Current trends in drug resistance of pathogens isolated from poultry and the use of commercial phage preparations to control infections

2.1. E. coli

Pathogenic strains of E. coli exhibit a high level of drug resistance, most often to several groups of antimicrobial agents simultaneously. Our own research (Stępień-Pyśniak et al., 2025) determining the drug resistance profiles of avian pathogenic Escherichia coli (APEC) strains isolated from laying hens, breeding hens, broiler chickens, and turkeys in Poland revealed a high rate of resistance to the drugs tested, including amoxicillin (AMX, 100%), doxycycline (100%), enrofloxacin (ENR, 85%), chloramphenicol (75%), AMX  +  clavulanic acid (55%), sulfamethoxazole/trimethoprim (STX, 45%), and neomycin (NEO, 40%) (Table 1). Another of our studies (Nowaczek et al., 2021), using E. coli strains isolated from wild birds in Poland, confirmed resistance to three or more groups of antibiotics in more than 31% of strains tested. The most common resistance profile was simultaneous resistance to TET, STX, and ampicillin (AMP). It should be stressed that wild birds are most often reservoirs of pathogenic microbes, including E. coli strains, and are a very important vector in the transmission of drug resistance.

Earlier research conducted in Poland (Racewicz et al., 2022), in which commensal E. coli strains were isolated in 2019–2020 from litter swabs taken in poultry litter, showed the highest resistance against AMP and doxycycline (100%). In the case of E. coli isolate obtained from cloacal swabs, the highest resistance was observed against AMP (100%) and ciprofloxacin (CIP) (92%). The highest resistance to AMP (100%) and STX (94.7%) was observed in the case of strains isolated from chicken meat from slaughterhouses, while the lowest resistance was shown for gentamicin (GEN 12.5%, 36%, and 36.8%, respectively). Other research (Majewski et al., 2021) using pathogenic E. coli strains isolated from poultry in Poland, including APEC strains, confirmed high resistance to AMX (73.64%) and doxycycline (52.08%), whereas a high percentage of strains were susceptible to colistin (85.64%), NEO (80.62%), and AMX  +  clavulanic acid (73.05%).

Findings from Poland are largely consistent with the results of studies carried out by other research centres within and outside of Europe. For example, a study conducted in Portugal (Oliveira et al., 2022) using APEC strains from broiler chickens in the years 2009–2018 showed that resistance to the antimicrobials most often used in poultry ranged from 32.6% to 78%, i.e. 78% for AMX, 73.5% for AMP, 63.3% TET, 68.2% NEO, and 32.6% for ENR (Table 1). A study conducted in 2023–2024 in Spain, using E. coli strains isolated from broiler chickens, layers, and breeders (the drug susceptibility of 898 isolates in total was tested, among which 59.5% were classified as APEC), showed a high percentage of strains resistant to colistin (58.3%), β-lactams (99.1%), macrolides (99.2%), lincosamides (98.9%), and TETs (38%) (Monroy et al., 2025). A concerning finding is that as many as 99.3% of strains were classified as MDR, showing resistance to at least three families of antibiotics – β-lactams, macrolides, and lincosamides – at a rate of nearly 100%.

In Asian countries such as Nepal, the problem of drug resistance in E. coli from poultry was analysed in a study conducted on strains isolated from broiler chicken carcasses in 2021, which confirmed the presence of strains showing high resistance to GEN (90.2%), TET (67.2%), and AMP (54.1%) (Ranabhat et al., 2024). A study carried out in India (Patel et al., 2024), using E. coli strains isolated in 2019–2021 from chickens that had died with colibacillosis symptoms, confirmed high resistance to ENR (72.46%), levofloxacin (69.56%), ciprofloxacin (66.66%), AMX  +  clavulanic acid (63.77%), and TET (59.42%). Lower resistance was observed in the case of AMP  +  sulbactam (34.78%) and ceftriaxone  +  sulbactam (36.23%). The latest research conducted by Chinese scientists on APEC strains obtained in 2024 (Tian et al., 2025) also confirmed high resistance of isolates to TET (95%), AMP (84.6%), ceftiofur (73.1%), florfenicol (FLO, 80%), sulfisoxazole (80%), and STX (63.3%). MDR was observed in 74% of APEC strains (Table 1).

An equally high rate of drug resistance among APEC strains was observed by researchers in Brazil in 2022–2023, based on samples obtained from birds that had died with colibacillosis symptoms. The most frequently observed MDR profile was simultaneous resistance to β-lactams, fluoroquinolones, TETs, and aminoglycosides (Lúcio et al., 2025). The highest drug resistance was recorded for AMX (66.1%), ceftiofur (56.9%), and norfloxacin (47.7%), while resistance to FLO (25.7%), doxycycline (23.9%), and ENR (22.9%) was markedly lower (Table 1).

The problem of drug resistance in pathogenic E. coli strains isolated from poultry has also been demonstrated in Australia and Thailand (Thomrongsuwannakij et al., 2020). In that study, more than 60% of APEC strains isolated in Thailand were resistant to more than three antibiotics, whereas the percentage of MDR strains isolated in Australia was 10.7%. The highest drug resistance in strains isolated in Thailand was observed for TET (84.5%), AMX (70.2%), and STX (51.2%). In the case of Australian strains, the rates of resistance to these antibiotics were 36.9%, 29.8%, and 17.86%, respectively (Thomrongsuwannakij et al., 2020).

In a study using samples obtained in Algeria in 2019–2020 (Boulbair et al., 2025), 98 APEC strains isolated from chicken samples with characteristic colibacillosis signs showed the highest resistance rates for AMP (97.96%), AMX  +  clavulanic acid (96.94%), nalidixic acid (94.90%), TET (90.82%), and ciprofloxacin (79.59%). It is concerning that 92.86% of APEC strains showed resistance to at least three of the antibiotics tested, which is indicative of the serious problem resulting from the common use of antimicrobials on poultry farms in Algeria and the need for changes in flock health management, especially in poultry production.

Comparison of research results on the drug resistance of E. coli strains isolated from poultry in Poland and around the world reveals that the acquisition of resistance to antibiotics commonly used in poultry is trending upward (Table 1). In Poland as well, as the largest poultry producer in the EU, studies indicate a significant increase in the resistance of E. coli, including APEC strains, to the most important antibiotics in poultry production, such as TET, AMX, AMX + clavulanic acid, and colistin (Majewski et al., 2021). A similar opinion is shared by Ukrainian researchers (Nechypurenko et al., 2024), whose study of APEC strains isolated from broilers in 2015–2022 showed that the number of isolates resistant to colistin decreased in the years 2017–2018, but again increased from 2021 to 2022. In the case of AMX, AMX  +  clavulanic acid, spectinomycin, and doxycycline, a pronounced upward trend in drug resistance was observed in the years 2015–2022. The highest percentage of APEC strains exhibited resistance to flumequine (78.5%), AMX (78.4%), amoxiclav (69.3%), oxytetracycline (75.5%), and doxycycline (58.3%). This concerning phenomenon was again observed in 2022 in more than 40% of isolates, which showed MDR to more than ten antibiotics among polypeptides, aminoglycosides, TETs, beta-lactams, quinolones, and cephalosporins (Nechypurenko et al., 2024).

2.2. Campylobacter spp.

Infections caused by Campylobacter spp., especially Campylobacter jejuni (C. jejuni) and Campylobacter coli (C. coli), are a significant public health problem around the world. According to the World Health Organization (WHO), Campylobacter spp. are one of the four main causes of diarrhoeal diseases in the world, leading to gastroenteritis in humans, as well as extraintestinal complications such as Guillain-Barré syndrome, Miller Fisher syndrome (Yuki, 2001), and reactive arthritis (Keithlin et al., 2014). A report published by the European Food Safety Authority (EFSA) in November 2025 and a report created by the Foodborne Diseases Active Surveillance Network (FoodNet) in cooperation with the Centres for Disease Control and Prevention (CDC) in 2023 confirmed that campylobacteriosis is the most common zoonosis in EU countries and the United States (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025c; Delahoy et al., 2023). The main reservoirs for the microbes are poultry, pigs, and cattle (Al Hakeem et al., 2022; Wieczorek et al., 2021). The first-line drugs for treatment of Campylobacter spp. infections are usually macrolides (erythromycin, ERY and azithromycin), which have largely displaced fluoroquinolones. Fluoroquinolones, due to their widespread use in veterinary medicine, their non-selective use in treatment of humans, and the possibility of inducing drug resistance, are used as second-line drugs (Nunes et al., 2023).

