The Prevalence of Aliarcobacter Species in the Fecal Microbiota of Farm Animals and Potential Effective Agents for Their Treatment: A Review of the Past Decade

Abstract

There is an endless demand for livestock-originated food, so it is necessary to elucidate the hazard points for livestock breeding. Pathogens are one of the hazard points that threaten the biosecurity of farm-animal breeding and public health. As a potential foodborne pathogen, Aliarcobacter is a member of the intestinal microbiota of farm animals with and without diarrhea. Aliarcobacter spp. are capable of colonizing livestock intestines and are transmitted through the feces. Hence, they endanger slaughterhouses and milk products with fecal contamination. They also have other, rarer, vertical and horizontal transmission routes, including the offspring that abort in farm animals. Gastrointestinal symptoms and abort cases demonstrate potential financial losses to the industry. Viewed from this perspective, the global circulation of farm-animal products is a significant route for zoonotic agents, including Aliarcobacter. In the last decade, worldwide prevalence of Aliarcobacter in fecal samples has ranged from 0.8% in Italy to 100% in Turkey. Furthermore, antibiotic resistance is recognized as a new type of environmental pollutant and has become a hot topic in animal breeding and the food industry. Increasing antibiotic resistance has become a significant problem impacting productivity. The increase in antimicrobial resistance rates in Aliarcobacter is caused by the misuse of antimicrobial drugs in livestock animals, leading to the acquiring of resistance genes from other bacteria, as well as mutations in current resistance genes. The most resistant strains are A. butzleri, A. cryaerophilus, and A. skirrowii. This review analyzes recent findings from the past decade on the prevalence of Aliarcobacter in the intestinal microbiota and the current effective antibiotics against Aliarcobacter. The paper also highlights that A. cryaerophilus and A. skirrowii are found frequently in diarrheal feces, indicating that Aliarcobacter should be studied further in livestock diarrheal diseases. Moreover, Aliarcobacter-infected farm animals can be treated with only a limited number of antibiotics, such as enrofloxacin, doxycycline, oxytetracycline, and gentamicin.

1. Introduction

The genus Arcobacter belongs to the family Campylobactereaceae [1]. The number of novel species has increased dramatically in the last five years. The genus Arcobacter has been divided into six genera—Arcobacter, Aliarcobacter gen. nov., Pseudoarcobacter gen. nov., Halarcobacter gen. nov., Malaciobacter gen. nov., and Poseidonibacter gen. nov. The 16S rRNA genetic similarity of some species has been observed to be low. The genus Aliarcobacter gen. nov. comprises Aliarcobacter cryaerophilus comb. nov., Aliarcobacter butzleri comb. nov., Aliarcobacter skirrowii comb. nov., Aliarcobacter thereius comb. nov., Aliarcobacter trophiarum comb. nov., Aliarcobacter lanthieri comb. nov., and Aliarcobacter faecis comb. nov. [2,3]. While 29 species were identified before 2019 [4], this number was updated to 33 in 2020 [5]. A. vitoriensis sp. nov. [6] and A. vandammei sp. nov. [7] are recorded as the two most recently identified species. Furthermore, A. faecis, and A. lanthieri have been identified as emerging pathogens that could harm humans and animals [8].

The genus Aliarcobacter, with its new name, is a Gram-negative curved rod, and is motile with a single polar flagellum. It is 0.2 to 0.5 μm in diameter and 1 to 3 μm long, and is oxidase- and catalase-positive. Aliarcobacter do not produce fluorescent pigments. Some species may grow in the presence of safranin or oxgall, but they do not occur in the presence of 2, 3, 5-triphenyltetrazolium chloride (0.04%, w/v), glycine (1% w/v), or 4% NaCl [2]. Colonies on blood-agar plates after three days of incubation have a diameter of 2 to 4 mm, and most are round and whitish.

However, there is still no standard isolation protocol, so the current isolation techniques may not lead us to a reliable result [9]. Nevertheless, there have been different approaches for isolating Aliarcobacter in recent years. The study by Merga et al. [10] compared the five most commonly used isolation methods and found that the “Arcobacter broth-mCCDA-Columbia Agar” isolation method [11,12], in which the selectivity was achieved with selective antibiotics instead of filtration, was more specific and sensitive than the other methods. Aliarcobacter species were identified by Celik and Ikiz [13] using the multiplex polymerase chain reaction (mPCR) technique in all isolates, and this proved the selectivity of the “Arcobacter broth-mCCDA-Columbia Agar” method. Moreover, A. skirrowii was isolated at a high rate in Celik and Ikiz’s [13] investigation, which was similar to the results of Merga et al. [10]. This was surprising, as A. skirrowii strains were known to be the most susceptible strains to antibiotics [14]. It was reported that A. skirrowii was the species that showed the least sensitivity to the substances used in the medium, followed by A. butzleri and A. cryaerophilus [10].

Aliarcobacter has been isolated from cases with clinical symptoms, such as acute or chronic watery diarrhea (21%) in pigs and abortions (41.8%) in sows [15,16,17]. Nachamkin et al. [18] reported that A. butzleri was isolated from fecal samples of swine, cattle, horses, ostriches, and tortoises with diarrhea, and A. skirrowii was isolated from sheep and cattle with diarrhea and hemorrhagic colitis. Vandamme et al. [19,20,21] detected A. skirrowii and A. butzleri in lambs with enteritis. However, there have been many studies that have proven that Aliarcobacter strains can be detected in healthy cattle, sheep, and pigs [10,20,21]. Regarding healthy chicken fecal samples, the prevalence is low as a result of avian body temperature being 41.8 °C, being that the majority of strains grow at 18 °C to 37 °C [22,23]. To sum up, water, animal, human clinical specimens, foodstuffs, and food facilities are natural habitats and environments of Aliarcobacter [5].

