Multidrug-Resistant Staphylococcus aureus Strains Thrive in Dairy and Beef Production, Processing, and Supply Lines in Five Geographical Areas in Ethiopia

Livestock, farms, abattoirs, and food supply systems can become the source of foodborne pathogens, including S. aureus, in the absence of monitoring, general hygienic practices, and control. Studies are scarce on reservoirs (hiding places) and routes of entry of S. aureus into the food supply chain in Ethiopia. To fill these gaps, we evaluated the role of cows (milk), meat, equipment, and food handlers on the abundance and AMR of S. aureus in five geographical areas in central Oromia, Ethiopia. We isolated S. aureus from 10 different ecologies per area in 5 areas and tested their sensitivity to 14 antimicrobials of 9 different classes. We ranked the 5 areas and 10 ecologies by computing their multiple AMR index (MARI) at a cut-off value of 0.2 to determine 'high-risk' ecologies for AMR. We recorded as MDR if an isolate had resistance to ≥3 antimicrobial classes. We used a circos diagram to analyze if isolates with identical AMR patterns were shared between different ecologies. S. aureus is prevalent in central Oromia (16.1-18.3%), higher in dairy farms than in abattoirs, and varied among 10 ecologies (p < 0.001) but not among 5 areas (p > 0.05). Of the 92 isolates, 94.6% were penicillin-resistant. Their AMR prevalence was above 40% for 9 of 14 antimicrobials. All isolates (100%) had AMR in at least one antimicrobial class (range = 1-9; median = 5), indicating MDR was prevalent. The prevalence of MDR S. aureus varied (p < 0.05) among areas and 10 ecologies; the highest was in slaughter lines. All isolates had a MARI of >0.2, indicating drug overuse, and S. aureus's AMR burden is high in central Oromia. Dairy farms had higher MARI values (0.44) than abattoirs (0.39). Of 10 ecologies, the highest and lowest MARI values were in the beef supply chain, i.e., slaughter line (0.67) and butcher's hand (0.25). Of the 68 different AMR patterns by 92 isolates against 14 antimicrobials, 53 patterns (77.9%) were unique to individual isolates, indicating they were phenotypically dissimilar. MDR S. aureus was widespread in central Oromia in dairy and meat supply chains, contaminating milk, meat, equipment, and workers in farm and abattoir settings. In the absence of strict regulations and interventions, MDR S. aureus can be disseminated from these epicenters to the public.

Incidence and Predictors of Calf Morbidity and Mortality From Birth to 6-Months of Age in Dairy Farms of Northwestern Ethiopia

The Ethiopian government has initiatives for expanding the commercial and smallholder market-oriented urban and peri-urban dairy production systems to meet the demands for dairy products. However, there have been only limited on-farm studies on the health performance of commercial dairy breeds. The aim of this longitudinal study was to quantify the incidence and identify predictors of calf morbidity and mortality from birth to 6 months of age in urban and peri-urban dairy farms of Northwest Ethiopia. A total of 439 calves aged below 6 months from 174 dairy farms were included in the study. We collected data on 35 potential risk factors to determine their effect on calf morbidity and mortality in the area. Kaplan-Meier survival analysis was used to summarize survival probability. The Cox proportional hazard regression model with shared frailty to account for unmeasured herd-specific heterogeneity was also used to identify and quantify factors associated with time to morbidity and mortality. Among 439 calves enrolled for 6 months of follow-up period, a total of 141 morbidities and 54 mortality events were recorded. This gives an overall morbidity and mortality incidence rates of 64 per 100-calf 6-months at risk (risk rate of 47.3%) and 19 per 100-calf 6-months at risk (risk rate of 17.9%), respectively. Diarrhea was the most frequent calf health problem with a risk rate of 25.2%. It was the cause of death for 33.3% of all the 54 calf deaths. Next to diarrhea, pneumonia ranked second with risk rate of 8.6% and was responsible for death of 12.9% of all the 54 calf deaths. Among 35 potential risk factors, calf age, vigor status at birth, calf breed, colostrum ingestion, and herd size were significant (p < 0.05) predictors of calf morbidity and mortality. The Cox-shared frailty model revealed that the herd frailty component had no significant effect on hazard estimates of the covariates of all-cause morbidity and mortality. This implies that the dairy herds participated in the study were homogeneous in the distribution of unmeasured random effects. In conclusion, the magnitude of calf morbidity and mortality was higher and above economically tolerable level in this study. This could impede the success of Ethiopia's dairy development initiative in general, and the livelihood of smallholder dairy producers in particular. Therefore, educating farmers aimed at mitigating the identified risk factors can reduce calf morbidity and mortality in the study areas.