Mechanisms of resistance transfer in Campylobacter spp., including both chromosomal mutations and horizontal gene transfer (HGT), have been described in detail in the literature (Urban-Chmiel et al., 2022). However, trends in the resistance of Campylobacter spp. strains to specific groups of antibiotics are continually changing. For example, a study conducted by Australian researchers using C. jejuni and C. coli strains isolated from chicken broilers showed that most strains of both C. jejuni (63%) and C. coli (86.5%) were susceptible to the antibiotics used in the study, i.e. FLO, GEN, azithromycin, ERY, clindamycin, and telithromycin, with C. coli strains shown to be much more susceptible than C. jejuni. A large discrepancy in resistance was noted for TET, 22.2% for C. jejuni but only 3.1% in C. coli. The level of resistance to both ciprofloxacin and nalidixic acid was 14.8% for C. jejuni and 5.2% for C. coli. The results also confirmed the presence of strains resistant to fluoroquinolones, which are not approved for use in poultry production in Australia. The authors emphasize that the ban on the use of fluoroquinolones in poultry farming does not itself guarantee that bacteria will not be resistant, if there are other routes by which resistant strains can be introduced, such as humans, pests, or wild birds. Genetic analysis of the isolates showed that the most frequently detected resistance gene was bla _OXA, determining resistance to β-lactam antibiotics. Its presence was confirmed in 64.8% of C. jejuni isolates and in 72% of C. coli isolates (Table 2). A mutation in the gene encoding the DNA gyrase A subunit (gyrA) was detected in all C. jejuni and C. coli strains resistant to fluoroquinolones. The tetO gene, determining resistance to TETs, was identified in 28.4% of C. jejuni isolates, which was correlated with the phenotypic assessment of resistance to TET (22.2%). In C. coli, the TET resistance gene was detected in only one isolate (Abraham et al., 2020).

Another study, conducted in China (Tang et al., 2020) using 70 strains of Campylobacter spp., confirmed a high rate of resistance to fluoroquinolones, in which the resistance of C. jejuni to ciprofloxacin and nalidixic acid was high, at 66.7% and 80%, respectively. For C. coli strains, the values were 100% and 92%, respectively (Table 2), which is an alarming phenomenon and, as stressed by the authors, directly linked to the intensive use of these drugs in the poultry sector. High resistance to ERY, clindamycin, azithromycin, GEN, and TET was also noted among Campylobacter spp. strains, ranging from 60% to 80% (Table 2). Genetic testing identified key mechanisms of resistance in Campylobacter spp., such as a point mutation in the gyrA gene (C257T), detected in all strains that were phenotypically resistant to ciprofloxacin and/or nalidixic acid, mutation A2075G in the V domain of the 23S rRNA gene in both C. jejuni and C. coli isolates that were highly resistant to macrolides, and the presence of the gene ermB in nearly 65.7% of strains (Table 2). Among genes responsible for TET resistance, the genes tetO and tetA were detected (Abraham et al., 2020). Similar drug resistance results in Campylobacter spp. strains were obtained in a study carried out in Brazil (Paravisi et al., 2020) on 54 strains of C. jejuni, obtained from bird carcasses, cloacal swabs, and environmental samples. One strain was shown to be susceptible to all antimicrobials tested: ciprofloxacin, nalidixic acid, ERY, TET, GEN, and chloramphenicol. The study showed an extremely high level of resistance to ciprofloxacin (94.4%) and nalidixic acid (94.4% according to CLSI criteria), which was linked to specific mutations in the gyrA gene. In the case of other antimicrobials, the level of resistance varied depending on the standards used Clinical and Laboratory Standards Institute (CLSI) vs European Committee on Antimicrobial Susceptibility Testing (EUCAST) and ranged from 46.3% to 51.8% for TET and from 42.6% to 48.1% for ERY (Table 2). Only 42.8% of strains phenotypically resistant to TET possessed the gene tetO, which suggests that other mechanisms, such as efflux pumps, may be responsible for resistance in the remaining strains (Paravisi et al., 2020). All strains were shown to be clinically susceptible to GEN and chloramphenicol, which the authors link to bans or restrictions on their use in poultry production in Brazil. A particularly concerning phenomenon is the high resistance to ERY and ciprofloxacin shown in the study, as both of these substances are first-line drugs for campylobacteriosis treatment in humans. In addition, the multiple antibiotic resistance (MAR) index of 0.5 suggests high selection pressure in the study area resulting from frequent use of antibiotics in poultry farming (Paravisi et al., 2020). The results are also similar to those of a study conducted in Chile on 118 Campylobacter strains (C. jejuni n = 75, C. coli n = 43) isolated from poultry carcasses (Concha-Toloza et al., 2023). C. jejuni strains showed the highest resistance to ciprofloxacin (37.3%) and TET (20%), and 5.3% of strains were resistant to both antibiotics (Table 2). C. coli strains showed the highest rate of resistance to ciprofloxacin (55.8%), while by far the lowest percentage of strains were resistant to TET (4.7%). In addition, 16.3% of isolates were resistant to ERY, and all of these strains were also resistant to ciprofloxacin. A much lower percentage of C. coli strains showed simultaneous resistance to ciprofloxacin and TET (2.3%) than in the case of C. jejuni, but all strains of Campylobacter spp. were susceptible to GEN, and C. jejuni was additionally susceptible to ERY (Table 2). The genetic analysis detected molecular determinants of resistance to antibiotics; in all Campylobacter spp. strains resistant to ciprofloxacin, the C257T mutation was detected in the quinolone resistance-determining regions (QRDR) of the gyrA gene. The tetO gene was also present in all TET-resistant strains. In addition, determinants of resistance to antimicrobials that were not tested phenotypically were present: lnuC determining resistance to lincomycin (LIN), bla _OXA-61, which encodes the enzyme oxacillinase responsible for Campylobacter resistance to β-lactam antibiotics, aph(3’)-III and aadE-Cc, responsible for resistance to some aminoglycoside antibiotics, and cfrC, associated with resistance to linezolid and phenicols (Concha-Toloza et al., 2023).

In a study conducted in the United States, Poudel et al. (2022) tested 414 samples from conventional chicken farming and farming without antibiotics for the presence of Campylobacter spp. The overall prevalence of Campylobacter was 25.4%. C. jejuni was the dominant species, accounting for 78.1%. C. lari and C. volucris were isolated as well, accounting for 6.7% and 1.9%, respectively. C. coli was not detected in that study. Among the C. jejuni isolates, 13.6% were resistant to three or more classes of antibiotics. C. jejuni showed the highest resistance to nalidixic acid (49.2%) and the highest susceptibility to GEN, ciprofloxacin, ERY, clindamycin, and TET, ranging from 76% to 93%. In C. lari, the highest rate of resistance was noted for nalidixic acid (71.4%) and for ciprofloxacin and TET (57.1%), and the lowest for ERY, azithromycin, and GEN (14.3%). Among 82 C. jejuni isolates, 52.4% possessed the gyrA gene. Other resistance genes were detected as well: tetO, aph(3′)-IIIa, bla _OXA-184, and bla _OXA-61. Only bla _OXA-61 was identified in C. lari. The study demonstrated that Campylobacter spp. is present on farms without antibiotics, and antibiotic resistance, while lower than in conventional farming, still occurs; the absence of antibiotics reduces but does not fully eliminate the problem of resistance (Poudel et al., 2022).