The purposes of this review were to (i) show the prevalence rates of Aliarcobacter species in the feces of farm animals and the change in antibiotic-resistance rates from 2012 to 2022, as well as to (ii) indicate effective antibiotics for treatment and to (iii) describe the factors influencing prevalence.

Research information was focused on studies of the prevalence of A. butzleri, A. cryaerophilus, and A. skirrowii in the feces of farm animals over the past decade. A database was gathered from experiments where Aliarcobacter species were specified. This included publications that were obtained from the ISI Web of Science database, Scopus, and Springer Link using the words as keywords.

1.1. Virulence Factors

In the last 20 years, research on Aliarcobacter pathogenicity and virulence mechanisms has contributed to the fight against the disease [1,24]. Putative virulence determinants have been identified in Campylobacter. However, until recently, little was known about the genes that directly generate the infection of Aliarcobacter, although recent research has shed some light on virulence factors.

A. butzleri has been described as potentially the most virulent Aliarcobacter species, and the fecal shedding was observed to be longer for A. Butzleri than for other Aliarcobacter species. Furthermore, A. Butzleri was detected to have spread to the majority of tissues, including the liver, kidney, ileum, and brain. On the contrary, A. Cryaerophilus and A. Skirrowii were not seen in these tissues, indicating that these agents may not pass through the intestinal wall [25].

The pathogenesis of A. Butzleri is dependent on the host species and breed. In contrast to the colonization and mortality found in Beltsville white turkeys, A. Butzleri was unable to colonize standard chickens and turkeys [26]. Rats that had been infected with A. Butzleri or A. Cryaerophilus strains developed diarrhea, electrolyte imbalance, and changes in haematological parameters. Aliarcobacter disease may be dose-dependent, indicating that oral doses resulted in varying the progress of disease between mild and diarrhea [27].

Villarruel-Lopez et al. [28] sampled beef, pork, and chicken meat to determine Aliarcobacter cytotoxicity against Vero cells. Only the pork meat was found to have A. Butzleri, A. Skirrowii, and A. Cryaerophilus. It was reported that 95% of the Aliarcobacter isolates produced a virulence mechanism against Vero cells, including cell elongation and the formation of vacuoles. It was the first time that Aliarcobacter spp. Were recorded as producing a vacuolating toxin. By using PCR, Miller et al. [29] detected that A. Butzleri ATCC 49616 had cadF and cj1349 genes encoding fibronectin-binding proteins, which promote the binding of bacteria to intestinal cells; ciaB, which encodes invasion antigen B that contributes to host cell invasion; the virulence factor mviN (inner membrane protein required for peptidoglycan biosynthesis); the gene pldA, which encodes outer membrane phospholipase A associated with lysis of erythrocytes; the hemolysin gene tlyA; the iron-regulated outer membrane protein (irgA); filamentous hemagglutinin (hecA); and hemolysin-activation protein (the gene hecB).

There are other important factors, such as enterotoxins, adherence, invasiveness, and penetrability, that influence the pathogenesis of bacteria. Aliarcobacter was determined to be capable of generating disease by attaching to the surface of epithelial cells or invading the intestinal epithelial cells and replicating in the intestinal lumen [30]. Douidah et al. [31] designed a rapid detection method (PCR) for putative virulence genes for Aliarcobacter strains. hecA and hecB were detected significantly more in cattle strains than in pig and chicken strains (p < 0.05). tlyA was found more frequently in A. cryaerophilus strains from pigs than in those from chickens (p < 0.05).

Levican et al. [24] emphasized that Aliarcobacter species are potential pathogens of humans and also described A. trophiarum and A. defluvii as potentially more virulent. In their research, they isolated Aliarcobacter species mostly from animal feces and sewage and nearly all were found to be adhesive to Caco-2 cells. Among their isolates the most invasive strains were detected from A. trophiarum (3/3), A. skirrowii (1/2), A. cryaerophilus (1/5), A. butzleri (2/12), and A. defluvii (1/8). As a remarkable result, A. trophiarum (all from feces of pig and chicken) was significantly (p < 0.05) more invasive than the other species.

The authors continued to detect putative genes by PCR from different isolates in livestock. Sekhar et al. [32] studied fecal samples and predominantly detected the genes of ciaB, cj1349, mviN, cadF, pldA, and tlyA. In addition, the presence of cytolethal distending toxin (cdtA, cdtB, and cdtC) genes in A. faecis and A. lanthieri reference strains was revealed with high frequencies. cadF, ciaB, mviN, pldA, and tylA are considered common virulence genes in A. butzleri and A. skirrowii strains [33]. Although A. thereius and A. mytili lack virulence genes, they were able to bind and invade Caco-2 cell lines [24].

Potential virulence factors must be evaluated in order to determine their clinical significance in humans and animals. Based on the data so far, we understand that Aliarcobacter species are capable of attaching to and penetrating the host’s intestinal epithelial cells, causing inflammatory reactions, septicemia, and enteritis [31]. The presence of virulence genes and their cytopathogenic activity on in vitro cell lines led the International Commission on Microbiological Specifications for Foods to classify A. butzleri as a “serious hazard” to human health [34].

In brief, the way Aliarcobacter creates disease and its virulence factors have been better understood after the development of in vivo laboratory animal models, cell culture techniques, and rapid and accurate PCR assays.

