | |
P. fellutanum
| Medical | Worldwide | Animal pens, dump sites | Larvae | 11.9% | Field | External surfaces | [57] | |
P. verrucosum
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] | |
P. aurantiogriseum
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] | |
Others | Medical | Worldwide | Human habitation, Cattles diagnosed with bovine ringworm, hospitals, slaughter houses | adult | 3.4–21% | Field/lab | External surfaces | ||
Aspergillus
|
A. flavus
| Medical | Worldwide | Animal pens, dump sites, poultry farms, dairy, piggery, slaughter houses, open field | Adult/larvae | 23.8% | Field | External surfaces | |
A niger
| Medical | Worldwide | Animal pens, dump sites | Adult/larvae | 14.4–85.71% | Field | External surfaces | ||
A fumigatus
| Medical | Worldwide | Cafeteria and food centers | Adult | 85.71 | Field | External surfaces | [7] | |
A tamari
| Medical | Worldwide | Fresh fish | Larvae | – | Field | External surfaces | [53] | |
A parasiticus
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] | |
Others | Medical | Worldwide | Human habitation, Cattles diagnosed with bovine ringworm, hospitals, slaughter houses | Adult | 2.8–67.4% | Field/lab | External surfaces | ||
Beauveria
|
B. bassiana
| Medical | Worldwide | Poultry farms, dairy, piggery, open field, slaughter houses | Adult | – | Field | External surfaces | [52] |
Mucor
|
M. cirinelloides
| Medical | Worldwide | Cafeteria and food centers | Adult | – | Field | External surfaces | [7] |
Others
| Medical | Worldwide | Human habitation | Adult | 2% | Field | External surfaces | [55] | |
Alternaria
|
A. alternata
| Medical | Worldwide | Animal pens, dump sites | Adult/larvae | 1.4–11.9% | Field | External surfaces | |
Fusarium
|
F. oxysporum
| Medical | Worldwide | Fresh fish | Larvae | – | Field | External surfaces | [53] |
F. verticilliodes
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] | |
F. proliferatum
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] | |
Others | Medical | Worldwide | Animal pens, dump sites, Human habitation, hospitals, slaughter houses | Larvae | 4.7–17% | Field | External surfaces | ||
Curvularia
|
C. brachyspora
| Medical | Worldwide | Animal pens, dump sites | Adult | 2.4% | Field | External surfaces | [57] |
Mycelia
|
M. sterilia
| Medical | Worldwide | Animal pens, dump sites | Adult | 2.4% | Field | External surfaces | [57] |
Candida
|
C. albicans
| Medical | Worldwide | Pig pen, Human habitation | Adult | 44.6% | Field | External surfaces | |
C. glabrata
| Medical | Worldwide | Human habitation | Adult | 23% | Field | External surfaces | [51] | |
C. krusei
| Medical | Worldwide | Human habitation | Adult | 19.6% | Field | External surfaces | [51] | |
C. tropicalis
| Medical | Worldwide | Pig pen, Human habitation | Adult | 7.4% | Field | External surfaces | ||
C. dubliniensis
| Medical | Worldwide | Human habitation | Adult | 3.6% | Field | External surfaces | [51] | |
C. parapsilisis
| Medical | Worldwide | Human habitation | Adult | 1.8% | Field | External surfaces | [51] | |
Others | Medical | Worldwide | Human habitation | Adult | 10.5% | Field | External surfaces | [59] | |
Microsporum
|
M. canis
| Veterinary | Worldwide | Laboratory experiment | Adult/larvae | – | Field | External surfaces/internal organs | [85] |
M. gypseum
| Medical | Worldwide | Hospitals, slaughter houses | Adult | – | Field | External surfaces | [58] | |
Chrysosporium
|
Chrysosporium spp.
| Medical | Worldwide | Human habitation | Adult | 2% | Field | External surfaces | [55] |
Curvalaria
|
Curvalaria spp.
| Agricultural | Worldwide | Human habitation | Adult | 0.4% | Field | External surfaces | [55] |
Epicoccum
|
Epicoccum spp.
| Medical | Worldwide | Human habitation | Adult | 1% | Field | External surfaces | [55] |
Eupenicillium
|
Eupenicillium spp.
| Medical | Worldwide | Human habitation | Adult | 1% | Field | External surfaces | [55] |
Moniliella
|
Moniliella spp.
| Medical and veterinary | Worldwide | Human habitation | Adult | 9% | Field | External surfaces | [55] |
Nigrospora
|
Nigrospora spp.
| Agricultural | Worldwide | Human habitation | Adult | 1% | Field | External surfaces | [55] |
Rhizopus
|
Rhizopus spp.