Findings obtained by researches from Iraq (Shakir et al., 2021) for 36 Campylobacter spp. strains isolated from 179 samples (including 150 faecal samples and 29 cloacal swabs) also revealed an alarmingly high level of resistance to commonly used drugs, including 100% resistance to representatives of quinolones – nalidixic acid – and fluoroquinolones – ciprofloxacin (Table 2). High resistance to TET (88.8%), AMP (83.3%), and STX (80.5%) was noted as well. Half of the strains were resistant to ERY (50%) and ceftriaxone (50%). The study confirmed MDR among the Campylobacter spp. strains. The researchers also determined the MAR index, which was 0.3 or higher in 97.2% of isolates, suggesting that these bacteria come from environments in which antibiotics are overused (Shakir et al., 2021).

A large study using 2,367 swabs collected from broiler chicken carcasses in Poland (Wieczorek et al., 2020) showed a very high (>50%) prevalence of Campylobacter spp. strains, among which the dominant species was C. coli (n = 738). Among C. jejuni isolates, 108 (20.6%) were resistant to three or more classes of antibiotics; for most strains (17.9%), the resistance profile included ciprofloxacin, nalidixic acid, streptomycin, and TET. In the case of C. coli, 25.1% of isolates exhibited MDR; the resistance pattern was identical to that of C. jejuni and was found in 18.8% of strains. Only two C. jejuni isolates and one C. coli strain proved to be resistant to all antimicrobials used in the study (Wieczorek et al., 2020). In another study (Casalino et al., 2022), German researchers demonstrated high prevalence of Campylobacter spp. strains (90.4%), which were isolated from 177 of samples collected from layers. C. jejuni was identified in 43.5%, C. coli was detected in 38.9%, and mixed infections were shown in 7.9% of birds. Resistance to antimicrobials was considerable and more often observed in C. coli than in C. jejuni. Higher values for fluoroquinolones were noted in C. coli, amounting to 20.6% for ciprofloxacin, 17.5% for nalidixic acid, and 15.9% for ENR. In C. jejuni, resistance to this group of antibiotics was lower: 18.4% for ciprofloxacin, 13.1% for nalidixic acid, and 11.8% for ENR. Significant differences were also observed for TET resistance, which was much higher in C. coli (39.7%), while only 5.3% of C. jejuni strains were not susceptible to this antibiotic. Resistance to STX was detected in 13.1% of C. jejuni strains and 9.5% of C. coli strains. In the case of ERY, chloramphenicol, and azithromycin, resistance was only observed in single strains, and resistance to GEN was not found in either species. Despite the fact that resistance was higher in C. coli, MDR was shown in more strains of C. jejuni (19.7%) than C. coli (17.5%) (Casalino et al., 2022). A high rate of resistance to TET: 88.5%, ERY (73%), and ciprofloxacin (57.7%) was also observed in a study conducted on 26 Campylobacter spp. isolates from samples of caecal contents collected from poultry in Ukraine (Shchur et al., 2023).

To sum up, resistance of Campylobacter spp. to antimicrobials is dynamic, changing constantly depending on the region, time, and type of antibiotic use. The findings of research conducted in the last 5 years in various parts of the world show a clear upward trend in the acquisition of drug resistance among Campylobacter spp. strains, particularly to ciprofloxacin and nalidixic acid, for which it often exceeds 80–90%, and in some cases, even reaches 100%. This is indicative of the global nature of the problem of drug resistance among Campylobacter spp. isolated from poultry. At present, studies indicate that the efficacy of macrolides remains relatively high, but the appearance of localized cases of resistance indicate that it will gradually decline in the future. Differences in resistance profiles between countries (very high values in Asia vs lower ones in parts of Europe and Australia) confirm the impact of local farming practices and antibiotic policies. The presence of resistant strains is observed even in countries with restrictive antibiotic policies (Australia), which suggests the role of alternative routes of transmission among bacteria. Especially increasing occurrence of MDR strains indicates a growing treatment problem and may limit available treatment options. The trends observed suggest that without effective control measures (rational antibiotic therapy, epidemiological supervision, and biosecurity), the level of resistance may continue to rise.

2.3. Enterococcus spp.

Bacteria of the genus Enterococcus are part of the gut microbiota in poultry. Due to high genome adaptability and plasticity, they are an important reservoir of resistance genes in the animal production environment. In recent years, the role of enterococci in the epidemiology of resistance to antimicrobials has been clearly highlighted in both the scientific literature and reports of European institutions functioning within the framework of the integrated One Health approach (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2023b, 2025b). Despite the decrease in selection pressure associated with the use of antibiotics, resistance to many classes of antimicrobial agents among Enterococcus spp. isolated from poultry remains high. This is due to several overlapping mechanisms, i.e. the durability of resistance determinants encoded on mobile elements (plasmids and transposons), the capacity of enterococci for horizontal transfer of resistance genes, and their natural adaptation to the environment of the digestive tract of animals (Clewell et al., 2014; Partridge et al., 2018). In addition, the phenomenon of co-selection makes exposure to factors other than antibiotics (e.g. heavy metals) conducive to the persistence of resistance genes. In consequence, restricting the use of antibiotics does not always eliminate resistance, which may persist in bacterial populations for a long time (Seiler & Berendonk, 2012). This underscores the need for continued monitoring and the implementation of comprehensive measures within the framework of the One Health approach, encompassing the health of animals, humans, and the environment.

Enterococcus faecalis and Enterococcus faecium are among the enterococcal species most commonly isolated from the gut of poultry. In recent years, other species have increasingly been identified as well, including those of clinical importance in poultry, such as Enterococcus cecorum, Enterococcus hirae, Enterococcus durans, Enterococcus gallinarum, and Enterococcus thailandicus (Stępień-Pyśniak et al., 2016; Velhner et al., 2024; Wigmore et al., 2024). Enterococci are used as indicator bacteria to assess the selection pressure of antibiotics, which results from their ability to accumulate and transfer resistance genes (Hollenbeck & Rice, 2012). Reports by the European Food Safety Authority and the European Centre for Disease Prevention and Control from the years 2020 to 2023 indicate significant geographic variation in levels of resistance in Enterococcus spp. in EU member states (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2023a, 2024a, 2025c). This may be linked to differences in antibiotic use practices, animal production systems, and degrees of implementation of surveillance programmes. Nevertheless, a common feature observed in all regions is the high occurrence of MDR strains, defined as resistant to at least three classes of antibiotics. Especially high MDR levels are noted in isolates from poultry farms, where environmental selection and stocking density are conducive to the persistence and spread of resistance. In many cases, genes of resistance to antibiotics of critical importance for human medicine co-occur, which underscores the importance of the One Health approach in monitoring and curbing this phenomenon.

5.1. Listeria spp.

Antibiotic resistance in Listeria spp., as described in earlier works (Charpentier & Courvalin, 1999; Urban-Chmiel et al., 2022), is primarily determined by the presence of resistance genes in mobile fragments and by plasmid transfer through conjugation with plasmids present in bacteria, mainly Enterococcus spp., Staphylococcus spp., and Streptococcus spp. Drug resistance in Listeria is also associated with transposons carrying resistance genes from the above-mentioned bacterial species to Listeria, or between Listeria species. Changes in determinants of drug resistance acquisition in those bacterial species also influence resistance in Listeria. These mechanisms, known as efflux pumps, are significantly linked to the occurrence of resistance to fluoroquinolones, macrolides, and cefotaxime in L. monocytogenes.