1.2. Livestock as a Reservoirs of Aliarcobacter

Aliarcobacter spp. may be found all over the world, with infectious sources including livestock and water [35,36,37]. The routes of transmission of Aliarcobacter among animals are still under investigation. In a study conducted in the Netherlands on pregnant pigs, it was investigated whether the mother could transmit the agent to her offspring through the intrauterine route, and A. skirrowii has been observed to be the most prominent Aliarcobacter species in intrauterine transmission. In addition, postpartum infections caused by Aliarcobacter in piglets were also investigated, and it was stated that the agent was transmitted to the offspring from the mother, other newborns, and the environment. Therefore, it is clear that Aliarcobacter can be transmitted to animals both vertically and horizontally [38]. Aliarcobacter spp. has been investigated many times in the stools of livestock animals in the last decade (

Table 1. Relative (%) prevalence rates of Aliarcobacter in intestinal samples of farm animals over the past decade.

Sample	Animal	Sample Size (n)	Prevalence of Aliarcobacter Strains (%)	Clinical Status of Animals	Identification Techniques	References
Fecal samples	Cattle	200	Ab: 58.3	Healthy	PCR	[40]
			Ac: 16.6
			As: 8.3
			Ab+Ac: 16.6
	Sheep	108	Ab: 55	Healthy
			Ac: 10
			Ab+Ac: 35
Chicken swab samples; feces of cattle, sheep and goats	Goats	100	Ab: 18.8	Healthy	PCR and 16S rDNA-RFLP	[44]
			Ac: 31.3
			As: 12.5
			A.cl: 12.5
			An: 6.3
			Ah: 6.3
	Sheep	100	Ac: 33.3	Healthy
			As: 25
			Ah: 16.7
			A.cb: 16.7
			Ab: 8.3
	Cattle	100	Ab: 38.5	Healthy
			Ac: 23.1
			A.cl: 15.4
			As: 7.7
			An: 7.7
	Chickens	100	Ab: 30.3	Healthy
			Ac: 27.3
			As: 15.2
			A.cl: 12.1
			Acb: 6.1
Fecal samples	Water buffaloes	30	Ac: 56.6	Healthy and lactation period	PCR and mPCR	[45]
			As: 6.6
			Ab: 3
			Ab and Ac: 20
			As and Ac: 10
Fecal swabs	Pigs, chickens, turkeys, cattle, sheep, ducks	21	Ab: 16	Healthy	PCR and mPCR	[32]
			Ac: 13
			As: 12
Fecal swabs	Cattle	200	Ab: 100	Healthy	PCR and mPCR	[46]
	Sheep	200	Ab: 100
	Goats	200	Ab: 87.5
			Ac: 12.5
Fecal samples	Pigs	135	Ab: 40.7	Healthy	mPCR	[47]
			Ac: 9.6
			Ab and Ac: 8.9
	Bovines	75	Ab: 26.7	Healthy
			Ac: 6.7
			Ab and Ac: 4
	Chickens	20	Ab: 10.7	Healthy
			Ac: 20
Fecal samples	Sheep	50	Ab: 2	Diarrhea	mPCR	[13]
			Ac:16
			As: 50
Fecal samples		50	Ab: 0	Healthy
			Ac: 0
			As: 10
Fecal samples	Cattle	170	Ab: 0.8	Healthy	mPCR and PFGE	[48]
			Ac: 12.9
			As: 11.2
Cloacal Swabs and Stool	Ducks, geese, broiler chickens, laying hens	100	Ab: 55	Healthy	PCR and mPCR	[49]
			Ac: 30
			As: 0
Fecal samples	Swine	100	Ab: 0	Healthy	mPCR	[50]
			Ac: 12
Fecal samples	Cattle and calves	792	Ab: 34	Healthy	MLST, WGS, PCR	[51]
			Ac: 49
			As: 55
Fecal samples	Cats, cattle, dogs, pigs	197	A.f: 28	Healthy	Real-time (qPCR)	[52]
			A.l: 10
Fecal samples	Cattle, sheep and broiler chickens	NM	Ab: 67.2	Healthy	PCR	[53]
			Ac: 23.8
			As: 88.92
Rectal swabs	Adult cattle (>3 years of age)	110	Ab: 75	Healthy	mPCR	[54]
			As: 12.5
			Ab + Ac: 12.5
	Young cattle (<1 year of age)	83	Ab: 0
			Ab + Ac: 50
			As + Ac: 25
			Ab +Ac + As: 25
	Goats	93	Ab: 0
			Ac: 0
			As: 0

Ab: A. butzleri, Ac: A. cryaerophilus, As: A. skirrowii, Af: A. faecis, Al: A. lanthieri, Acl: A. cloaca, An: A. nitrofigilis, Ah: A. halophilus, A.cb: A. Cibarus, PCR: polymerase chain reaction, mPCR: multiplex polymerase chain reaction, qPCR: quantitative PCR, RFLP: restriction fragment length polymorphism, MLST: multilocus sequence typing, PFGE: pulsed-field gel electrophoresis, WGS: whole genome sequencing, NM: not mentioned.

) using various isolation methods and molecular techniques [10,13,20,39]. The results indicate that cattle and sheep are significant intestinal carriers of Aliarcobacter spp. [40]. Moreover, Aliarcobacter is found in pigs at all stages of production, from piglets through to ground-meat [41]. A. butzleri, A. cryaerophilus, and A. skirrowii have been related to animal diseases and have been isolated from milk samples from a mastitis-affected cow, aborted livestock fetuses, and diarrhea-affected cattle [42,43].

