E. coli is a gram-negative, non-acid-fast, uniform staining, non-spore-forming bacillus that grows both aerobically and anaerobically and may be variable in size and shape. Many strains are motile and have peritrichous flagella. E. coli is considered as a member of the normal microflora of the poultry intestine, but certain strains, such as those designated as avian pathogenic E. coli (APEC), spread into various internal organs and cause colibacillosis characterized by systemic fatal disease [22,23]. E. coli isolates pathogenic for poultry commonly belong to certain serogroups, particularly the serogroups O78, O1, and O2, and to some extent O15 and O55 [24,25]. In domestic poultry, avian colibacillosis is frequently associated with E. coli strains of serotypes O78:K80, O1:K1 and O2:K1 (2- Filali E). The avian colibacillosis was found widely prevalent in all age group of chickens (9.52 to 36.73%) with specially high prevalence rate in adult layer birds (36.73%) [26].

The most important reservoir of E. coli is the intestinal tract of animals, including poultry. In chickens, there are about 10⁹ colony forming units (CFU) of bacteria per gram of feces and of these, 10⁶ CFU are E. coli. E. coli has also been commonly isolated from the upper respiratory tract. In addition, it is present on the bird’s skin and feathers. These strains always belong to both pathogenic and non-pathogenic types [27]. In the caecal flora of healthy chickens, 10 to 15% of the E. coli strains may belong to an O-serotype that can also be isolated from colibacillosis lesions [28]. As soon as the first hours after hatching, the birds start building up their E. coli flora. The bacteria drastically increase their numbers in the gut. In a single bird a large number of different E. coli types is present, obtained via horizontal contamination from the environment, more specifically from other birds, faeces, water and feed [29]. Moreover, rodents may be carriers of APEC and hence a source of contamination for the birds [22].

The risk for colibacillosis increases with increasing infection pressure in the environment. A good housing hygiene and avoiding overcrowding are very important. Other principal risk factors are the duration of exposure, virulence of the strain, breed, and immune status of the bird [30–34]. Every damage to the respiratory system favours infection with APEC. Several pathogens, like NDV, IBV and MG, both wildtype and vaccine strains, may play a part in this process. An unfavourable housing climate, like an excess of ammonia or dust, renders the respiratory system more susceptible to APEC infections through deciliation of the upper respiratory tract [22].

Pulsed field gel electrophoresis (PFGE) is considered to be the most reliable molecular finger-printing technique to differentiate organisms but restriction fragment length polymorphism (RFLP) is the one that is used most frequently. However, both techniques require large quantities of DNA, are time consuming, and require expensive equipment [35]. Other techniques such as ERIC–PCR and REP–PCR [36,37] and random amplification of polymorphic DNA (RAPD)–PCR [38] have been proposed as alternatives and used to characterize Escherichia coli isolates of avian origin [39,40]. Other molecular techniques such as ribotyping and isoenzyme profile have also been used to evaluate the clonality of avian E. coli [41]. Some clones are specific to APEC and a small-scale comparison of commensal and pathogenic isolates revealed that 83% of pathogenic strains belong to only five clones, whereas each of the 10 non-pathogenic strains belong to different clones [42]. On the other hand, clonal relationships were found for O2:K1 isolates from humans and chickens [43] and for O78 isolates from humans, cattle, sheep, pigs and chickens [44], indicating that these species too might act as a source of infection for chickens.

Even though certain O-types are more frequently detected in APEC than in commensal E. coli [45], the isolates are very heterogenous, both in their pheno- and genotype [43,45–47]. On the other hand, the prevalence of certain serotypes is linked with the geographical localisation of a flock [48].