| Veterinary | Worldwide | Human habitation | Adult | 2% | Field | External surfaces | [55] |
Scopulariopsis
|
Scopulariopsis spp.
| Veterinary | Worldwide | Human habitation | Adult | 2% | Field | External surfaces | [55] |
Mucorales
|
Mucorales spp.
| Medical | Worldwide | Hospitals | Adult | 11% | Field | External surfaces | [59] |
Rhodotorula
|
Rhodotorula spp.
| Medical/veterinary | Worldwide | Hospitals | Adult | 8.4% | Field | External surfaces | [59] |
Moniliella
|
M. suaveolans
| Medical | Worldwide | Human habitation | Adult | – | Field | External surfaces | [60] |
Parasite genera | Species | Medical or veterinary importance | Geographical occurrence | Site of specimen collection | Host stage infected | Prevalence | Lab or field study | Site of isolation | References |
---|---|---|---|---|---|---|---|---|---|
Ascaris
|
A. lumbricoides
| Medical | Worldwide | Slaughter houses, dump sites, human habitation, open fields | Adult | 12.6–14.29% | Field | External surfaces | |
A. suum
| Veterinary | Worldwide | piggery | Adult | 62% | Field/lab | External surfaces/internal organs | [54] | |
Entamoeba
|
E. histolytica
| Medical | Worldwide | Slaughter houses, dump sites, human habitation, open fields | Adult | 35.43–53.57% | Field | External surfaces | |
Hookworm |
Ancylostoma duodenale/Necator americanus
| Medical | Worldwide | Slaughter houses, dump sites, human habitation, open fields | Adult | 8.93% | Field | External surfaces | |
Trichuris
|
T. trichiura
| Medical | Worldwide | Slaughter houses, dump sites, human habitation, open fields, piggery | Adult | 12.5–74.0% | Field | External surfaces | |
T. suis
| Medical/veterinary | Worldwide | Piggery | Adult | – | Field/lab | External surfaces/internal organs | [54] | |
Strongyloides
|
S. stercoralis
| Medical | Developing countries | Slaughter houses, dump sites, human habitation, open fields | Adult | 10.7% | Field | External surfaces/internal organs | [61] |
S. ransomi
| Veterinary | Tropical regions | Piggery | Adult | 21% | Field | External surfaces | [54] | |
Metastrongylus |
M. spp
| Veterinary | Worldwide | Piggery | Adult | – | Field | External surfaces/internal organs | [54] |
Haematopinus |
H. suis
| Veterinary | Worldwide | Piggery | Adult | – | Field | External surfaces/internal organs | [54] |
Crytosporidium
|
C. parvum
| Medical/ Veterinary | Worldwide | Laboratory experiment | Adult/larvae | – | Lab | Internal organs | [65] |
Giardia
|
G. lamblia
| Medical | Developing countries | Human habitation, refuse dumps, tomato/vegetable and soft drink shops | Adult | 23.62% | Field | External surfaces | |
Enterobius
|
E. vermicularis
| Medical | Worldwide but more prevalent in developed world | Poultry | Adult | – | Field | External surfaces | [3] |
Taenia
|
T. spp.
| Medical/veterinary | Worldwide | Human habitation, refuse dumps, tomato/vegetable and soft drink shops | Adult | 15.75% | Field | External surfaces | |
Hymenolepis
|
H. nana
| Medical | Worldwide | Human habitation, refuse dumps, tomato/vegetable and soft drink shops | Adult | 5.51% | Field | Internal organs | [63] |
Virus family | Common name | Medical or veterinary importance | Geographical occurrence | Site of specimen collection | Host stage infected | Prevalence | Lab or field study | Site of isolation | References |
---|---|---|---|---|---|---|---|---|---|
Picornavirus | Senecavirus A | Medical/veterinary | Worldwide | Laboratory experiment | Adult | – | Lab | Internal organs | [65] |
Filoviridae | Ebola virus | Medical | West and Central Africa | Laboratory experiment | Adult | – | Lab | Internal organs | [68] |
Arteriviridae | Porcine reproductive and respirator syndrome virus | Veterinary | Worldwide | Piggery | Adult | – | Lab | Internal organs | [86] |
Orthomyxoviridae | Avian Influenza virus H5N1 | Veterinary | Worldwide | Laboratory experiment | Adult | – | Lab | Internal organs | [66] |
Hytrosaviridae | Musca domestica salivary gland hypertrophy virus (MdSGHV) | Veterinary | Worldwide | Laboratory experiment | Adult | 3–24% | Lab | Internal organs | [88] |
Paramyxoviridae | Newcastle disease virus | Medical/veterinary | Worldwide | Laboratory experiment | Adult | – | Lab | Internal organs | [67] |