Drug resistance in Listeria spp. is highly varied, and as shown in the studies cited below, depends on the part of the world where the bacteria are isolated. A recent study conducted by Chinese researchers in 2024 (Chen et al., 2024) showed a considerable decrease in the percentage of strains resistant to β-lactams, whose resistance was at a level of 5.26% in 2020 but is currently zero. Similarly, in the case of ERY, representing macrolides, previous research showed a resistance rate of 15.79%, but current values are close to 0 (Chen et al., 2024). In the case of LIN and TET, resistance rates have increased, amounting to 36.36% and 18.18%, respectively, while earlier resistance was at 10.53% for LIN and 15.70% for TET.

Previous research by Hailu et al. (2021) showed that L. monocytogenes strains obtained from poultry manure were 100% resistant to kanamycin, nalidixic acid, and levofloxacin, with MDR to cephem, LIN, antitubercular drugs, folic acid antagonists, penems, and macrolides. Research conducted previously in Poland (Skowron et al., 2020) also confirmed high resistance of L. monocytogenes to cotrimoxazole (45.8%), meropenem (43.3%), ERY (40.0%), penicillin (PEN, 25.8%), and AMP (17.5%).

In Spain, the latest research (Panera-Martínez et al., 2022; Martinez-Laorden et al., 2024) has demonstrated very high resistance of L. monocytogenes strains to cephalosporins and beta-lactams (Table 3). The prevalence of resistance to oxacillin, cefoxitin, cefotaxime, cefepime, ciprofloxacin, ENR, and nitrofurantoin in the Listeria isolates ranged from 97.3% to 100%. The authors cited (Panera-Martínez et al., 2022) suggest that the increase in drug resistance observed in these strains in recent years in comparison to the period before 2020 seems to be due in part to the activation of MGEs associated with plasmids or transposons, through horizontal transfer mechanisms. A fairly concerning phenomenon is the appearance of L. monocytogenes resistance to nitrofurantoin, a substance whose use in livestock has been banned for many years. The authors cited indicate that this may be due to mechanisms of cross-resistance or co-resistance, which could have contributed to the persistence of resistance genes over time. The latest research (Martinez-Laorden et al., 2024) revealed a significant increase in the drug resistance of L. monocytogenes to oxacillin, to 100%, in contrast to data from 2015, in which drug resistance ranged from 75% to 93.3% (Aras & Ardıç, 2015). These findings clearly indicate a concerning phenomenon of intensive acquisition of resistance to an increasingly large group of antimicrobials among Listeria spp. strains.

5.2. Staphylococcus spp.

Bacteria of the genus Staphylococcus are ubiquitous in the environment, including in the water, soil, and air, and are isolated from various animal species, including poultry, in which they colonize the digestive and respiratory systems and are present as physiological flora on the skin and mucous membranes. In the external environment, they can be present in the air, dust, soil, water, and wastewater (Götz et al., 2006). The latest phylogenetic analysis of Staphylococcus led to the separation of ​​a new genus, Mammaliicoccus, within this group of bacteria. The species previously called Staphylococcus sciuri, S. fleurettii, S. lentus, S. stepanovicii, and S. vitulinus were assigned to the new genus Mammaliicoccus, with M. sciuri as the type species (Lory, 2014; Madhaiyan et al., 2020). Coagulase-negative species belonging to both genera can be harmless commensals in poultry and wild birds or invasive opportunistic pathogens with varying virulence potential (Becker, 2020). Among coagulase-positive staphylococci, Staphylococcus aureus is regarded as the most pathogenic, causing a wide range of illnesses, not only in birds, from superficial skin infections to life-threatening conditions such as toxic shock syndrome and sepsis (Mehrotra et al., 2000). Infections caused by S. aureus are a worldwide problem in poultry production and encompass arthritis, synovitis, chondronecrosis, osteomyelitis, gangrenous dermatitis, subcutaneous abscesses, and sepsis (Meyer et al., 2021; Mohibbullah et al., 2022). In addition, strains producing enterotoxins can cause food poisoning in consumers of poultry meat (Franjus et al., 2026). Of particular concern, however, is the growing frequency of isolation of multidrug-resistant Staphylococcus strains, both coagulase-positive and coagulase-negative, including methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase-negative Staphylococcus (CoNS) strains (Gómez-Sanz et al., 2013; Katkowska et al., 2025). Poultry is currently regarded as an important reservoir of livestock-associated MRSA (LA-MRSA) strains (Hado & Assafi, 2021). According to the latest estimates, the prevalence of LA-MRSA is 2.5% in chickens and 5% in turkeys (Chen & Wu, 2021). LA-MRSA strains have also been isolated from poultry products, which indicates that LA-MRSA can spread between humans and animals (da Silva et al., 2020; Tuominen et al., 2022). The local environment is also a significant factor. According to research carried out in Denmark by Friese et al. (2013), residents living in the vicinity of poultry farms are at 15% greater risk of LA-MRSA exposure. One reason for this is undoubtedly the use of poultry manure to fertilize crop fields, but various insects and rodents can also be vectors for these bacteria (Hamza et al., 2020).

An alternative PEN-binding protein 2a, encoded mainly by the gene mecA and displaying low affinity for β-lactam antibiotics, underlies resistance to methicillin in staphylococci (Katayama et al., 2000). The mecA gene is part of the mec complex located on MGEs known as staphylococcal chromosomal cassette mec (SCCmec) (Lakhundi & Zhang, 2018). In 2011, a new type of mec gene was discovered in S. aureus, showing about 70% overlap with the nucleotide sequence of mecA (Shore & Coleman, 2013). This mec homologue was initially called mecALGA251, and later renamed mecC. A plasmid-borne mecB gene has also recently been identified in S. aureus (Becker et al., 2018). The presence of the methicillin resistance gene mecC in coagulase-negative bacteria of the genera Staphylococcus spp. and Mammaliicoccus spp. is rare. In practice, the fact that phenotypic resistance to cefoxitin and oxacillin has been demonstrated in Staphylococcus aureus isolates suggests methicillin resistance (MRSA), which can be confirmed by the detection of mecA or mecC at the molecular level (Fernandes et al., 2005). A much less common and less known phenotype is borderline oxacillin-resistant Staphylococcus aureus (BORSA). BORSA strains show reduced oxacillin susceptibility, with minimum inhibitory concentrations (MICs) ranging from 1 to 8 mg/l. While S. aureus strains with MIC > 2 mg/l are generally considered methicillin-resistant due to the presence of mecA or mecC, BORSA strains do not possess these genes (Hryniewicz & Garbacz, 2017).