Since avian pathogenic E. coli (APEC) and human uropathogenic E. coli (UPEC) may encounter similar challenges when establishing infection in extraintestinal locations, they may share a similar content of virulence genes and capacity to cause disease. In this regard, Rodriguez-Siek et al. [49] compared 200 human uropathogenic E. coli (UPEC) and 524 avian pathogenic E. coli (APEC) isolates for their content of virulence genes (Table 1), including many implicated in extraintestinal pathogenic E. coli (ExPEC) virulence as well as those associated with APEC plasmids for assessing the potential of APEC to cause human extraintestinal diseases and a well-documented ability of avian E. coli to spread to human beings, the potential for APEC to act as human UPEC or as a reservoir of virulence genes for UPEC should be considered.

Avian pathogenic E. coli strains are often resistant to antimicrobials approved for poultry including cephradine [66], tetracyclines [66–70], chloramphenicol [66], sulfonamides [67,69–71], amino-glycosides [68–70,72,73] and β-lactam antibiotics [66,67,69,71]. Resistance to fluoroquinolones was reported within several years of the approval of this class of drugs for use in poultry [45,71,74,75]. There is reason for concern that genes conferring resistance to extended-spectrum beta-lactams will emerge in avian pathogenic E. coli strains [76] and reduce the efficacy of ceftiofur, which is currently used on a limited basis in poultry breeding flocks and hatcheries. In one study, conducted at the University of Georgia, 97 of 100 avian pathogenic E. coli isolates were resistant to streptomycin and sulfonamide and 87% of these multiple antimicrobial resistant strains contained a class 1 integron, intI1, which carried multiple antibiotic resistance genes [70]. Multiple antimicrobial resistance traits of avian pathogenic E. coli have also been associated with transmissible R-plasmids [77].

Avian Salmonella infections are important as both a cause of clinical disease in poultry and as a source of food-borne transmission of disease to humans. Under the family of Enterobacteriaceae, the genus Salmonella is a facultative intracellular pathogen causing localized or systemic infections; as well as a chronic asymptomatic carrier state [78]. The etiological agent of fowl typhoid and pullorum disease is Salmonella enterica subsp. enterica serovar Gallinarum, which is divided into two distinct biovars under the serogroup D1, Gallinarum and Pullorum, which are denoted as S. gallinarum and S. pullorum, respectively [78,79]. In addition to S. gallinarum-pullorum, other salmonellae such as S. enteritidis, S. panama and S. dublin also belong to the serogroup D1 [79]. The various motile and non-host adapted highly invasive serotypes such as Salmonella enteritidis and Salmonella typhimurium are commonly referred to as paratyphoid salmonellae [80]. Age wise prevalence of avian salmonellosis showed highest infection rate in adult layers (53.25%) in comparison to brooding (14.55%), growing (16.10%) and pullet (16.10%) chickens [26].

Various routes of infection have been described. Oral route of infection represents the normal route of infection [81]. Although infection in newly hatched chicks by nasal and cloacal route are also considered as the important route of transmission. Chicks may be infected early by vertical transmission either from an infected ovary, oviduct or from the infected eggs during the passage through the cloacal faeces from infected or carrier hens. The birds survive from clinical disease when infected in young stage may show few signs of infection but they become carriers [82]. In adult carriers the reproductive organs are the predilection sites that often lead to the infection of ovarian follicles and as a result transovarian transmission of the disease occurs. The bacteria are passed out through the faeces and lateral spread takes place through the fecal contaminated feeds, water and litter [78].

Although more than 2,300 serotypes of Salmonella have been identified, only about 10% of these have been isolated from poultry [80]. Chickens are the natural hosts for the highly host adapted biovar S. gallinarum and S. pullorum, but natural outbreaks have also been reported in turkeys, guinea fowl, quail and pheasants [83]. Fowl typhoid is a peracute, acute or chronic form of disease affecting mostly adult chickens, whereas pullorum disease affects the very young chickens, mostly 2−3 weeks of age. In the adult it tends to be chronic [78,84]. Fowl typhoid is frequently referred to as a disease of adult birds; still, there are also reports of high morbidity and mortality in young chickens [85]. S. gallinarum can produce lesions in chicks, which are indistinguishable from those associated with pullorum disease [78]. A certain percentage of chickens that survive from the initial infection become carriers with or without presence of clinical signs and pathological lesions [83]. Crowding, malnutrition, and other stressful conditions as well as unsanitary surroundings can exacerbate mortality and performance losses due to salmonellosis, especially in young birds [86]. The potential risk factors responsible for Salmonella contamination of broiler-chicken flocks are summarized in Table 2.