Moreover, water, domestic pets, migratory birds, farm equipment, transport vehicles, feed, and farmers may play an important role in spreading Aliarcobacter spp. [32,55,56]. Farm animals are accepted as a potential source of disease since they have higher prevalence rates of Aliarcobacter species [57]. There was no disease connection in chickens, ducks, turkeys, and domesticated geese. However, it was suggested that diverse poultry species could act as a natural reservoir for Aliarcobacter spp. [58,59]. The gut content of chickens was found to be the source of transmission of Aliarcobacter spp. into slaughterhouses. Aliarcobacter species from the intestine contaminate the environment [58]. Small ruminants endanger slaughterhouses and milk products with fecal contamination, so they pose possible sources of foodborne infections.

There may be some cases of change in the recovery of Aliarcobacter isolates over time in the same animal. Temporary colonization of sheep, low diagnostic levels, or irregular excretion of Aliarcobacter in feces has shed light on this inconsistency [60]. Poultry products, as reservoirs for Aliarcobacter, may pose a hazard for public health, although they are incapable of colonizing the gut of chickens, as the internal temperature of chickens (40.5 to 42 °C) may not provide an optimal environment for Aliarcobacter species because their growth temperature range is between 26 and 30 °C. However, Aliarcobacter can be transmitted to consumers through poultry products due to the processing and storage of poultry meat below 4 °C and at room temperature. In humans, diarrheal illness-associated Aliarcobacter can be spread through drinking water and surface and ground water and, in addition, livestock animals and raw meat are considered a source of Aliarcobacter infection in humans. Although A. butzleri and A. cryaerophilus have been found in slaughter equipment, the mechanism of transmission of Aliarcobacter spp. to humans has not yet been clarified [61]. Infections with A. butzleri cause diarrhea and abdominal pain, as well as nausea, vomiting, and fever in humans, whereas A. skirrowii strains lead to diarrhea. A. butzleri shows similar symptoms to Campylobacter jejuni, but a noteworthy difference is that Aliarcobacter causes more persistent, watery, and less-bloody diarrhea [62].

1.3. Factors Affecting Aliarcobacter Prevalence

There are many factors that affect the colonization of Aliarcobacter, such as animal age, the season of the sampling, geographical location, isolation method, sampling type, farm management, and symptoms of gastrointestinal disease [10,26]. Although Kabeya et al. [20] reported that season does not affect Aliarcobacter prevalence, many studies have found a positive or negative correlation between temperature and prevalence. It was observed that Aliarcobacter was present in almost all of the samples collected by Fisher et al. [63] in August, but during January or April, they observed Aliarcobacter species in a only a few samples. Similarly, the prevalence of A. butzleri was found to be higher in July (76.9%) and August (77.8%), compared to September (42.9%), in the study of Levican et al. [64], and Wesley et al. [65] detected Aliarcobacter more frequently in cattle fecal samples that were taken after the start of May (26.7%) than in those taken earlier (16.6%). Significantly, contrary to these findings, A. butzleri was detected more in samples collected during the winter–spring period (29%) than from those of the summer–autumn period (8%) [66]. Furthermore, an increase in the prevalence of Aliarcobacter strains in sheep was seen in autumn and in winter [13,67]. According to Grove-White et al. [67], the effect of variation in farm-management between dairy cattle and sheep was revealed, with Aliarcobacter spp. being isolated at a greater rate in ruminants raised in closed barns (50.1%) than in animals raised in pastures (20.9%); however the opposite was detected in Camplylobacter samples [68]. The reasons for this difference might be due to variations in the sources of bacterial fecal contamination, as well as the geographical and climatic features of farm sites [66].

Ho et al. [58] reported that the recovery of Aliarcobacter species depends on the sampling size and place. For instance, in chickens, aerotolerant Aliarcobacter species may prefer the ileum over the anaerobic caecum. It is also necessary to consider the difference in culturing methods and incubation conditions that can affect the prevalence and diversity of Aliarcobacter spp. [64,69]. Golla et al. [70] observed that there was a positive correlation between age and the prevalence of Aliarcobacter. In healthy cattle, 16% of rectal swab samples were found to be A. butzleri, whereas only 2% of those from healthy young cattle were identified as A. butzleri. In contrast to this result, De Smet et al. [41] found that the number of excreting animals and Aliarcobacter in the feces did not rise as the animals became older. Giacometti et al. [48] stated that young animals had a much larger proportion of positive samples (27.2% versus 13.15% for adult animals). In another study [13], the number of A. cryaerophilus was found to be greater in sheep aged from 1 month to 3 years (11.5%), but it showed a reverse slope for A. butzleri (1.6%). The incidence of A. skirrowii reached its highest rate between 1 and 3 years (36.1%).

According to sample type, the frequencies of Aliarcobacter species differed considerably in most of the research. Giacometti et al. [48] found that A. butzleri was the only species isolated from milk (80%), while A. cryaerophilus (12.9%) and A. skirrowii (11.2%) were detected as major Aliarcobacter species in fecal samples. Celik and Ikiz [13] reported similar results, indicating the sample type was found to be 99% statistically significant (p < 0.05), and they also stated that the presence of diarrhea was also found to be statistically significant in the isolation rates (p < 0.001) of A. cryaerophilus and A. skirrowii. In accordance with their results, Hassan [71] stated that cloacal swabs and intestinal samples collected from birds (chickens and turkeys) suffering from enteritis had a greater prevalence rate than samples acquired from healthy birds.

