4. Antibiotic resistance of some selected organisms in poultry
The bacterial genus Staphylococcusis a Gram-positive cocci and a facultative anaerobe which appears in clusters when viewed under the microscope . They are etiological agents of staphylococcosis, pododermatitis (bumblefoot) and septicaemia which affect mostly chicken and turkeys. Coagulase-negative species have also been implicated in human and animal infections [38, 39].
β-lactams were considered the first line of drugs for treatment of staphylococcal infections but due to emergence of high level of resistance to these and other drugs, there are currently very few drugs available for treatment of these infections . Methicillin resistant Staphylococcus aureus(MRSA), now known as a superbug, is resistant to almost every available antibiotic used against Staphylococcus.
A study to detect the presence of MRSA in broilers, turkeys and the surrounding air in Germany reported the prevalence of MRSA in air as high as 77% in broilers compared to 54% in Turkeys. Ten different spa types were identified with spa type t011 and clonal complex (CC) 398 being the most prevalent. It was also found that for every farm, the same sequence types were present in both the birds and the environment . This pattern of resistance was also reported in India with 1.6% of staphylococcal isolates containing mecA resistant gene .
In Africa, studies carried out in Ghana and Nigeria have shown that livestock-associated Staphylococciare susceptible to amoxicillin/clavulanic acid, amikacin, ciprofloxacin, gentamycin and cephalexin [39, 44], whereas in the US, most of the staphylococcal isolates were susceptible to rifampin, cotrimoxazole, gentamycin, vancomycin and chloramphenicol [45, 46]. It is worth noting that most of these organisms showed a high level of resistance to oxacillin and tetracycline, which would be disastrous if these oxacillin-resistant strains are transferred to humans [39, 44, 45].
Pseudomonasis a genus of Gram-negative, aerobic bacteria that belongs to the family Pseudomonadaceae . The genus Pseudomonasis ubiquitous in soil, water and on plants. It consists of 191 subspecies belonging to species groups including P. fluorescens, P. pertucinogena, P. aeruginosa, P. chlororaphis, P. putida, P. stutzeriand P. syringae. Pseudomoniasis, which is an opportunistic P. aeruginosainfection, is common in poultry birds like chickens, turkeys, ducks, geese and ostriches where infections in eggs destroy embryos .
P. aeruginosacauses respiratory infection, sinusitis, keratitis/keratoconjuctivitis and septicemia and responsible for pyogenic infections, septicemia, endocarditis and lameness along with many diverse diseases . Infections may occur through skin wounds, contaminated vaccines and antibiotic solutions or needles used for injection. The disease may be systemic, affecting multiple organs and tissues or localized in tissues as infraorbital sinus or air sacs producing swelling of the head, wattles, sinuses and joints in poultry birds. P. aeruginosahas been isolated from many poultry farms and birds worldwide .
A study carried out in Ghana show that P. aeruginosaisolated from poultry litter were all susceptible to levofloxacin in the range of 20–100% and nearly 75% demonstrated intermediate susceptibility to aztreonam. The organisms showed resistance to cephalosporins, carbapenems, penicillins, quinolones, monobactam and aminoglycoside. Metallo β-Lactamase encoding genes (blaIMP, blaVIM) were not detected in any of the isolates but the class 1 integron which is known to carry multiple antibiotic resistant genes were detected in 89.4% of the multi-drug resistant strains . This is contrary to a report by Zhang and his Colleagues , who identified the blaVIM gene in P. aeruginosaand P. putidafrom chicken that resembled corresponding regions in clinical isolates of P. aeruginosa.These isolates were resistant to all β-lactam antibiotics tested, including meropenem, imipenem, aztreonam, and ceftazidime [33, 51].
Another study in Nigeria reported that the P. aeruginosaisolates were highly resistant to β-lactams, tetracycline, tobramycin, nitrofurantoin and sulfamethoxazole-trimethoprim, while ofloxacin, imipenem and ertapenem were highly effective against the bacterial pathogens .
In Pakistan, a study which investigated the causative agents for necropsy in chicken, recorded a 28% prevalence for P. aeruginosa. These isolates were found to be 100% resistant towards ceftriaxone, meropenem, ciprofloxacin, erythromycin and colistin, while 60% sensitivity was observed against ampicillin sulbactam, ceftazidime, cefoperazone and rifampicin. Isolates exhibited variable multidrug resistance patterns to other antibiotics .