In more recent years, the use of DNA-related techniques such as plasmid analysis [95,96], ribotyping [97–100], and PFGE [101,102] have proved to be useful in discriminating isolates of Salmonella species. Lapuz et al. [103] investigated the prevalence of Salmonella in four layer farms in eastern Japan between 2004 and 2006 to determine the role of roof rats (Rattus rattus) in the epizootology of Salmonella enterica subsp. enterica serovar Enteritidis (S. enteritidis) and they suggested that roof rats were carriers of S. enteritidis and S. infantis and that persistent S. enteritidis and S. infantis infections in a rat population might play an important role in the spread and maintenance of these pathogens inside the layer premises.

Fowl typhoid and pullorum disease are distributed in many countries of the world, and have economic significance [104]. They are mainly distributed in Latin America, the Middle East, the Indian subcontinent, Africa and perhaps other parts of the world [78,105]. Salmonellosis has also been reported in many countries of South-East Asia including Bangladesh [106,107], India [108,109], Pakistan [110,111] and Nepal [112]. Fowl typhoid is common in both backyard chickens and in commercial poultry [113].

Salmonella and other food borne pathogens acquire antibiotic resistance by random chromosomal mutations, mutation of existing genes, and through specific mechanisms such as transduction, tranformation, and conjugation [114]. These mechanisms involve transfer of drug resistant genes by means of circular DNA plasmids such as R-factor, conjugative plasmid, or chromosomal elements [115–122]. The occurrence and proliferation of antibiotic-resistant Salmonella in environmental samples, poultry, and other animals and humans may be due to the use of medicated feeds [123–125], the practice of dipping hatching eggs in solutions containing antimicrobial agents [126–128], routine inoculation of day-old poults with antibiotics [126–128] and treatment of other animals [129] and humans [117] with antibiotics. Salmonella strains of avian origin are also often resistant to variety of antimicrobials approved for poultry including tetracycline [130–133], oxytetracycline [134], penicillin [66,130–134], aminoglycosides [130,132,133], sulfisoxazole [133] and fluoroquinolones [135]. On the other hand, Manie et al. [136] found several strains of multiple antibiotic-resistant Salmonella strains in chicken.

The mechanisms by which avian pathogenic E. coli cause infection are largely unknown. The virulence factors contributing to the pathogenesis of avian colibacillosis are summarized in Table 3.

Recently, Hughes et al. [155] described a cross-sectional study of wild birds in northern England to determine the prevalence of E. coli-containing genes that encoded Shiga toxins (stx1 and stx2) and intimin (eae), important virulence determinants of STEC associated with human disease and they stated that while wild birds were unlikely to be direct sources of STEC infections, they did represent a potential reservoir of virulence genes.

APEC are responsible for a considerable number of various diseases at different ages. Neonatal infection of chicks can occur horizontally, from the environment, or vertically, from the hen. A laying hen suffering from E. coli-induced oophoritis or salpingitis may infect the internal egg before shell formation. Faecal contamination of the eggshell is possible during the passage of the egg through the cloaca and after laying. The latter possibility is considered as the main route of infection for the egg [22]. Before hatching, APEC causes yolk sac infections and embryo mortality. The chick can also be infected during or shortly after hatching. In these cases, retained infected yolk, omphalitis, septicemia and mortality of the young chicks up to an age of three weeks is seen [22]. Broilers may be affected by necrotic dermatitis, also known as cellulitis, characterized by a chronic inflammation of the subcutis on abdomen and thighs [22].