One of the factors that can contribute to an increase in bacterial resistance is the widespread use of subtherapeutic doses of antibiotics in poultry production. This is often referred to as “metaphylaxis” and is aimed at preventing the consequences of infections before clinical symptoms or a reduction in production are observed in the flock. The antibiotics most commonly used in high-risk situations, such as transport or the post-vaccination period, include TETs, aminoglycosides, macrolides, and quinolones, which may explain the high rate of resistance to them in Staphylococcus strains isolated from poultry (Van Cuong et al., 2021; Singh et al., 2025). Due to the conditions mentioned above, the level of resistance in both commensal and pathogenic Staphylococcus and Mammaliicoccus strains of various species isolated from birds and from henhouse environments varies depending on geographic location, the degree of development of a given region, and awareness among farmers and veterinarians. It most likely also depends on the source of the samples (henhouse environment, dead birds, healthy birds, or slaughterhouse) and on poultry species and production types, probably due to differences in antibiotic use practices and management systems. Another factor is the legal provisions in force in a given country, particularly discrepancies in regulations between the EU and countries outside the EU. These determinants underscore the importance of regional programmes for monitoring antibiotic resistance in bacteria and the need to tailor strategies for combating antimicrobial resistance to local conditions. The collection and analysis of data on antibiotic resistance is a difficult challenge given the large number of Staphylococcus and Mammaliicoccus species, which can constitute microflora colonizing the skin and mucous membranes or can be pathogens in poultry. Currently available literature from various parts of the world indicates that the frequency of isolation of Staphylococcus bacteria in samples from farming environments and from birds has ranged from 29% to 64%, with S. aureus being the dominant species. The percentage of MRSA strains on poultry farms ranged from about 30% in Algeria to 95% in samples collected in Egypt (Benrabia et al., 2020; Ahmed et al., 2021). Analysis of samples of retail poultry meat has shown widespread contamination with Staphylococcus aureus (34–57% of samples), with MRSA strains identified in 1.8–21% of isolates, depending on the country and the study. The typical resistance patterns in staphylococci isolated from poultry show a high percentage (53–97%) of strains resistant to β-lactam antibiotics (PEN G, AMP, and oxacillin), and in most cases, these were MRSA strains in which the gene mecA was detected. Many MRSA strains and coagulase-negative Staphylococcus strains possessing the mecA gene also harboured other genes of resistance, to TETs (tetK/L/M/O) and macrolides (ermA/B/C and mphC). The percentage of strains resistant to antibiotics of the TET group (TET and doxycycline) ranged from 60% to 95%. A similar percentage (∼50–95%) was shown for strains resistant to macrolides and lincosamides (ERY and clindamycin), while the percentage of staphylococci resistant to fluorinated quinolones (ciprofloxacin and ENR) ranged from 23% to 66%. Moreover, several studies have shown MDR ( ≥ 3 classes of antibiotics) in 39–95% of isolates. The examples of data presented in Table 4 reveal higher rates of resistance among staphylococci isolated from poultry or poultry products and from the environment. For example, studies of retail chicken and turkey meat samples in Czechia in 2017–2018 showed a very high percentage (36.4%) of methicillin-resistant S. aureus strains (Tegegne et al., 2021). Data gathered in 2022 by the EFSA indicate that a high percentage of Staphylococcus and Mammaliicoccus strains in EU countries are resistant to TETs (even 96.7%), clindamycin (95%), trimethoprim (88.3%), and ERY (85%) (Annex E – EUSR on AMR, 2025). A similar high percentage of tiamulin (TIA)-resistant strains (90%) was reported, particularly in turkey samples (Kovács et al., 2025). European strains showed the lowest rate of resistance to vancomycin and chloramphenicol. The low resistance to vancomycin is most likely due to the fact that its use has been highly restricted in veterinary practice, as it has never been approved for use in poultry and is currently banned for use to protect animal health due to its critical importance in human medicine. Strains isolated from poultry and poultry products in other parts of the world (Asia, the Near East, and Africa) have also showed varying degrees of resistance to antibiotics. A study conducted in Egypt showed a 95% MRSA rate in strains isolated from samples from broiler farms, poultry hatcheries, and slaughterhouses (Ahmed et al., 2021). Available data also indicate a high percentage of strains resistant to β-lactam antibiotics. For example, a study of samples collected from poultry carcasses in Nigeria in 2018–2019 showed 100% resistance to PEN and other β-lactam antibiotics among S. aureus isolates (Igbinosa et al., 2023). The high prevalence of resistance to AMX, an antibiotic commonly used to treat bacterial infections in humans, raises particular concern. Troubling data from 2025 from South America indicated that 100% of S. aureus strains isolated from samples of retail chicken meat sold on street markets and in butcher shops in Brazil were resistant to several groups of antibiotics (macrolides, aminoglycosides, lincosamides, and TETs). In contrast, a low percentage of strains (Table 4) were resistant to fluorinated quinolones, sulfonamides with trimethoprim, and chloramphenicol (da Silva et al., 2025). The authors of most of the studies cited also demonstrated the presence of isolates resistant to more than three groups of antibiotics, which indicates MDR in these strains and suggests high selection pressure resulting from long-term or improper exposure to antibiotics. This finding additionally underscores the possibility of horizontal transfer of resistance genes via plasmids, transposons, and various other MGEs. Molecular detection of resistance genes reveals the common occurrence of mecA, blaZ, ermA, ermB, ermC, msr(A), and tet(K/L\M\O), which mediate resistance to these antibiotics, in staphylococci (Krupa et al., 2015; Silva et al., 2022; Syed et al., 2020; Seyedeh Mozhgan et al., 2025).

5.3. Salmonella spp.

Salmonellosis is globally reported as a major foodborne gastrointestinal infection in humans, with an estimated 90 million cases of gastroenteritis worldwide annually and approximately 155,000 deaths (Majowicz et al., 2010). In 2024, salmonellosis was the second most frequently reported zoonotic disease in Europe, with 79,703 confirmed cases in the EU The overall trend for Salmonella infections in Europe showed a significant increase in the years 2020–2024 (European Food Safety Authority, & European Centre for Disease Prevention and Control 2025c). Poultry and its products continue to be the primary source of Salmonella, with eggs and egg products identified as infection vehicles in strong-evidence outbreaks (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2023a, 2024a, 2025c).

The Salmonella genus consists of over 2,600 serovars, classified into typhoidal (S. enterica subspecies enterica serovar Typhi) and non-typhoidal serotypes (NTS) (Grimont & Weill, 2007). All serovars have pathogenic potential and are considered potentially harmful to human health. NTS are the most predominant zoonotic pathogens and can easily adapt to a wide range of hosts. Various Salmonella serovars are identified in various poultry species, among which S. Gallinarum and S. Pullorum are host-adapted and cause disease in chickens. In Gallus gallus (chickens), several Salmonella enterica serovars are especially common and important for both poultry health and human food safety. The distribution varies by region, production system, and control programmes, but S. enteritidis, S. typhimurium, and S. infantis consistently rank among the most significant globally (European Food Safety Authority, & European Centre for Disease Prevention and Control 2023a, 2024a, 2025c; Borges et al., 2019). In Europe, S. enteritidis is associated with laying hens, whose eggs are the source, while S. infant is is strongly associated with chicken consumption (Table 5) (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025a, 2025c). Turkeys are more commonly linked with S. agona, S. infantis, or S. kentucky, but S. Reading was commonly noted in the USA (Cason et al., 2024). In China, S. enteritidis is associated with broilers (Wang et al., 2024, Liu et al., 2025a), whereas S. kentucky was the dominant serovar in the USA (Table 1) (Obe et al., 2023). Duck production is mainly associated with Asian countries, where S. typhimurium and S. indiana are frequently isolated (Song et al., 2024; Chu et al., 2024).

AMR has contributed to the emergence and proliferation of individual NTS serovars and strains within animal and human populations (Ao et al., 2015) The occurrence of resistance in Salmonella depends on several important factors, including the serovar, selective pressure from antimicrobial use in animal populations, the clonal spread of resistant strains within production sectors, and the horizontal transfer and dissemination of resistance determinants, such as resistance plasmids. The importance of resistance to last-resort antimicrobials such as cephalosporins, carbapenems, quinolones, or polymyxins was underlined in the WHO Bacterial Priority Pathogens List (World Health Organization 2024). Fluoroquinolone-resistant Salmonella enterica is classified as a high-priority pathogen because of its increasing resistance trends, global disease burden, and limited treatment options. Moreover, isolates resistant to cephalosporins or carbapenems are ranked as a “critical group” on the priority pathogens list (World Health Organization 2024). Levels of antimicrobial resistance remain consistently high, varying between regions and countries. Resistance levels in laying hens are generally lower than in broilers, but infections may persist longer because laying hens remain in production for extended periods (Table 5).

