Antimicrobial resistance studies from Atlantic Canada with a focus on extended-spectrum cephalosporin resistance in dairy cattle and humans

The first major objective of this thesis was to determine the antimicrobial\nsusceptibilities from the most common pathogens isolated from clinical samples, from\nfood animals and companion animals submitted to the bacteriology diagnostic laboratory\nat Atlantic Veterinary College over a 20 years period, which is described in chapters 2\nand 3. The second major objective was to determine the antimicrobial resistance and the\nassociated resistance genes to extended-spectrum cephalosporins (ESC) and\nfluoroquinolones in enteric bacteria from dairy cattle and humans within the Maritime\nProvinces using selective culture (chapters 4 to 6). Chapter 5’s objective was to explore if\ncolostrum was a potential source of ESC and fluoroquinolone resistance identified in\ncalves from chapter 4.\nAntimicrobial susceptibility patterns and resistance trends in pathogens from\ncattle, small ruminants and pigs were described in chapter 2. Staphylococcus aureus,\nStreptococcus uberis, and Escherichia coli were the predominantly isolated agents of\nbovine mastitis, while E. coli, P. multocida, M. haemolytica, and H. somni were the\nmajor bacteria isolated from small ruminants and non-mastitis clinical samples of cattle.\nEscherichia coli, S. suis, and P. multocida accounted for over 70% of the total pathogens\nisolated from clinical samples originating from pigs. A high proportion of the food animal\npathogens were susceptible to the antimicrobials tested over the entire study period,\nespecially the mastitis pathogens and pathogens isolated from small ruminants.\nDecreased resistance to aminoglycosides was consistent in all three food animal species.\nHowever, increased resistance to ceftiofur was found in E. coli from cattle and pigs over\nthe period. In general, multi-drug resistance (MDR) was higher in cattle and pigs compared to small ruminants. In cattle isolates (mastitis and non-mastitis pathogens),\nMDR was higher in Gram-negative pathogens, especially E. coli, and in small ruminants,\nMDR was most commonly found in M. haemolytica and P. multocida. Interestingly in\nswine, MDR was common in Gram-positive isolates, such as Erysipelothrix\nrhusiopathiae and Staphylococcus spp.\nAntimicrobial susceptibility patterns and AMR trends in pathogens from horses,\ncats, and dogs were described in chapter 3. Streptococcus zooepidemicus and E. coli were\nthe most commonly isolated pathogens of horses. Similar bacterial pathogens were\nisolated from both dogs and cats with E. coli and Staphylococcus spp. being the most\nfrequently isolated Gram-negative and Gram-positive pathogens, respectively. Among\nthe horse pathogens, lower susceptibility frequencies were common to tetracycline, TMS,\nand ampicillin, while isolates were frequently susceptible to ceftiofur. Higher\nsusceptibilities (compared to horses) were seen in dog and cat pathogens, although cat\npathogens were more likely to be susceptible to tested antimicrobials compared with\nbacterial species recovered from dogs. Generally, among the companion animals, most\nAMR trends were stable over the study period. While increased resistance was seen to\nboth amikacin and gentamicin in Actinobacillus spp., and Streptococcus zooepidemicus to\nTMS in the horse. Increased antimicrobial resistance trends were commonly seen to\nenrofloxacin and amoxicillin-clavulanate in dog pathogens. Increased resistance to\ncefovecin was also observed in coagulase-positive Staphylococcus spp. in dogs.\nDecreasing AMR trends were found to the aminoglycosides in dog and cat pathogens.\nMulti-drug resistance in equine pathogens was low, however, when it was seen, it was\nmore commonly found in Gram-negative pathogens, especially Klebsiella spp. and E. coli. Multi-drug resistance was generally low in dog and cat pathogens, but the frequency\nwas significantly higher in dogs compared to cats and horses. All methicillin-resistant\nStaphylococcus spp. from dogs were MDR in this study.