Escherichia coliis a Gram-negative bacterium that has been known for ages to easily and frequently exchange genetic information through horizontal gene transfer with other related bacteria. Hence, it may exhibit characteristics based on the source of isolation. E. coliis a commensal organism living in the intestines of both humans and animals. However, some strains have been reported to cause gastrointestinal illnesses . Tetracycline which is commonly used in poultry has been reported to be one of the drugs bacteria are most resistant to. There is a reported tetracycline resistance in poultry even without the administration of this antibiotic .
A study carried out on fecal isolates of E. coliin the Netherlands showed that there is a high level of multidrug resistance occurring in broilers, turkeys while majority of those from laying hens were susceptible. It was observed that the isolates from birds had high rates of resistance to amoxycillin alone and others had resistance to amoxicillin as well as oxytetracycline, streptomycin, sulfamethoxazole and trimethoprim. .
E. colihad a prevalence of 46.98% among the other bacteria isolated in Ghana. All isolates showed some degree of resistance to ceftriaxone (1.34%), cefotaxime (0.67%), gentamycin (2.01%), cotrimoxazole (1.34%), tetracycline (2.01%) and ampicillin (3.36%) . Resistant genes have been found in E. coliisolates from Nigeria and these include bla-TEM (85%), sul2 (67%), sul3 (17%), aadA (65%), strA (70%), strB (61%), catA1 (25%), cmlA1 (13%), tetA (21%) and tetB (17%) which conveyed resistance to the following antibiotics; tetracycline (81%), sulfamethoxazole (67%), streptomycin (56%), trimethoprim (47%), ciprofloxacin (42%), ampicillin (36%), spectinomycin (28%), nalidixic acid (25%), chloramphenicol (22%), neomycin (14%) gentamicin (8%). In this study the isolates were susceptible to amoxicillin-clavulanate, ceftiofur, cefotaxime, colistin, florfenicol and apramycin. Class 1 and 2 integrons were found in five (14%) and six (17%) isolates, respectively, while one isolate contained both classes of integrons. There is that suggestion that poultry production environments represent important reservoirs of antibiotic resistance genes such as qnrS that may spread from livestock production farms to human populations via manure and water .
Salmonellaspp. are Gram-negative, facultative anaerobic, non-spore forming, usually motile rods belonging to the Enterobacteriaceae family, which are found in the alimentary tract of animals [37, 58]. Fecal shedding allows Salmonellato be transmitted among birds in a flock. Salmonellaspp. is widespread in poultry production. Prevalence varies considerably depending on country and type of production as well as the detection methods applied. It is known to be the etiological agent responsible for salmonellosis by Salmonellaspp. in both humans and animals. Food-borne salmonellosis caused still occurs throughout the world . The risk factors associated with Salmonellainfections and contamination in broiler chickens include contaminated chicks, size of the farm and contaminated feed and these risk increase when feed trucks are parked near the entrance of the workers’ change room and when chicken are fed with meals [59, 60]. It also depends on age of the chicken, animal health, survival of organism in the gastric barrier, diet and genetic constitution of the chicken could also affect the colonization ability of Salmonellaspp. in poultry .
Pullorum disease in poultry is caused by the S. pullorum. Transmission of the disease in birds can be vertical (transovarian) but also occurs through direct or indirect contact with infected birds via respiratory route or fecal matter or contaminated feed, water, or litter. Antimicrobials used to treat pullorum disease are furazolidone, gentamycin sulfate and antimetabolites (sulfadimethoxine, sulfamethazine and sulfamerazine) .
Salmonellaspp. have increasingly been isolated from poultry with prevalence of 2.7% in Brazil and the most common isolates were Salmonella enteritidis(48.8%), S. infantis(7.6%), S. typhimurium(7.2%), and S. heidelberg (6.4%). All the isolated strains were resistant to at least one class of antimicrobial and 53.2% showed multidrug resistance to three or more classes, with streptomycin (89.2%), sulfonamides (72.4%), florfenicol (59.2%), and ampicillin (44.8%) .
Salmonellaspp. are one of the commonest microbial contaminants in the poultry industry. In Ghana, there is high prevalence rate of 44.0% in poultry with main isolates being S. kentucky(18.1%), S. nima(12.8%), S. muenster(10.6%), S. enteritidis(10.6%) and S. virchow(9.6%). Resistance of these isolates to the various antibiotics were nalidixic acid (89.5%), tetracycline (80.7%), ciprofloxacin (64.9%), sulfamethazole (42.1%), trimethoprim (29.8%) and ampicillin (26.3%).