In Europe, Salmonella most commonly shows resistance to ciprofloxacin, TET, and AMP, ranging from moderate to very high in isolates from food-producing animals and imported poultry meat (Table 6). The exception was in laying hens, where low levels of resistance were reported. Large differences in resistance levels between countries were observed, especially in Salmonella isolates from broilers (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025a, 2025c). At the EU level, a statistically significant decreasing trend in TET resistance was observed in Salmonella from broilers. Between 2022 and 2024, a decreasing trend in AMP resistance was identified in isolates from turkeys and broilers, while in the case of laying hens, no changes in resistance to these antimicrobials were observed. A significant decrease in ciprofloxacin resistance was also noted in broilers and turkeys. In contrast, laying hens showed a statistically significant increasing trend in ciprofloxacin resistance (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025c). For cefotaxime and ceftazidime, representing third-generation cephalosporins, resistance levels were generally low among Salmonella spp. The occurrence of presumptive extended spectrum beta lactamases (ESBL)-/AmpC beta-lactamases (AmpC)-producing Salmonella was low in 2024, ranging from 0.2% in turkeys to 1.2% in broilers. Only a few countries, mainly Italy and Malta, reported moderate cephalosporin resistance. Analysis of WGS data for Salmonella spp. reported by Germany, Italy, and the Netherlands revealed the bla _CTX-M-1 gene to be the most common resistance determinant. No carbapenem-resistant isolates derived from poultry have been identified thus far in European countries (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025a, 2025c). In the USA in 2024, resistance among Salmonella chicken isolates was most commonly reported against TET (60.7%), sulfamethoxazole-sulfisoxazole (46.8%), AMP (15.6%), and ceftriaxone (15.6%), as compared to 51.4%, 17.6%, 16.2%, and 6.8%, respectively, in turkey isolates. A total of 4.5% chicken and 2.7% turkey isolates were resistant to cefoxitin (Food and Drug Administration, 2026). Isolates were frequently resistant to at least one antibiotic (91.2%) or MDR (45.5%). Resistance was observed to TET (82.8%), minocycline (42.3%), nitrofurantoin (40.3%), cefazolin (38.3%), AMP (32.1%), and ceftriaxone (26%). All isolates were susceptible to fluoroquinolones, carbapenems, and glycylcyclines (Food and Drug Administration 2026).

Research conducted on the Brazilian poultry production chain demonstrated a high prevalence of resistance in Salmonella isolates, with the highest resistance percentage noted for sulfamethoxazole (91%), followed by sulfonamides (51%) and ceftiofur (28.9%). The serovars showed no resistance to ciprofloxacin (Moraes et al., 2024). In the case of China’s study, research from broiler farms, layer farms, slaughterhouses, and retail chicken meat consistently shows high levels of Salmonella resistance to sulfisoxazole (100%), nalidixic acid (54.3%), TET (47.8%), streptomycin (39.86%), AMP (39.1%), and chloramphenicol (30.4%) (Wang et al., 2024). Other studies have found that 41–62.5% of isolates were ESBL-producing strains (Shu et al., 2023; Zhou et al., 2025). Three serotypes of carbapenem-resistant Salmonella from chickens, S. Kentucky, S. Indiana, and S. Idikan, were shown to carry bla _NDM-5 (Zhou et al., 2025). In India, AMR was observed across regions, revealing substantial variation. Studies have reported high resistance to antibiotics such as AMP, TET, and colistin (Shil et al. 2026).

Research in Bangladesh found that S. enterica prevalence in layers was significantly higher than in broilers. Broiler isolates showed considerable resistance, particularly to sulfamethoxazole (100%), streptomycin/sulfonamide (88.9%), nitrofurantoin (66.7%), and AMP (55.6%). Layer isolates demonstrated lower resistance overall, though resistance to AMP (52%) and sulfonamide/sulfamethoxazole (92%) was still prevalent (Popy et al. 2025). Most Salmonella isolated from Thai poultry samples were phenotypically resistant to doxycycline (84.4%) and colistin (68.75%), while the same study showed no resistance in isolates obtained in Japan (Noenchat et al., 2023). Interestingly, higher NTS prevalence in Vietnam was reported in ducks (94.3%) than in chickens (64.7%), with a high rate of resistance to TET (58.5%), STX (58.1%), streptomycin (47.3%), AMP (39.8%), and chloramphenicol (37.3%). The diversity of Salmonella serotypes may reflect differences in geographic location, collection time, or identification methods (Starkova et al., 2025).

Among African countries, AMR testing of Salmonella serovars in Egypt revealed that all isolates were completely resistant (100%) to ceftazidime, cefepime, and ERY. High resistance was also observed against AMX (94.7%), AMX  +  clavulanic acid (94.7%), ceftriaxone (84.2%), chloramphenicol (84.2%), doxycycline (84.2%), ciprofloxacin (89.5%), GEN (89.5%), streptomycin (89.5%), and STX (94.7%). In contrast, a high level of sensitivity to meropenem was observed (Salem et al., 2025). In another Egyptian study, S. enteritidis isolates from broiler and layer farms were found to be extremely resistant to NEO (100%), nalidixic acid and cefoxitin (95.4%), norfloxacin (86.3%), cefotaxime (81.8%), AMX (77.2%), amikacin (72.7%), and ERY (68.1%). The presence of the bla _CTX-M gene and gyrA mutation was high (Elsayed et al., 2024). In Uganda, Salmonella species isolated from broiler samples were highly resistant to AMP (80%), ERY (70%), TET (67.5%), and ciprofloxacin (62.5%) (Ssemakadde et al., 2025). Similarly, in Tanzania, the highest resistance was also observed against AMP (92.9%), followed by TET (71.43%), ciprofloxacin (42.9%), sulfonamide (42.85%), GEN (35.7%), and azithromycin (28.9%) (Mwambene et al., 2025).

The widespread use of antimicrobials to enhance poultry meat production has facilitated the increase in MDR Salmonella spp. Studies show significant differences among MDR Salmonella spp. strains isolated from various poultry species and geographic regions (Di Taranto et al., 2025). In general, Asian and African countries have reported increasing levels of MDR Salmonella on poultry farms and in poultry meat. Broilers consistently show the highest MDR prevalence globally. S. Infantis, S. Enteritidis, S. Typhimurium, and S. Heidelberg are the dominant poultry MDR Salmonella serovars worldwide. In European countries, a slight decrease in MDR Salmonella was observed between 2022 and 2024 (European Food Safety Authority, & European Centre for Disease Prevention and Control 2025a, 2025c). MDR was observed at high levels in Salmonella spp. recovered from broilers and turkeys in 2024 (35.1% and 22.9%, respectively). Salmonella spp. isolates from laying hens showed a markedly lower MDR level (6.0%). The highest levels of MDR were observed in S. Infantis isolates, particularly those derived from broilers and turkeys (European Food Safety Authority, & European Centre for Disease Prevention and Control, 2025c). In the USA, the MDR Salmonella rate in 2024 was higher in isolates recovered from chickens (47.4%) compared to turkeys (16.2%). In Brazil, depending on the study, approximately 18–51.1% of Salmonella strains were classified as MDR strains. The majority of MDR strains belonged to the serotypes S. Enteritidis, S. Typhimurium, S. Bredeney, or S. Agona (Borges et al., 2019; Moraes et al., 2024). Asia and Africa often report high MDR prevalence linked to intensive antibiotic use and poorer antimicrobial stewardship. The highest MDR rates have been noted in South and Southeast Asia (Starkova et al., 2025). China has reported extensive MDR Salmonella circulation, with antimicrobial resistance profiles showing a 61.6% MDR rate in Salmonella from broilers (Shu et al., 2023). Similarly, India reports an alarming increase in MDR isolates in 2021–2025, particularly in resistance to commonly used antibiotics such as TET, AMP, and third-generation cephalosporin, and especially in S. Typhimurium (Shil et al., 2026). Research conducted in Bangladesh classified 86.1% of isolates as multidrug-resistant (Popy et al., 2025), whereas a 29.1% rate of MDR Salmonella was noted in Thailand, and no MDR isolates were identified among Japanese Salmonella isolates (Noenchat et al., 2023). In Africa, MDR Salmonella isolates have been detected in many studies, with prevalence ranging from 12.1% in Zimbabwe to 100% in Egypt, Ethiopia, Nigeria, Senegal, and South Africa (Salem et al., 2025; Ramtahal et al., 2022). In contrast to broiler chickens and turkeys, MDR prevalence in laying hens is comparatively lower. In Europe, surveillance programmes, vaccination programmes, and stricter antimicrobial regulation have contributed to relatively lower MDR Salmonella prevalence (European Food Safety Authority, & European Centre for Disease Prevention and Control 2025c). Similarly, in North America, the prevalence of MDR Salmonella in laying hens is generally lower than in broilers and turkeys due to long-term surveillance and control programmes. In Asia and Africa, MDR Salmonella isolated from laying hens is reported more frequently than in North America or Europe, but is lower than in chickens. Recent global analyses suggest that the intensification of poultry production, inadequate antimicrobial stewardship, and limited surveillance systems may contribute substantially to the spread of MDR Salmonella across continents.