2. Prevalence and Antibiotic Resistance of Aliarcobacter Species

2.1. Aliarcobacter Prevalence Rates in Farm Animal Fecal Content

Due to a lack of specific guidelines, Aliarcobacter isolation may not be adequately achieved during regular diagnostic procedures [9], but Aliarcobacter has been isolated from the intestines and feces of a variety of domestic animals on several occasions. In a study by Duncan et al. [68], where the researchers worked with dairy cattle and sheep fecal pat, 55.3% and 13.7% of the samples were detected as Aliarcobacter spp. in dairy cattle and sheep, respectively. Co-colonization of Aliarcobacter species is a widespread situation, and samples containing multiple Aliarcobacter species have been found in certain investigations [45,54]. The dominant species isolated from cows was A. Cryaerophilus, and co-colonizations, on the other hand, occurred in 26% of the Aliarcobacter-excreting animals [21]. The most common species isolated from healthy cattle and sheep was A. butzleri, followed by A. cryaerophilus and A. skirrowii [39,40,72]. Unlike their results, in other investigations, almost all of the species found in the feces were A. cryaerophilus and A. skirrowii [13,48]. Enteritis, diarrhea, and hemorrhagic colitis have also been associated with A. butzleri, A. skirrowii and A. cryaerophilus [13,73].

2.2. Antibiotic Resistance Rates of Aliarcobacter Species in Farm Animals

Increasing antimicrobial drug resistance in food-borne zoonotic pathogens has widespread implications for public health [74]. Phenotypic antimicrobial resistance of Aliarcobacter isolates from different sources can be performed with different techniques, including disc diffusion [13,75,76], ETEST^® bioMerieux [77,78], agar dilution [79], and broth microdilution [80,81]. Disc diffusion is a culture-based assay that uses antibiotic-containing paper disks to determine antimicrobial susceptibility, and the most popular approaches for determining the minimal concentration of antimicrobial (MIC) drugs that kill or inhibit the growth of microorganisms are agar dilution and broth dilution. The E-test is also used to detect the MIC value of bacteria.

There has been little previous research on the rate of antibiotic resistance genes in Aliarcobacter spp. A few studies have demonstrated the antimicrobial resistance mechanism of Aliarcobacter with only its chromosomal structure [29,82], but then, as the plasmids that are in charge of antibiotic resistance have been described, the prevalence of the plasmid genes among Aliarcobacter spp. has been revealed. Many studies on the antimicrobial susceptibilities of Aliarcobacter have been limited mainly to three species: A. butzleri, A. cryaerophilus, and A. skirrowii. Two decades ago, several antimicrobials were recommended for the treatment of Aliarcobacter infections. According to Yan et al. [83], cefuroxime (cephalosporin) was the most effective antibiotic used in Aliarcobacter medication. Fluoroquinolones have been proposed as an alternative treatment of related intestinal diseases. According to the case, some antibiotics can be used in gastro-intestinal infections, along with quinolones, including tetracycline, macrolide, and b-lactams [84]. Gentamicin and enrofloxacin [54], gentamicin, streptomycin and tetracycline [85], tetracycline, oxytetracycline, erythromycin, ciprofloxacin, kanamycin, amikacin, gentamicin, and enrofloxacin [40] were found as suitable antibiotics that can be used to treat Aliarcobacter infections. However, antibiotics that had been chosen for the treatment of Aliarcobacter infections started to show resistance against the strains [84]. Some studies have shown that quinolone group antibiotics have started to gain resistance. Quinolone resistance has been connected to the regular use of the drug in animals to prevent disease [86,87]. In Aliarcobacter species, a mutation in the quinolone-resistance-determining region of the gyrA gene has resulted in significant levels of resistance [16].

Tetracyclines are used to a great extent as therapeutics or growth promoters in livestock in China, India, and the United States. That has led to an increase in antibiotic-resistant strains, allergic reactions in humans and animals, and changes in microflora and bacterial populations, but their use as a growth promoter has been prohibited in Europe [88]. The ribosomal protection from tetracycline is given by tetracycline-resistance genes, tet(O) and tet(W), and Sciortino et al. [89] detected tet(O) and tet(W) in all resistant Aliarcobacter isolates, which was confirmed by disc-diffusion method. tet(O) and tet(W), present in A. cryaerophilus, have been found in high frequency in A. lanthieri and A. faecis [33].

In another study, rectal swabs of cattle and goats were examined, but Aliarcobacter species were not found in any of the samples from a goat farm. Resistance against ampicillin, cefotaxime, and ciprofloxacin was detected in A. butzleri at 55.6%, 33.4%, and 33.4%, respectively [54]. A. butzleri has a large amount of genetic variety and is resistant to several antibiotics, such as amoxycillin+clavulonic acid, nalidixic acid, and ampicillin [80,85].

An increasing number of studies have illustrated that there are differences in susceptibility tests due to the variety of drugs used in animals or the lack of standard susceptibility techniques in Aliarcobacter [84,90]. In order to read the results properly, specific breakpoints should be established for defining the resistance in Aliarcobacter species. Therefore, to conclude the research, different breakpoint criteria in the Clinical Laboratory Standards Institute (CLSI) have been used. In previous studies, MIC results were compared with breakpoints for Enterobacteriaceae or Staphylococcus spp., as defined by the CLSI, with breakpoints for Campylobacter, or with EUCAST breakpoints for Enterobacteriaceae, Campylobacter, or non-species-related breakpoints [84,91,92]. Recently, Brückner et al. [9] evaluated MICs with ECOFFs, defined by EUCAST for C. jejuni.