Genetic diversity and virulence characteristics of Staphylococcus aureus isolates from cases of bovine mastitis

Staphylococcus aureus is one of the major bacterial mastitis pathogens with significant effects on animal and human health. Some studies showed that S. aureus strains that infect different host species are genetically distinct, although most strains can infect a wide range of host species. However, there are no clearly defined clonal patterns of S. aureus strains that are known to infect a specific host. The objectives of this study were to evaluate the clonal diversity and virulence characteristics of S. aureus isolates from cases of bovine mastitis. Bacteriological tests were conducted on milk samples from cases of bovine mastitis from 11 dairy farms including some milk samples from unknown farms in Eastern Tennessee. Overall, a total of 111 S. aureus were isolated and identified, and further evaluated for their genetic diversity by pulsed-field gel electrophoresis (PFGE) and virulence characteristics by PCR. Genotypic virulence factors including staphylococcal enterotoxins, and toxic shock syndrome toxin 1 (tsst-1) were tested by PCR. In addition, the association among several known virulence factors of these isolates based on our current and previous studies in our lab were evaluated. Previously generated data that were included in the analysis of association among virulence factors were the presence of biofilm production associated genes in the ica operon such as icaA, icaD and icaAB, and phenotypic virulence characteristics such as hemolysis on blood agar, slime production and resistance or susceptibility to ten commonly used antimicrobials in dairy farms. The PFGE results showed the presence of 16 PFGE types (designated A - P) throughout farms, of which three pulsotypes, I, M and O were the most frequently isolated PFGE types from most farms. The PFGE type M was the most prevalent of all 16 PFGE types, with 64 isolates being present among nine farms. The PCR results of enterotoxin genes showed that out of the total 111 tested 84 (75.7%) were negative whereas 13 (11.7%), 2 (1.8%), 3 (2.7%), 1 (0.9%) and 8 (7.2%) were positive for seb, seb and sec, sec, see, and tsst-1, respectively. All 111 isolates were negative for sea and sej. Results of the evaluation of I, M and O strains adhesion to and invasion into mammary epithelial cells showed that the total count of each strain of bacteria adhered to and invaded into mammary epithelial cell line (MAC-T cells) was not significantly different (P > 0.05). This may be an indication that there is no significant difference in their ability to establish early host-pathogen interaction and colonization of the host. There were no statistically significant associations among PFGE types and other known virulence factors of these strains. However, PFGE types O and M tend to cluster with β-hemolysin, absence of enterotoxins and susceptibility to antimicrobials. In conclusion, there was not any association between pulsotype and genotypic and phenotypic virulence factors. S. aureus isolates from cases of bovine mastitis had diverse genotypes that possessed variable virulence factors.

Distribution and antimicrobial resistance profile of coagulase-negative staphylococci from cattle, equipment, and personnel on dairy farm and abattoir settings

BACKGROUND

Safe food is central to social wellbeing. Coagulase-negative staphylococci (CNS) are a threat to food safety because they may harbor multiple enterotoxins and antimicrobial resistance (AMR) genes. CNS bacteria are an emerging nosocomial pathogen in public health. CNS also cause bovine mastitis with a significant economic loss in the dairy industry and may introduce toxins to the food supply chain resulting in foodborne illnesses. However, information on CNS and their AMR status are scarce in food animal production and processing lines in Ethiopia.

METHODOLOGY

This cross-sectional study evaluated the prevalence and AMR patterns of CNS in dairy farms and abattoirs using samples (n = 1001) from udder milk, beef carcass, personnel, and different abattoir and dairy equipment across five locations of central Oromia. The CNS isolates were identified via standard microbiological protocols and evaluated using disc diffusion test against 14 antimicrobials belonging to nine different broad classes. Uni-and-multivariable logistic regressions were used to analyze the association between potential risk factors (location, sample source, and sample type) and positivity to CNS.