Streptococcus is Gram-positive bacteria. Streptococcus gallolyticusis a common member of the gut microbiota in animals and humans; however, being a zoonotic agent, it has been reported to cause mastitis in cattle, septicemia in pigeons, and meningitis, septicemia, and endocarditis in humans . A study carried out in Japan isolated Streptococcus gallolyticusfrom pigeons with septicaemia. Most of the isolates were susceptible to vancomycin, penicillin G and ampicillin, while some were resistant to tetracycline, doxycycline and lincomycin. All the isolates were resistant to tetracycline had tet(M) and/or tet(L) and/or tet(O) genes .
Campylobacter jejuniand Campylobacter coliare the most prevalent disease causing species of the genus Campylobacter. They are mostly responsible for foodborne gastroenteritis in humans [66, 67, 68]. Campylobacteriosis is often associated with handling of raw poultry or eating of undercooked poultry meat . Cross-contamination of raw poultry to other ready-to-eat foods via the cook’s hands or kitchen utensils has been reported. Erythromycin is usually the drug of choice for the treatment of Campylobacterinfections . However, fluoroquinolones, gentamicin, and tetracycline are also clinically effective in treating Campylobacterinfections when antimicrobial therapy is required .
Resistance of C. jejuniand C. coliisolates to fluoroquinolones, tetracycline, and erythromycin has been reported. The increased resistance is partly due to the wide use of these antimicrobials in animal husbandary, especially in poultry [71, 72].
A study carried out by Elz’bieta and his colleagues, in their quest to compare the prevalence and genetic background of antimicrobial resistance in Polish strains of C. jejuniand C. coliisolated from chicken carcasses and children reported a slight difference in resistance between human and chicken strains. The isolated Campylobacterstrains were found to be resistant to gentamycin, tetracycline, ampicillin, ciprofloxacin and erythromycin and tet(O)gene and mutations in the gyrAgenes were found to be associated with the observed antibiotic resistance in the study .
Another study carried out in Kenya isolated thermophilic Campylobacterspecies (C. jejuniand C. coli) from feces and clocal swabs of chicken. These isolates showed a high rate of resistance to nalidixic acid, tetracycline and ciprofloxacin of 77.4, 71.0 and 71.0%, respectively. Low resistance (25.8%) was detected for gentamicin and chloramphenicol and 61.3% of C. jejuniisolates exhibited multidrug resistance and 54.5% of the C. jejuniisolates possessed the tet(O)gene whereas all of C. colihad the tet(A)gene .
C. jejuniand C. coliare the predominant species of Campylobacterusually isolated from poultry farms. In Ghana, other species such as Campylobacter lari, Campylobacter hyo-intestinalisand C. jejuni sub sp. doyleihave been isolated from poultry. These organisms have been found to be resistant to β-lactams, quinolones, aminoglycosides, erythromycin, tetracycline, chloramphenicol and trimethoprim-sulfamethoxazole and all isolated species were sensitive to imipenem [75, 76].
It is a Gram-negative non-spore-forming rod, a psychrotrophic bacterium and able to survive and multiply at cold temperatures. Poultry meat is one of the most important sources of Yersiniaspp. infections in humans. Yersinia enterocoliticais the predominant specie mostly isolated from poultry and poultry products . In humans, Y. enterocoliticais an enteric pathogen which commonly causes acute enteritis associated with fever, bloody diarrhea and inflammation of lymph nodes. Contaminated food is one of the main sources of yersiniosis in humans .
Y. enterocoliticais widely distributed in nature and animals; food and environment are routinely contaminated with this organism. Major reservoir of Y. enterocoliticais swine. However, Y. enterocoliticahas been frequently isolated from poultry and ready-to-eat foods . A study in Iran reported a prevalence rate of Y. enterocoliticaof 30% of among chicken meat samples . Yersiniaisolates (16%) from chicken and beef meat samples were mostly resistant to cephalotin (98%) and ampicillin (52%) .
Y. enterocoliticaisolated from poultry raw meat and retailed meats in Poland were classified as biotype 1A and exhibited moderate ability of producing biofilms and ystB was the predominant virulence gene. In biofilms, a multi-system that include poor antibiotic penetration, nutrient limitation and slow growth, adaptive stress responses, and formation of persister cells are hypothesized to constitute the organisms’ resistance to antibiotics .