Ferreira et al. [87] reviewed the results that were obtained from Aliarcobacter antibiotic resistance investigations. The antibiotic resistance variation range was found to be between 4.3 and 14.0% for fluoroquinolones, 0.7 and 39.8% for macrolides, 1.8 and 12.9% for aminoglycosides, and 0.8 and 7.1% for tetracyclines. The high resistance rate reported for A. butzleri further shows that this species might behave as a reservoir of genes contributing to antimicrobial resistance transmission through the animal–human–environment interaction, indirectly leading to the failure to treat more severe infections. In addition, A. butzleri presented higher resistance rates to penicillin and cephalosporin.

Most Aliarcobacter isolates were found to be resistant to β-lactam antibiotics. The most effective compound against Aliarcobacter isolates was imipenem [87,93]. The fluoroquinolones, including levofloxacin, marbofloxacin, enrofloxacin, and ciprofloxacin, were detected as effective against A. butzleri and A. cryaerophilus [93]. According to previous studies conducted on the intestinal content of livestock (

Table 2. Aliarcobacter antibiotic resistance rates in percentages in farm animals over the past decade.

Sample	Isolates	AMP	CIP	NAL	GEN	CLOX	TET	ERY	CHL	CTX	ENR	OFX	AMK	OTC	CFZ	GEN + AMX	CEF	DOX	AMC	STM	VAN	CLI	AMX	MET	Reference
Rectal swab and water swabs	Ab	56	33	7	4	ND	7	7	7	33	4	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	[54]
Fecal samples of cattle and sheep	Ab (Cattle)	84.1	0	46.1	0	ND	0	0	38.4	ND	7.6	ND	ND	0	92.3	ND	ND	ND	ND	ND	100	84.1	ND	ND	[40]
	Ac (Cattle)	100	0	0	0	ND	0	0	33.3	ND	0	ND	ND	0	100	ND	ND	ND	ND	ND	100	100	ND	ND
	Ab (Sheep)	88.8	0	55.5	11.1	11.1	0	0	44.4	ND	0	ND	ND	0	100	ND	ND	ND	ND	ND	100	100	ND	ND
	Ac (Sheep)	50	0	0	0	0	0	0	0	ND	0	ND	ND	0	100	ND	ND	ND	ND	ND	100	100	ND	ND
Chicken swab samples; faeces of cattle, sheep, goat, dog and rabbit	Ab	90	ND	70	ND	100	100	60	ND	ND	5	ND	ND	ND	ND	20	20	10	30	30	25	ND	ND	ND	[44]
	Ac	92	ND	75	ND	100	92	63	ND	ND	8	ND	ND	ND	ND	16	13	21	33	25	36	ND	ND	ND
	As	100	ND	64	ND	100	100	64	ND	ND	9	ND	ND	ND	ND	18	9	18	18	27	18	ND	ND	ND
Faeces and carcass swabs from sheep	Ab	ND	44.4	100	0	ND	22	0	ND	ND	22	88.9	0	44.5	ND	ND	88.8	11	33	ND	100	ND	22	0	[13]
	Ac	ND	44.4	66	0	ND	0	0	ND	ND	33	100	0	0	ND	ND	88.8	0	44	ND	100	ND	55	88.8
	As	ND	22.5	25.8	6.5	ND	0	3,2	ND	ND	6.5	29	3	0	ND	ND	90.3	3	32	ND	93.5	ND	35.5	54.8
Faeces of pig, poultry, cattle, sheep, and other non-fecal samples	Ab	ND	0	37.5	18.7	ND	0	50	81.2	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	100	ND	ND	ND	[94]
	Ac	ND	7.6	30.7	7.6	ND	0	54	76.9	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	100	ND	ND	ND
	As	ND	2.4	25	0	ND	0	51	75	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	100	ND	ND	ND
Meat samples of livestock	Ab	ND	ND	63.4	0	ND	0	49	87.8	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	70.7	ND	ND	[95]
	Ac	ND	ND	28.6	0	ND	0	71	42.9	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	71.4	ND	ND
	As	ND	ND	50	0	ND	0		50	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	ND	50	ND	ND
Broiler cloacal swab	Ab	0	ND	100	0	ND	0	100	ND	ND	100	ND	ND	ND	ND	ND	ND	ND	0	100	ND	ND	ND	ND	[85]
Cattle rectal swabs		71	ND	28.5	0	ND	0	0	ND	ND	0	ND	ND	ND	ND	ND	ND	ND	14.28	100	ND	ND	ND	ND
Cloacal swabs from domestic geese	Ab	66.6	ND	ND	ND	ND	ND	0	66,6	ND	0	0	0	0	100	ND	0	ND	66.6	ND	100	ND	100	ND	[76]
	Ac	85.7	ND	ND	ND	ND	ND	0	0	ND	14.2	0	0	0	100	ND	42.8	ND	28.5	ND	100	ND	14	ND
	As	71.4	ND	ND	ND	ND	ND	0	28.5	ND	0	0	0	0	100	ND	100	ND	0	ND	100	ND	0	ND

AMX: amoxycillin, AMP: ampicillin, CLOX: cloxacillin, CHL: chloramphenicol, CTX: cefotaxime, CFZ: cefazolin, CEF: cefalotin, AMC: amoxicillin+clavulanic acid, STM: streptomycin, CLI: clindamycin, CIP: ciprofloxacin, OFX: ofloxacin, ENR: enrofloxacin, NAL: nalidixic acid, AMK: amikacin, DOX: doxycycline, OTC: oxytetracycline, ERY: erythromycin, TET: tetracycline, VAN: vancomycin, MET: methicillin, GEN + AMX: gentamicin+amoxicillin, GEN: gentamicin, Ab: A. butzleri, Ac: A. cryaerophilus, As: A. skirrowii.