RESULTS

The overall prevalence of CNS in the five different geographic locations studied was 9.6% (range: 6.7-12.4%) and varied between abattoirs (11.3%) and dairy farms (8.0%). CNS were prevalent on the carcass, milk, equipment, personnel hands, and nasal samples. Of all CNS isolates, 7.1, 10.7, 7.1, 12.5, 17.9, 10.7, 12.5, 7.1, 1.8, 5.4, 1.8, and 5.4% exhibited AMR simultaneously to single, double, 3, 4, 5, 6, 7, 7, 8, 9, 10, 11, and 13 antimicrobials, respectively. Overall, the isolates displayed 51 different AMR phenotypic patterns in which 50% of the isolates exhibited quadruple-resistance simultaneously based on the nine broad antimicrobial classes tested using 14 representative antimicrobials. The prevalence of multidrug-resistant (MDR) CNS (i.e. ≥ 3 classes of antimicrobials) was significantly (p = 0.037) different between locations with 100, 57.1, 50, 86.7, and 76.9% in Addis Ababa, Adama, Assela, Bishoftu, and Holeta, respectively. However, the prevalence of MDR CNS was not significantly (p = 0.20) different between dairy farms (87.5%) and abattoirs (71.9%). We evaluated the effect of acquiring cefoxitin-resistance of the isolates on the efficacy (i.e. inhibition zone) of the rest antimicrobials using General Linear Model after adjusting geographical locations as a random effect. Isolates with cefoxitin-resistance significantly displayed resistance to eight antimicrobials of 14 tested including amoxicillin, penicillin, cloxacillin, chloramphenicol, nalidixic acid, nitrofurantoin, and tetracycline (p = 0.000), and erythromycin (p = 0.02). On the other hand, cefoxitin-resistant isolates were susceptible to gentamicin, ciprofloxacin, kanamycin, streptomycin, and sulphamethoxazone trimethoprim (p = 0.000). Thus, antimicrobials such as gentamicin and ciprofloxacin may be an alternative therapy to treat cefoxitin-resistant CNS, as 96.4% of CNS isolates were susceptible to these antimicrobials. Overall, 94.1 and 54.5% of the CNS isolates among cefoxitin-resistant and cefoxitin-susceptible, respectively, harbored resistance to 3 or more classes of antimicrobials i.e. MDR.

CONCLUSION

The overall prevalence of CNS in milk, meat, equipment, and food handlers in central Oromia was 9.6% but varied by location and sample source. Some specific niches such as equipment, hands, and nasal cavities of personnel are significant sites for the source of CNS. Most, but not all, MDR CNS isolates were cefoxitin-resistant. Overall, 78.6% of the CNS tested were MDR and 50% had resistance to four or more broad classes of antimicrobials. CNS in food animals (raw milk and meat), equipment, and food handlers can be the source of MDR to the public. Personnel safety and hygienic food handling practices are needed. In addition, further investigation into the risk factors for the transmission and mechanisms of resistance of the CNS is required for intervention.

Comparison of Staphylococcus aureus surface protein extraction methods and immunogenicity

Staphylococcus aureus is the major contagious bovine mastitis pathogen and has no effective vaccine. Strain variation and limited knowledge of common immunogenic antigen/s are among major constraints for developing effective vaccines. S. aureus cell surface proteins that are exposed to the host immune system constitute good vaccine candidates. The objective of this study was to compare two novel S. aureus surface protein extraction methods with biotinylation method and evaluate immune-reactivity of extracted proteins. Surface proteins were extracted from nine genetically distinct S. aureus strains from cases of bovine mastitis. After extraction, bacterial cell integrity was examined by Gram staining and electron microscopy to determine if extraction methods caused damage to cells that may release non-surface proteins. The extracted proteins were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and evaluated for immune-reactivity using western blot. Results showed that all three extraction methods provided multiple protein bands on SDS-PAGE. Western blot result showed several immunoreactive surface proteins, in which some proteins strongly (well-resolved, thick, dark, and intense band) reacted across the nine strains tested. The three methods are valid for the extraction of surface proteins and hexadecane, and cholic acid methods are more feasible than biotinylation since both are easier, cheaper, and have minor effects on the bacterial cell. Strongly immune-reactive surface proteins may serve as potential candidates for a vaccine to control S. aureus mastitis in dairy cows.