Clostridiumis a genus of Gram-positive obligate anaerobic bacteria which includes several significant human pathogens. Spore of Clostridiumnormally inhabits soil and intestinal tract of animals and humans . Common infections caused by Clostridiainclude botulism caused by C. botulinum¸ pseudomembranous colitis caused by C. difficile,cellulitis and gas gangrene caused by C. perfringens, tetanus caused by C. tetaniand fatal post-abortion infections caused by C. sordellii.
High-dose penicillin-G remains sensitive to Clostridiaspecies and thus widely used to treat Clostridial infections. Clostridiaspecies such as welchiiand tetani respond to sulfonamides . Tetracyclines, carbapenems, metronidazole, vancomycin and chloramphenicol are effective options for treatment of Clostridiainfections .
C. perfringensis known to cause necrotic enteritis in poultry. Bacitracin or virginiamycin is an effective treatment option when administered in the feed or drinking water. C. colinumis responsible for ulcerative enteritis. Bacitracin and penicillins are the most effective drugs in the treatment and prevention of this infection [85, 86].
A study in Egypt, identified 125 isolates of C. perfringensfrom clinical cases of necrotic enteritis in broiler chickens from 35 chicken coops and the all isolates were resistant to gentamycin, streptomycin, oxolinic acid, lincomycin, erythromycin and spiramycin. Over 95% of isolates were resistant to sulfamethoxazole-trimethoprim, doxycycline, perfloxacin, colistin and neomycin. Most of the isolates were susceptible to amoxicillin, ampicillin, fosfomycin, florfenicol and cephradine .
Thirty strains of C. perfringensisolated from chickens with necrotic enteritis in Korea were found to susceptible to ampicillin, amoxicillin/clavulanic acid, cephalothin, cefepime, chloramphenicol, cefoxitin, ceftiofur, florfenicol and penicillin but resistant to gentamycin, neomycin, streptomycin, apramycin and colistin . This trend of resistance was similar to that observed in 43 C. perfringensisolates from the ileum of 5-week old broiler chicken in Taiwan. Most of the C. perfringensisolates were susceptible to amoxicillin, bacitracin and enrofloxacin but resistant to erythromycin, lincomycin and chlortetracycline .
Bacillusis a genus of Gram-positive, obligate aerobic or facultative anaerobic rod shaped bacteria of the phylum firmicutes. Bacillusspp. include both free-living non-parasitic and parasitic pathogenic species . Medically significant species include B. anthraciswhich causes anthrax and B. cereuswhich causes food poisoning . Other infections caused by Bacillispp. include pneumonia, endocarditis, ocular and musculoskeletal infections. Antibiotics usually used for Bacillusinfections include vancomycin, imipenem, ciprofloxacin, gentamycin, tetracycline, chloramphenicol, clindamycin and erythromycin. Most Bacillusspp. have been found to be resistant to broad spectrum cephalosporins and ticarcillin-clavulanate .
In a study involving 18 strains of B. cereusisolated from raw and processed poultry meat from supermarkets in Iasi county, all the isolates were found to be resistant to penicillin, amoxicillin, amoxicillin-clavulanate, colistin, cefoperazone, sulfamethizole and metronidazole but sensitive to erythromycin, cotrimoxazole, tylosin, flumequine, kanamycin, gentamycin, enrofloxacin, oxolinic acid, apramycin, tetracycline and doxacilin. All B. cereusisolates were resistant to nearly half of tested antibiotics . This pattern of resistance was also observed in 44 strains of B. cereusisolated from chicken and chicken products in the Jammu region of India. All isolates were resistant to penicillin G but sensitive to streptomycin. Over 60% of isolates were resistant to amoxicillin, ampicillin and carbenicillin .
Mycobacteriaare acid-fast, aerobic, nonmotile of bacteria of the genus Mycobacterium. Mycobacteriaare widespread organisms that live in water and food sources and can colonize their hosts without showing any adverse signs and symptoms. Pathogenic mycobacterial species including M. tuberculosis, M. bovis, M. africanum, M. macroticause tuberculosis whiles M. lepraeis responsible for leprosy. Mycobacteriaspp. are naturally resistant to penicillin and mostly susceptible to clarithromycin and rifamycin .
A study in Bangladesh identified three Mycobacteriumisolates from 80 poultry droppings and all isolates were found to be resistant to rifampicin but highly susceptible to azithromycin, ciprofloxacin, streptomycin and doxycycline. One isolate was identified as multi-drug resistant .