), enrofloxacin, gentamicin, and doxycycline have been understood to have the potential to show efficacy against Aliarcobacter strains.

3. Genomic Characterization of the Genus Aliarcobacter

More than two decades ago, the first entire genome of bacteria was sequenced by Fleischmann et al. [96] and, since then, the sequencing technology and the science of bacteria have developed dramatically. Bacterial diversity, population characteristics, operon structure, mobile genetic elements, and horizontal gene transfer are just a few of the essential issues that genomic data have helped us better comprehend. The accessibility of entire genome sequencing for pathogenic and commensal bacterial species has enabled a more in-depth investigation of their complex relationships with their plant or animal hosts [97].

Currently, a total of 325 genomes of Aliarcobacter genus are on the website of the National Center for Biotechnology Information [98]. Currently, 81 belong to A. butzleri, 33 belong to A. cryaerophilus, and 17 belong to A. skirrowii.

Bacterial genomes are now widely sequenced, and data from vast numbers of genomes have a significant influence on our understanding of bacteria. Through genome sequencing, the virulence and the resistance genes can be detected [99]. There are many studies proving this. The antibiotic and metal resistance, along with virulence determinants, were identified by WGS from A. butzleri [100]. and A. cryaerophilus [101]. The detection of phylogeny, resistance, plasmids, and virulence-associated genes (ciaB, pldA, tlyA, mviN, cadF, and cj1349) of A. cibarius and A. thereius was carried out by [102]. In another study, the biofilm activity of Aliarcobacter isolates on polystyrene, borosilicate, and stainless steel was investigated by biofilm-associated genes (flaA, flaB, fliS, luxS, pta, waaF, and spoT), and MLST was applied for the genetic characterization of Aliarcobacter strains [103].

Genomic sequencing plays a key role in assessing the risk that Aliarcobacter poses for human and animal health. Genomic sequence data may be exchanged to contribute to the understanding of evolution and transmission routes of viruses and bacteria, vaccine development, and diagnostic techniques [104].

4. Discussion

Livestock is an integral part of the agricultural production system. It has a key role in the national and global economy [105]. According to the Food and Agriculture Organization of the United States (FAO), livestock contributes 40% of worldwide agricultural production and supports the livelihoods and food and nutrition security of nearly 1.3 billion people. Over 70% of emerging human diseases are caused by animals [106]. Farm animals represent a major source of fecal contamination. Drinking water [107] and food sources [108] that are subjected to feces can lead to disease outbreaks and damage to the economy. The connection between gut microbiota and host health has become apparent over time [109]. Over the last decade, Aliarcobacter has been included in numerous studies to explore the gut microbiome. As Collado et al. [110] stated, Aliarcobacter may have a fecal origin, as it was detected in the intestinal contents of farm animals, such as chickens, pigs, cattle, sheep, and horses, so that the consumption of farm-animal products may have a potential influence on disease transmission. Although the cases in which Aliarcobacter is transmitted to humans from farm animals are rare, previous pathogenesis studies indicate that Aliarcobacter has a zoonotic potential [111]. This thought has been backed up by the evidence in a case study where A. butzleri was reported to be responsible for a foodborne (roasted chicken) outbreak that occurred at a wedding ceremony in the USA in 2013 [112]. Results obtained in the last decade from different regions showed that the prevalence of Aliarcobacter species in farm animal fecal samples ranged from 3 to 100% (Table 1) [45,46]. Generally, A. butzleri dominated the gut microbiome of healthy farm animals, as seen in Table 1. There have not been sufficient Aliarcobacter investigations in farm animals showing diarrhea symptoms, although many studies were carried out on the stool of humans with gastroenteritis or diarrhea [85,113,114]. However, Celik and Ikiz [13] recently discovered that A. cryaerophilus (16%) and A. skirrowii (50%) were the key agents in 50 sheep with diarrhea symptoms, whereas A. butzleri was found less frequently. Figueras et al. [113] also added that A. cryaerophilus was the leading agent of diarrhea. All these results have suggested that Aliarcobacter may be a bacteria that should be investigated more in diarrheal diseases in livestock.

There are many factors, including climate, age, and farm conditions, that may play a role in the differences in the prevalence of Aliarcobacter species. For instance, Golla et al. [70] explain that there is a direct correlation between age and the prevalence, as adult cattle may have been exposed to different environmental conditions than calves, which may have contributed to the higher A. butzleri occurrence. The gut microbiota of younger animals is less likely to be colonized with A. butzleri than that of older animals since they have been treated with different nutritional diet plans.

Several antibiotics have been suggested for the treatment of Aliarcobacter diseases, but antimicrobial resistance continues to be a major public health issue [115]. Amoxicillin/clavulanic acid, gentamicin, erythromycin, and fluoroquinolones, such as ciprofloxacin and doxycycline, have been reported to be the first-line antibiotics used in the treatment of intestinal infections caused by Aliarcobacter spp. [113,116]. As shown in Table 2, the most sensitive drugs were gentamicin, enrofloxacin, oxytetracycline, and doxycycline, which is consistent with findings reported in the last decade. On the contrary, according to many findings, amoxicillin+clavulanic acid, ciprofloxacin, and erythromycin appear to be gaining resistance [13,44,76,94,95]. Ferreira et al. [84] reviewed antibiotic resistance tests that were carried out before 2012. The results of the previous 10 years have been listed in Table 2 of our review, and, as a result, gentamicin and fluoroquinolones (enrofloxacin, oxytetracycline, and doxycycline) are suggested to be used in Aliarcobacter-infected animals.