Immunological responses and evaluation of the protection in dairy cows vaccinated with staphylococcal surface proteins

Bovine mastitis is a significant cause of economic losses in the dairy industry. Staphylococcus aureus is one of the most common contagious mastitis pathogens, whereas Staphylococcus chromogenes increasingly became a significant cause of subclinical mastitis in dairy cows. Current mastitis control measures are not effective on all mastitis pathogens. There is no effective vaccine to control Staphylococcal mastitis in dairy cows. The objective of this study was to evaluate the immune responses and protection in dairy cows vaccinated with S. aureus surface proteins (SASP) or S. chromogenes surface proteins (SCSP). We divided eighteen Holstein dairy cows randomly into three groups of 6 animals each. We vaccinated group 1 and 2 animals with SASP and SCSP with Emulsigen-D adjuvant, respectively. We injected control (group 3) animals with PBS (pH 7.2) in Emulsigen®-D. We vaccinated animals three times at 28 and 14 days before drying off, and at dry off. Two weeks after the third vaccination, we challenged each animal by dipping all teats in S. aureus culture suspension once daily for 14 consecutive days. We evaluated milk or mammary secretion and serum antibody titers during vaccination and challenge periods. We evaluated milk samples for the number of bacteria shedding and somatic cell counts (SCC). Out of six cows vaccinated with SASP, one cow was removed from the study due to injury, two were infected clinically, another two were infected subclinically, and the remaining cow was not infected. No SCSP vaccinated cows developed clinical or subclinical mastitis. Out of six control cows, two developed clinical mastitis whereas four were infected subclinically. The SCSP vaccine cross-protected against S. aureus mastitis and reduced number of S. aureus shedding in milk. We concluded that the SCSP is a promising vaccine to control Staphylococcal mastitis in dairy cows.

Analysis of milk-derived isolates of E. coli indicating drug resistance in central Ethiopia

Mastitis is one of the most important diseases in dairy cows throughout the world and is responsible for significant economic losses to the dairy industry. This study was performed to characterize the genetic basis of drug resistance in Escherichia coli isolated from cases of clinical and sub-clinical bovine mastitis. A total of 224 California mastitis test (CMT)-positive milk samples were collected from December 2015 to April 2016 to characterize the phenotypic and genetic basis of antimicrobial resistance in E. coli isolated from raw milk from dairy farms found in Burayu, Sebeta, and Holeta areas of Ethiopia. The prevalence of E. coli was 7.1% (16) and both phenotypic and molecular techniques were used to identify E. coli antimicrobial susceptibility trait. The most commonly observed phenotypic resistance was against ampicillin (68.7%), sulphamethazole-trimethoprim (50%), and streptomycin (25%). Multidrug resistance phenotypes were found in 11 of 16 (68.7%) of E. coli isolates. Tetracycline (tet (A)) and chloramphenicol (cml (A)) genes were the most predominant encoding resistance genes identified (50%) each, followed by gentamycin resistance encoding gene (aac (3)-IV) (37.5%). Overall, 11 (68.7%) of the isolates had multidrug resistance genes responsible to two or more classes of antibiotics. The most common pattern detected was cml (A) and tet (A) together 37.5% followed by aac (3)-IV and tet (A) 25%. The current study indicated that raw milk could be regarded as critical source of antibiotic-resistant pathogenic E. coli.

Determination of the sources and antimicrobial resistance patterns of Salmonella isolated from the poultry industry in Southern Ethiopia

BACKGROUND

Ethiopia set an ambitious masterplan to increase chicken meat and egg production from 2015 to 2020. Poultry breeding, multiplication and distribution centers in the country have received executive order to import, amplify and distribute commercial chickens to end users. The biosecurity and the pathogen fauna of the centers have not been evaluated as to whether the centers could implement the mission effectively without any risk. Thus, the aim of this study was to evaluate the biosecurity practices and the pathogen prevalence, risk factors and their antimicrobial resistance (AMR) using Salmonella as case study.

METHODS

Routine farm workers of the centers were interviewed about the different management (biosecurity) practices using a checklist. Samples (n = 270) from different sources consisting of chicken's cloacal swab (n = 244), personnel hand swab (n = 9) and bedding (n = 17) were collected from three chicken multiplication centers. Standard bacteriological methods were used for the isolation of Salmonella. Disk diffusion method was used for drug sensitivity testing.