Swollen head syndrome (SHS), mainly a problem in broilers, causes oedema of the cranial and periorbital skin. SHS can cause a reduction in egg production of 2 to 3%, and a mortality of 3 to 4% [156]. Data on this disease are contradictory. Picault et al. [157] and Hafez & Löhren [158] considered SHS as a disease caused by avian pneumovirus (APV), usually followed by an opportunistic E. coli infection. Nakamura et al. [159] however reported that APEC were probably playing a significant part in the disease, but that the role of APV was not at all clear. This had been confirmed by Georgiades et al. [160], who did not detect APV in any of the flocks affected by SHS during a field study, but instead detected infectious bronchitis virus (IBV), avian adenovirus, avian reovirus, and Newcastle disease virus (NDV), as well as Mycoplasma synoviae and M. gallisepticum (MG).

APEC probably do not cause intestinal diseases. Nevertheless, enterotoxigenic E. coli (ETEC) are occasionally isolated from poultry suffering from diarrhoea [161–163] and diarrhoea was experimentally induced after intramuscular inoculation of APEC [164]. On the other hand, enteropathogenic E. coli (EPEC) were isolated from clinically healthy chickens [165]. In turkeys, experimentally inoculated EPEC can only cause enteritis in combination with coronavirus [166].

Layers as well as broilers may suffer from acute or chronic salpingitis [167,168]. Salpingitis can be the result of an ascending infection from the cloaca [167,168] or an infection of the left abdominal airsac [22], although Bisgaard and Dam [167] considered the latter possibility less likely than an ascending infection. Salpingitis can lead to the loss of egg-laying capacity [163]. In the case of chronic salpingitis, the oviduct has a yellowish-gray, cheese-like content, with a concentric structure [168]. In layers, salpingitis can cause egg peritonitis if yolk material has been deposited in the peritoneal cavity, characterised by a sero-fibrinous inflammation of the surrounding tissues [22].

Airsacculitis is observed at all ages. The bird is infected by inhalation of dust contaminated with faecal material, which may contain 10⁶ CFU of E. coli per gram [169]. This aerogenic route of infection is considered as the main origin of systemic colibacillosis or colisepticemia [33,143,170].

Septicemia also affects chickens of all ages, and is mainly described in broilers. It is the most prevalent form of colibacillosis, characterised by polyserositis [143]. It causes depression, fever and often high mortality. Although its pathogenesis has not been elucidated, several routes of infection are possible: neonatal infections [22], infections through skin lesions [171], infection of the reproductive organs [22,167,168], of the respiratory tract [33] and even infection per os [172]. When E. coli reaches the vascular system, the internal organs and the heart are infected. The infection of the myocard causes heart failure [173]. Septicemia occasionally also leads to synovitis and osteomyelitis [22,174] and on rare occasions to panophthalmia [22]. Coligranuloma or Hjarre’s disease is characterised by granulomas in liver, caeca, duodenum and mesenterium, but not in the spleen. It is a rare form of colibacillosis, but in affected flocks it may cause up to 75% mortality [22].

Further studies are needed to determine the role of newly identified putative virulence genes and genes with unknown functions as virulence markers of APEC to strengthen the current understanding of mechanisms underlying the pathogenesis of avian colibacillosis.

The pathogenicity of Salmonella depends on the invasive properties and the ability of the bacteria to survive and multiply within the cells, particularly macrophages [175]. The main site of multiplication of these bacteria is the digestive tract, which may result in widespread contamination of the environment due to bacterial excretion through feces. Following invasion through the intestinal mucosa, cecal tonsils and Peyer’s patches, the organisms are engulfed by macrophages, and through the blood stream and/or lymphatic systems, they spread to organs rich in reticuloendothelial tissues (RES), such as liver and spleen, which are the main sites of multiplication [176]. In case of inadequate body defense mechanism, they may lead to second invasion and be localized in other organs, particularly ovary, oviduct, myocardium, pericardium, gizzard, yolk sac and/or lungs [177]. In the bird challenge, S. typhimurium rapidly caused inflammation of the intestinal mucosa, but S. pullorum preferentially targeted the bursa of Fabricius prior to eliciting intestinal inflammation [178]. Pullorum disease manifests itself predominantly as an enteric disease of chickens, while fowl typhoid shows signs of septicemic disease [78]. Both biovars can cause septicemic infections, which may be acute or chronic, but unlike S. pullorum, S. gallinarum is capable of producing peracute infection and hemolytic anemia in both young and adults [84]. S. gallinarum is extremely pathogenic to young broiler chicks [179].