When the results are compared, it is clear that the antimicrobial resistance rates in Aliarcobacter change over time. For instance, prior to 2012, the majority of Aliarcobacter were ciprofloxacin-susceptible [91,117,118], but, recently, some studies conducted with livestock fecal samples have indicated that the rates of resistance to ciprofloxacin have risen (ranging between 22.5% and 44.4%) (Table 2). The resistance range of nalidixic acid changed from 0–64% [117,119] to 25–100% [13,94], and the resistance range of tetracycline expanded from 0–3% [120,121] to 0–100% [40,44]. Moreover, the highest rate of erythromycin resistance was 5% before 2012 [116], whereas it was 100% in 2012 [85].

Multi-drug resistance (MDR) has been seen in many farm animals in the past decade. According to Jasim and Al-Abodi [122], there is a significant relationship between some MDR strains and virulence genes in A. butzleri and A. cryaerophilus. The virulence genes cadF, irgA, tylA, cdtC, and cdtA were detected in all A. butzleri and A. cryaerophilus isolates. Furthermore, some A. butzleri strains were found to be resistant to tetracycline (72%), amoxicillin (69%), erythromycin (67%), cefoxitin (66%), norfloxacin (43%), and ciprofloxacin (35%), whereas all were found to be susceptible to amikacin, gentamicin, colistin, and fosfomycin. These results highlight the danger of antibiotic resistance in Aliarcobacter. This issue can be explained by several molecular mechanisms, including plasmids, transposons, multidrug efflux pumps, and integrons, which have all been implicated in the evolution and spread of multidrug resistance in Aliarcobacter [121]. Plasmids are the extrachromosomal element that can transfer genes encoding antimicrobial and heavy-metal resistance, toxins, and virulence phenotypes, and efflux pumps are transport proteins that allow the microorganisms to remove toxic substances from within cells into the surrounding environment [84]. Quinolone remains effective in the treatment of Aliarcobacter, but may acquire resistance via efflux and plasmids [123]. As a result, the efficient first-line treatment choices have changed over the last decade, which leaves the breeding and food industries with a number of problems. While aminoglycosides and tetracycline were recommended in 2014 [81] for Aliarcobater diseases, now, antibiotic-treated farm animals are becoming less attractive to consumers. This is something that should be borne in mind in future studies. A common source of the antimicrobial resistance of Aliarcobacter has been the misuse of antimicrobial drugs, leading to the bacteria acquiring resistance genes from other bacteria and mutations in current resistance genes.The past decade has seen an increase in antimicrobial resistance and, since this can have serious consequences, it is imperative that researchers gain a better understanding of the sources of this issue so that the livestock and human medicine industries can take effective action.

An important point should also be taken into consideration regarding the differences in the susceptibility of test results. There is still no standard for the Aliarcobacter disc-diffusion test, since CLSI has not yet stated any specific breakpoints for evaluating it. This may lead the investigators to misinterpret the results [84].

All these studies highlight the need for updated antibiotics for treatment and for further investigation of cases of Aliarcobacter in farm animals with diarrhea. More research into the pathogenicity and virulence potential of Aliarcobacter species is necessary.

5. Conclusions

Over the last decade, Aliarcobacter has been included in numerous studies to explore the gut microbiome. Farm animals may be a potential source of Aliarcobacter, since high prevalence rates have been detected by many researchers. The fact that Aliarcobacter causes diarrhea, enteritidis, and abortion symptoms demonstrates its potential impact on farming and the food industry. Recent research on Aliarcobacter distribution and antimicrobial resistance profiles in farm animals has provided a complete understanding of prevention of the disease. However, many factors have been observed to influence the rates. Although the general prevalence was high in autumn and winter, some authors have revealed higher rates of Aliarcobacter in summer. In cold and rainy weather, animal welfare and barn hygiene on farms may be poorer. The prevalence of Aliarcobacter species might be higher mainly in these seasons, as the animals stay longer in closed barns. For this reason, it is understood that the hygiene of barns should be taken into consideration more since farm animals live in closed areas in winter. The age of farm animals was also not found to be a determinant indicator for the prevalence. Most research has been limited to three species of Aliarcobacter—A. butzleri, A. cryaerophilus, and A. skirrowii. Further studies, therefore, appear necessary to understand the pathogenesis of other Aliarcobacter species, but, based on what we know from limited studies, A. cryaerophilus and A. skirrowii were found frequently in diarrheal cases, indicating that Aliarcobacter should be studied more in livestock diarrheal diseases. Despite the fact that Aliarcobacter has been found abundant in a small number of studies with farm animals having symptoms of diarrhea, the number of diarrheal cases where Aliarcobacter has been investigated is scarce. Researchers need to focus more on this issue. Furthermore, a thorough investigation of the virulence properties of potentially emerging pathogenic bacteria in animals and in foods of animal origin is required for food security. The role of putative virulence determinants in the pathogenicity of Aliarcobacter species is still contradictory. Moreover, antibiotic resistance has become a hot topic in animal breeding and the food industry. In the last decade, results showed that Aliarcobacter-infected animals could be treated with enrofloxacin, doxycycline, oxytetracycline, and gentamicin. However, these antibiotics are also under threat of acquiring resistance, so a new approach is needed to improve antimicrobial therapeutics.