RESULTS

Antimicrobials were often over prescribed without confirming the cause of ill health and without susceptibility testing. The general biosecurity and flock management practices were substandard. Salmonella was isolated from 45 (16.7%) of the 270 samples. Its prevalence was significantly (p<0.05) associated with location of the multiplication center, 27% at Bonga and 10.6% at Hawassa. Sample type was also significantly (p<0.05) affected in that it was higher in the bedding (35.3%) and personnel hand swabs (33.3%) than in the chicken cloaca (14.8%), which demonstrates the poor biosecurity and personnel hygienic practices in the centers. All of the 45 isolates (100%) exhibited resistance to kanamycin and sulfamethoxazole-trimethoprim, nalidixic acid (97.8%), ampicillin (97.8%), cefoxitin (97.8%), streptomycin (97.8%) tetracycline (97.8%), chloramphenicol (91.3%), ciprofloxacin (31.1%), and gentamicin (0%). Alarmingly, 42 isolates (93.4%) exhibited multidrug resistance (MDR) to ≥ 8 drugs and all 45 isolates had resistance to ≥ 3 drugs. The high rate of Salmonella isolation from (i) bedding, (ii) personnel hand swabs (iii) chickens, (iv) presence of more MDR isolates, (v) coupled with poor biosecurity practices in the centers could pose a risk for spreading of pathogens and drug resistant genes to the smallholder chicken producers and the public.

CONCLUSIONS

We conclude that the poultry breeding, multiplication and distribution centers in Ethiopia, as they stand currently, seem to be a source of pathogens and AMR isolates at least for Salmonella. Therefore, strict biosecurity, personnel safety, prudent drug use, regular monitoring and traceability of Salmonella serotypes or genotypes and AMR are recommended.

Prevalence and antimicrobial resistance profile of Staphylococcus in dairy farms, abattoir and humans in Addis Ababa, Ethiopia

Background

Staphylococcus species cause mastitis and wound infection in livestock and food poisoning in humans through ingestion of contaminated foods, including meat and dairy products. They are evolving pathogens in that they readily acquire drug resistance, and multiple drug-resistant (MDR) isolates are increasing in human and veterinary healthcare. Therefore, this study was conducted to evaluate the prevalence of Staphylococci and their drug resistance in dairy farms and abattoir settings of Addis Ababa.

Methods

In this cross-sectional study, 193 samples of milk, meat, equipment and humans working in the dairy farms and abattoir were collected (dairy farms = 72 and abattoir sources = 121). Staphylococcus isolation and identification at the species level was done according to ISO-6888-3 using biochemical characteristics. An antimicrobial susceptibility test was conducted for 43 of the isolates using 15 antimicrobial agents commonly used for humans and livestock by the Kirby Bauer disk diffusion method following CLSI guidelines.

Results

Staphylococcus organism were isolated from 92 (47.7%) of the total 193 samples, 50% in the dairy farms and 46.3% in the abattoir. The isolated species were S. aureus (n = 31; 16.1%), S. intermedius (n = 21; 10.9%), S. hyicus (n = 16; 8.3%), and coagulase negative Staphylococcus (CNS) (n = 24; 12.4%). Gentamycin was effective drug as all isolates (n = 43; 100%) were susceptible to it and followed by kanamycin (n = 39; 90.7%). However, the majority of the isolates showed resistance to penicillin-G (95.3%), nalidixic acid (88.4%), cloxacillin (79.1%), vancomycin (65.1%) and cefoxitin (55.8%). Of the 15 S. aureus tested for drug susceptibility, 73.3% of them were phenotypically resistant to vancomycin (VRSA) and all of the 15 isolates showed multi-drug resistance (MDR) to >3 drugs. Also, all of the tested CNS (100%), S. hyicus (100%) and the majority of S. intermedius isolates (88.9%) developed MDR.

Conclusion

Alarmingly, the Staphylococcus isolates circulating in the dairy farms and abattoir in the study area harbor MDR. High level of Staphylococcus species isolation from personnel and equipment besides food (meat and milk) samples in dairy farms and abattoir settings reveals that the hygiene practice in the dairy farm and abattoir is substandard. Prudent drug use and improved hygienic practice is recommended in the dairy farms and abattoir to safeguard the public from the risk of acquiring infections and MDR pathogenic Staphylococcus.