Fowl typhoid is indistinguishable from pullorum disease unless the etiological agent is isolated and identified [113]. Clinical signs in chicks and poults include anorexia, diarrhea, dehydration, weakness and high mortality [83]. In mature fowls, fowl typhoid and pullorum disease are manifested by anorexia, drop in egg production, increased mortality, reduced fertility and hatchability [83]. S. pullorum infected adult birds may or may not exhibit any clinical signs, or they cannot be detected by their physical appearance [78]. Furthermore, the exact mechanisms of getting these poultry diseases are still remained to be obscured.

A first step is the prevention of egg contamination by fumigating them within two hours after lay, and by removing cracked eggs or eggs soiled with faecal material. It is recommended to vent the incubators and hatchers to the outside and to have as few breeder flocks as possible per breeding unit [22]. In chicks, contamination with APEC from the environment must be controlled by reduction and control of intestinal infection. This can be achieved using competitive exclusion (CE) [186–190], i.e., inoculating day-old chicks with normal bacterial flora of healthy adult chickens or a monoculture, for instance of Bacillus subtilis. Birds also need to be protected against pathogens that promote infections with APEC. This is possible by using Mycoplasma-free birds [22] and protecting the birds against mycoplasmas and viral diseases by vaccinations [170]. Disease introduction must also be avoided [170] by a suitable house infrastructure, the correct use of a transition zone (for changing clothes and shoes, and washing hands), and pest control: rodent faeces are a source of pathogenic E. coli [22]. The housing climate must be kept optimal for bird density, humidity, ventilation, dust and ammonia [29,170].

The great diversity among APEC strains limits the possibilities of vaccination, and vaccines are not used on a large scale. Several vaccines based on killed or attenuated strains have been tested experimentally. In general, they give sufficient protection against infection with homologous strains, but protection against heterologous strains is less efficient [29]. However, Melamed et al. [191] reported a certain degree of heterologous protection obtained with an inactivated vaccine. Passive immunisation of young birds via the breeder hens is efficient for two weeks [192], if the birds are challenged with homologous strains. Vaccines based on virulence factors like fimbriae, also give a good homologous protection, i.e., against APEC possessing the same fimbriae [193].

Although fowl typhoid and pullorum disease are widely distributed in most parts of the world, the diseases have been eradicated from commercial poultry in developed countries such as the United States of America, Canada and most countries of Western Europe [78]. Successful control programs can be achieved by developing good hygiene and management together with routine serological tests and slaughter policy [177]. The principal management procedures should include chicks free from infections, and the chicks should be placed in a cleaned, sanitized and S. gallinarum and S. pullorum free environment with strict biosecurity measures [194]. The feed and water should be free from Salmonella contamination. The dead birds need to be well disposed. Adequate precautions are needed to prevent infections from mechanical carriers like footwear, human clothing, hatchery disciplines, equipments, litters, crates, trucks and processing plants [195]. Wray et al. [196] described that the birds need to be tested at the age of 16 weeks due to immunologic maturity, at the point of lay due to stress and two consecutive times one month apart to provide the acceptable evidence that the flock is free from fowl typhoid [177]. Kabir et al. [189] and Kabir [190] demonstrated the potential role of probiotics for the controlling of Salmonella strains of poultry via the mechanisms of competitive exclusion. Vaccines may be used to control the disease, and antibiotics can be used for the treatment of fowl typhoid and pullorum disease.