Klebsiellais a genus of non-motile, Gram-negative, oxidase-negative, rod-shaped bacteria with a prominent polysaccharide capsule and belong to the family Enterobacteriaceae. Klebsiellaspecies are found everywhere in nature including soil, plants, insect, humans and other animals . Infections caused by Klebsiellaspp. include septicaemia, meningitis, urinary tract infections, pneumonia, diarrhea . Common pathogenic Klebsiellain humans and animals include K. pneumoniae, K. oxytocaand K. variicola. Antibiotics commonly used in the treatment of Klebsiellainfections include third-generation cephalosporins, carbapenems, aminoglycosides and quinolones .
A study in Langa, South Africa identified 102 sub-species of K. pneumonia(96 K. ozaenaeand 6 K. rhinoscleromatisstrains) from 17 free-range chicken samples. The isolates exhibited high level of resistance towards ampicillin (66.7%), nalidixic acid (61.8%), tetracycline (59.8%) and trimethoprim (50.0%) but highly susceptible towards gentamycin (3.9%) and ciprofloxacin (4.8%). Almost 40% of the isolates were found to be multi-drug resistant K. pneumoniastrains . Similar trend of resistance was observed among 77 K. pneumoniaeisolates from poultry birds in Ekiti-state, Nigeria. The isolates showed high level of resistance towards tetracycline (100%), amoxicillin (94.8%), cotrimoxazole (94.8%) and augmentin (85.7%) .
Enterococcusis a large genus of Gram-positive diplococci, lactic acid-producing bacteria of the phylum Firmicutes . Commonly found species include Enterococcus faecalisand Enterococcus faecium. Notable infections caused by Enterococciinclude urinary tract infections, bacteremia, meningitis, endocarditis . Antibiotics active against Enterococciinclude ampicillin, penicillin, nitrofurantoin and vancomycin . Enterococcioften possess intrinsic resistance towards β-lactam antibiotics and aminoglycosides. However, resistance of Enterococcito vancomycin has been reported in several studies [105, 106, 107].
A study in Czech Republic identified 228 enterococcal isolates from the intestinal tract of poultry. These isolates were found to be highly resistant to tetracycline (80%), erythromycin (59%) and ofloxacin (51%) but exhibited low resistance to ampicillin (3%) and ampicillin/sulbactam (3%) . A similar trend of resistance was reported among 163 Enterococcal isolates from poultry litter in the Abbotsford area of British Columbia, Canada. The identified enterococcal isolates were found to be highly resistant to lincomycin (80.3%), tetracycline (65.3%), penicillin (61.1%) but showed low resistance towards to nitrofurantoin (3.8%), daptomycin (3.5%) and gentamycin (0.8%) . There is a high possibility of multi-drug resistant enterococci in animal meat and fecal matter being transferred to humans .
Proteusis a genus of Gram-negative Proteobacteria which is widely distributed as saprophytes . They are mainly found in decomposing animal matter, sewage, manure, mammalian intestine, human and animal fecal matter. They are mainly opportunistic pathogens responsible for nosocomial urinary and septic infections . Three species, namely, P. vulgaris, P. mirabilisand P. penneriare the only opportunistic species responsible for human infections. Most strains of P. mirabilisare sensitive to ampicillin and cephalosporins whereas P. vulgarisstrains are not sensitive to these antibiotics .
A study in Iran identified 54 P. mirabilisisolates from chicken intestines and 54 P. mirabilisisolates were screened for antimicrobial susceptibility to 13 antimicrobial agents. None of the P. mirabilisisolates in this study were found to be resistant to gentamycin. Over 90% of isolates were resistant to nalidixic acid, doxycycline and tetracycline. Less than a quarter of isolates were resistant to norfloxacin, ampicillin, amikacin and ceftriaxone. Nearly 96% of the isolates were resistant to at least two or more antibiotics. One isolate exhibited resistance to 10 antibiotics whereas three and five isolates were resistant to nine and seven antibiotics, respectively. The results showed that chicken could be a source of antibiotic resistant and multi-drug resistant P. mirabilisstrains and these resistant strains can cause worldwide problem both for veterinary sector and public health .
A similar trend of antibiotic resistance was observed in 36 P. mirabilisisolates from chicken droppings from commercial poultry farms in Bangladesh. Nearly 95% of the isolates were resistant to tetracycline followed by nalidixic acid (89%) and almost 20% of the isolates were found to be resistant to ciprofloxacin and 84% of the isolates exhibited multidrug resistance .