6.1. Erysipelothrix rhusiopathiae

Erysipelothrix rhusiopathiae is a gram-positive, facultatively anaerobic bacillus responsible for erysipelas, an infectious disease affecting humans and numerous animal species, including birds. In poultry, erysipelas is most commonly reported in domestic geese, ducks, turkeys, and laying hens. Infection is believed to occur primarily via ingestion of contaminated feed or water, or through damaged skin resulting from feather pecking, scratching, or cannibalism. In laying hens, the poultry red mite, Dermanyssus gallinae, has also been suggested as a potential mechanical vector (Jordan & Bisgaard, 2011; Eriksson et al., 2025). The disease typically manifests as acute septicaemia with sudden mortality, accompanied by splenomegaly, hepatomegaly, renal enlargement, and multifocal haemorrhages. Flock mortality ranges from 1% to as high as 50%, depending largely on how quickly appropriate treatment is implemented (Jordan & Bisgaard, 2011; Bobrek et al., 2016; Nowak et al., 2024). The disease is observed mainly in maturing and adult birds. In commercial goose flocks in Poland, most outbreaks occur in younger birds aged 11–13 weeks, particularly between August and September, indicating a strong seasonal pattern associated with intensive production periods (Jordan & Bisgaard, 2011; Nowak et al., 2024). Importantly, erysipelas is a zoonotic disease, and E. rhusiopathiae may be transmitted from infected birds or contaminated biological material to humans, typically through skin injuries. Such infections may result in localized erysipeloid or, less commonly, systemic disease such as septicaemia or endocarditis (Rostamian et al., 2022).

As standard erysipelas treatment involves the administration of antibiotics, continuous monitoring of antimicrobial susceptibility in E. rhusiopathiae is essential. In particular, it is important to track the prevalence of resistant strains, identify their resistance mechanisms, and better understand the processes involved in the horizontal transfer of resistance genes. Currently available evidence indicates that poultry-derived E. rhusiopathiae isolates retain high susceptibility to β-lactam antibiotics, including PEN, AMP, and AMX, confirming that these agents remain the cornerstone of erysipelas treatment in poultry production (Bobrek & Gaweł, 2023; Dec et al., 2024a; Kerek et al., 2025b). In contrast, E. rhusiopathiae strains frequently exhibit high levels of resistance to TETs and fluoroquinolones. In a study by Dec et al. (2024a) involving 60 isolates from geese and ducks in Poland, 85.0% of isolates were resistant to TET and 80.0% to ENR. Similarly, Bobrek & Gaweł (2023) reported that among 47 goose-derived isolates, 76.6% were resistant to ENR, and nearly 64% exhibited resistance to TET. Interestingly, markedly lower resistance rates to these antimicrobials have been reported in poultry isolates from Hungary. According to Kerek et al. (2025b), only 10.5% of isolates were resistant to TET and 2.6% to ENR, indicating substantial geographic differences in resistance patterns, likely reflecting variation in antimicrobial use practices (Table 7). Acquired resistance to other antimicrobial classes, including macrolides (0–7.9%), lincosamides (2.6–16.5%), pleuromutilins (7.9–15%), and phenicols (0–5.3%), remains relatively uncommon in poultry-derived E. rhusiopathiae isolates in both Poland and Hungary (Dec et al., 2024a; Bobrek & Gaweł, 2023; Kerek et al., 2025b). However, co-occurrence of resistance to these agents alongside resistance to TETs and fluoroquinolones contributes to the emergence and spread of MDR strains. In Polish waterfowl isolates collected between 2019 and 2021, the proportion of MDR strains was estimated at 16.7% (Dec et al., 2024a), highlighting a growing concern for antimicrobial therapy and disease control (Table 7). In addition to acquired antimicrobial resistance mechanisms, E. rhusiopathiae exhibits intrinsic resistance to several antimicrobial classes that should be considered when selecting therapeutic agents. Notably, these bacteria are regarded as naturally resistant to aminoglycosides (gentamycin and NEO) and folate pathway inhibitors (STX) (MIC ≥ 512 µg/ml) (Dec et al., 2024a).

Whole-genome sequencing studies have revealed that resistance determinants identified in poultry-derived E. rhusiopathiae strains are located within various MGEs, whereas resistance to fluoroquinolones is associated with mutations in the gyrA and parC genes (Dec et al., 2024a, b; Borek & Gaweł, 2023). Resistance to TET is associated with the presence of the ribosomal protection protein gene tet(M), which in E. rhusiopathiae is typically carried on the 18-kb Tn916 transposon. This transposon may occur as an independent MGE or be integrated into larger genomic islands, such as 130-kb ICEEr1023, 74-kb ICEEr1012, and 98-kb GI_Er147. These MGEs may additionally harbour other resistance genes present either individually (erm(47)) or in MDR clusters (e.g. lsa(E)-lnu(B)-ant(6)-Ia-spw) (Dec et al., 2024b). Furthermore, the lincosamide and pleuromutilin resistance genes lsa(E) and lnu(B) identified in poultry-derived E. rhusiopathiae isolates may also be located within prophage-associated DNA regions, such as the 53-kb φEr670 prophage identified in MDR isolates belonging to serotype 8 (Dec et al., 2026) (Table 7). The presence of transposons, genomic islands, and prophage-associated DNA carrying resistance genes indicates that HGT plays a central role in the dissemination of antimicrobial resistance in E. rhusiopathiae.

Taken together, these findings indicate that although β-lactam susceptibility remains well preserved, the progressive emergence of MDR E. rhusiopathiae strains in poultry warrants continuous surveillance of antimicrobial susceptibility profiles and prudent antimicrobial stewardship to limit further spread of resistance in this zoonotic pathogen.

6.2. Riemerella anatipestifera corrig (R. anatipestifera)

Infections caused by Riemerella anatipestifera corrig (R. anatipestifera), previously called R. anatipestifer (https://lpsn.dsmz.de/species/riemerella-anatipestifera), are an important health and economic problem in poultry production, especially duck and goose farming. This bacterium is an etiological agent of disease with a high mortality rate, especially in young birds (Ruiz & Sandhu, 2013). The clinical picture includes sepsis, meningitis, airsacculitis, and fibrinous lesions in internal organs (Hao et al., 2025). The importance of R. anatipestifera in veterinary practice results not only from the severe disease course, but also from its high serotype variability, which makes it difficult to develop effective methods of immunoprophylaxis (Yang et al., 2024a). An additional challenge is growing resistance to antimicrobials, which limits therapeutic options and underscores the need for rational use of antibiotics (Hao et al., 2025).

R. anatipestifera shows a high capacity to acquire resistance owing to HGT, supported by an open pan-genome and mechanisms such as natural transformation and outer membrane vesicles (Huang et al., 2021; Wang et al., 2025). Resistance genes can originate in the core genome or be acquired by mobile elements, such as genomic islands. Resistance to fluoroquinolones is mainly due to mutations in the genes gyrA, parC, and parE, while plasmid-mediated mechanisms (plasmid-mediated quinolone resistance) play a smaller role (Pathomchai-Umporn et al., 2025; Zhu et al., 2019). Efflux pumps also play an important role (Li et al., 2016). In the case of aminoglycosides, the dominant mechanisms are modifying enzymes – aminoglycoside phosphotransferases, acetyltransferases, and nucleotidyltransferases – and efflux systems (e.g. RanB and RaeB) (Zhou et al., 2026; Li et al., 2020). TET resistance is associated mainly with the tetX gene, efflux pumps, and ribosomal protection proteins (Zhu et al., 2018). Macrolides and lincosamides lose their efficacy mainly through rRNA methylation (erm genes) and enzymatic inactivation by the enzyme lincosamide nucleotidyltransferase (lnu gene) (Luo et al., 2018; Yang et al., 2024b). Resistance to β-lactams results from the presence of β-lactamases (e.g. RAA-1, RASA-1, or RAD-1) (Luo et al., 2022a, b; Li et al., 2023), while resistance to sulfonamides and trimethoprim is associated with the genes sul and dfr (Ma et al., 2026; Jiang et al., 2023), and resistance to phenicols is associated with the cat and floR genes (Huang et al., 2017). R. anatipestifera makes use of numerous, often co-occurring resistance mechanisms, which promotes the rapid spread of MDR strains.

The results of research carried out in 2020–2022 in China provide detailed information on the phenotypic and genotypic resistance of R. anatipestifera in ducks. Testing of 74 representative strains showed very high resistance to commonly used drugs. The highest rates of resistance were noted for GEN (77%), ENR (73%), kanamycin (62.2%), and streptomycin (58.1%). All strains were susceptible to ceftriaxone. Ceftiofur (98.6%) and FLO (64.9%) were also highly effective. As many of 81.1% isolates were resistant to at least three classes of antibiotics. Genes determining resistance to specific groups were very common among the bacteria. The most frequently noted was tetX, associated with TET resistance, detected in as many as 95.9% of strains. The ermF gene determining resistance to macrolides was present in 77% of strains, half of the strains possessed the floR gene associated with resistance to amphenicols, and bla _TEM was detected in 10.8% of strains (Lyu et al., 2023).

Another study (Yan et al., 2026) analysed 88 R. anatipestifera strains isolated from ducks in 2023–2024. The highest resistance rates were noted for polymyxin B (97%), amikacin (91%), kanamycin (90%), and fluoroquinolones (about 90%). Resistance to TETs and doxycycline were 80% and 75%, respectively. More than half of strains were resistant to β-lactam antibiotics, including cefotaxime (60%), ceftazidime (55%), and ceftiofur (53%). Susceptibility to rifampicin was relatively high (78%). All strains were classified as MDR. Nearly half of strains (n = 41) were resistant to 6 antimicrobials. Three genes, tetX, floR and ermF, were detected the most often (90–95%). The presence of qnrS in 16% of strains and rmtB in 5% of isolates was noted as well (Table 8). However, the other authors (Xihui et al., 2023) in the study on 51 R. anatipestifera strains from ducks revealed 100% resistance to most aminoglycosides. A high level of resistance was also shown for amikacin, with only a few strains found to be susceptible. In addition, nearly total resistance to polymyxin B (98%), LIN (94%), and tobramycin (94%) was observed. In the case of azithromycin, resistance was at a level of 88%. Among quinolones, resistance to norfloxacin (55%) and ENR (45%) was highest. The strains largely remained susceptible to β-lactam antibiotics such as cefotaxime or cefepime, as resistance did not exceed 10%. All strains were classified as MDR, among which 88% were resistant to at least five different classes of drugs, and the most resistant strain showed resistance to as many as seven classes. The study identified a number of genes responsible for these phenotypes, which was confirmed by the presence of dominant genes in most strains, including ranB (98%), ranA (96%), and aadS (88%) associated with aminoglycoside resistance, as well as bla _OXA-209, tetX4, ermF, floR, ereD, and tetQ (Table 8). Another study carried out in China (Dong et al., 2024) on 157 strains of goose- and duck-derived R. anatipestifera confirmed previous findings on phenotypic and genotypic antimicrobial resistance. The strains were resistant to kanamycin (98.73%), amikacin (98.09%), GEN (98.09%), and streptomycin (94.91%). The most effective drugs proved to be FLO, ceftriaxone, spectinomycin, sulfafurazole, and cefepime. Each of the 157 strains possessed from 42 to 55 genes determining drug resistance, predominantly TET resistance genes (19), genes encoding efflux pumps (15), glycopeptide resistance genes (11), and macrolide resistance genes (7) (Table 8). The study showed a high level of agreement between the presence of genes and actual resistance for most drugs. For TET and polymyxin B, a 100% correlation was noted for tetB(P), tetM, tetT, and mcr-8.1. In the case of macrolides, the ermF, ermX, and ermE genes showed more than 91% correlation for ERY and azithromycin. For aminoglycosides, agreement between genes (aac(3)-Ig, aadS, and aac(3)-Ic) and phenotypic resistance was below 43%, which suggests the presence of as yet undiscovered mechanisms of resistance to these antibiotics in R. anatipestifera (Dong et al., 2024).

In another study conducted in Asia, using 69 strains of R. anatipestifera, most of the strains were resistant to nalidixic acid (89.9%), streptomycin (75.4%), norfloxacin (72.5%), and kanamycin (65.2%). All isolates were susceptible to AMX  +  clavulanic acid and imipenem. High susceptibility to piperacillin, cefoperazone, cefepime, cephalexin, FLO, and doxycycline (87–91.3%) was noted as well (Vo et al., 2022). A study carried out in Thailand on 37 strains of R. anatipestifera from ducks showed high MIC values for nalidixic acid, ranging from 16 µg/ml to ≥ 128 µg/ml, and low MIC values for ciprofloxacin and ENR, with values of 8 µg/ml and 4 µg/ml, respectively. The main resistance mechanism identified in the study was chromosomal mutations in the gene gyrA, where all isolates possessed a single point mutation in codon 83. Neither mutations in the QRDR region of the parC gene nor the presence of genes PMQR was noted in any of the strains (Pathomchai-Umporn et al., 2025).

Analysis of the literature reveals that research on resistance in R. anatipestifera is mainly concentrated in Asia, whereas other geographic regions remain little studied, which may influence the global assessment of the problem. A study using R. anatipestifera strains from Poland (Nowaczek et al., 2023), assessing phenotypic resistance of bacteria by determining MICs, showed very high MIC values for GEN, amikacin, and colistin ( ≥ 128 µg/ml). Low MICs, indicating that the antibiotics were effective, were obtained for AMX, cefuroxime, cefoperazone, piperacillin, and the STX combination. At least one resistance gene was detected in 72% of isolates; tetX and ermF were the most frequently identified. The presence of other resistance genes was noted as well: aph(3′)-VII, aac(3′)-IV, cmlA bla _TEM, aadA, strA/strB, and sulI (Table 8). Another study, conducted in Poland (Tyc et al., 2026) using the disc-diffusion method, showed considerable variation in resistance between strains, with the largest inhibition zone diameters noted for cephalexin and ceftazidime. Antibiotics with moderate inhibition zones, measuring 20 mm, included amikacin and chloramphenicol. More than 70% of strains showed no visible growth inhibition zone in response to ENR, clindamycin, ERY, or streptomycin (Tyc et al., 2026).

It can be concluded from the studies cited that R. anatipestifera is a significant and growing problem in the context of antimicrobial resistance. Analysis of the results clearly reveals the widespread occurrence of MDR, irrespective of geographic region, although the phenomenon is particularly well documented in Asian countries. The highest level of resistance is shown mainly against aminoglycosides, polymyxins, TETs, and fluoroquinolones. At the same time, some β-lactam antibiotics, FLO, and certain drug combinations (e.g. AMX  +  clavulanic acid) remain relatively effective, which may be of importance in treating infections. Genotype testing confirms wide dissemination of resistance genes, especially tetX, ermF, and floR, present in most strains analysed. The high number of resistance genes and their diversity suggest strong selection pressure resulting from the use of antibiotics in poultry farming.