\nIn chapter 4, the frequency and risk factors of reduced susceptibility to extendedspectrum\ncephalosporin resistance were examined in Salmonella enterica and E. coli\nfrom fecal samples from 488 dairy calves from eight herds using selective culture. The\nfrequency of fecal carriage of Salmonella enterica was low (3.3%). The recovered\nSalmonella isolates were pan-susceptible, and ESC resistance was not detected. All the\nSalmonella enterica isolates belonged to three serovars: Senftenberg, Typhimurium\nDT02, and Derby. Eighty-one percent of calves were positive for E. coli with reduced\nsusceptibility to ESC (sESC-R E. coli). From the selected sESC-R E. coli (n=100), 88%\ndemonstrated phenotypic resistance to ESC (ceftriaxone and/or ceftiofur) based on MIC\ntesting. From these 88 ESC-R E. coli; blaTEM was detected in 84.1%, blaCMY-2 was\ndetected in 52.2%, 15.9% were blaCTX-M-9 positive, 9.1% blaCTX-M-1 positive, 9.1% were\nblaCTX-M-2 positive, and blaSHV was detected in 1.1% of isolates. Sixty percent (60%) of\nthe ESC-R E. coli had two or more β-lactamase resistance genes. Plasmid-mediated\nquinolone resistance genes were detected from seven of the nine isolates with reduced\nsusceptibility to quinolones. Five isolates were positive for qnrB alone, and two isolates\nwere positive for both qnrB and qnrS. Neonatal age calves (OR=2.42), regular ceftiofur\nuse on the farm (OR=3.83) feeding of unpasteurized, non-saleable milk (OR=1.6), use of\nflorfenicol (OR=2.02) and use of ceftiofur for the treatment of respiratory diseases\n(OR=0.57) were associated with the fecal recovery of E. coli with reduced susceptibility\nto ESC. In chapter 5, the potential role of dairy colostrum as a source of antimicrobial\nresistant bacteria to newborn dairy calves was examined. ESC-R E. coli were detected\nin 20 (4.43%) of the 452 colostrum samples. At least one ESC-R E. coli isolate was\ndetected in 6 (75%) of the 8 dairy herds. All ESC-R E. coli had phenotypic MDR\nprofiles. No blaCTX-M group genes were detected, but blaCMY-2 and blaTEM genes were\ndetected in nine (45%), and seven (35%) of the twenty ESC-R E. coli isolates recovered.\nIn chapter 6, the frequency of humans’ fecal carriage of vancomycin-resistant\nEnterococcus spp., carbapenem-resistant E. coli, and generic E. coli with reduced\nsusceptibility to ESC and fluoroquinolones were examined. The recovery of ESCresistant\nand quinolone-resistant E. coli was low (<10%) out of 489 human fecal samples.\nCarbapenem-resistant E. coli and vancomycin-resistant Enterococcus faecalis or faecium\nwere not detected in any samples in this study. The β-lactamase-resistance gene profile of\nthe 26 ESC-R E. coli isolates was as follows: 25 (96.2%) of harbored blaTEM, 18 (69.2%)\nharbored blaCMY-2, 16 (61.5%) harbored blaCTX-M groups (blaCTX-M-1 = 9, blaCTX-M-9 = 5,\nand blaCTX-M-2 =2 isolates), and two (7.7%) isolates harbored blaSHV resistance genes.\nThe majority of isolates (92.3%) harbored two or more resistance genes. Twenty-one\n(8.3%) out of 253 human fecal samples were positive for qnr-producing E. coli isolates.\nOf the E. coli isolates, Three (14.3%) harbored qnrB, five (23.8%) harbored qnrS, and\nthirteen (61.9%) were positive for both qnrB and qnrS genes.\nOverall, this research has provided valuable information on the antimicrobial\nsusceptibility patterns of commonly cultured pathogens from food and companion\nanimals from the Atlantic region of Canada. This information may influence the rational\nuse of antimicrobials by clinicians in choosing empirical therapies and treatment protocols within the food animal industries and companion animal veterinary practices in\nAtlantic Canada. Also, this study has provided an estimate of extended spectrum\ncephalosporin and fluoroquinolone resistance in dairy calves and humans, as well as\ncarbapenem and vancomycin resistance in humans within Prince Edward Island.\nAdditionally, this research has provided information on the resistance genes associated\nwith the occurrence of ESC and fluoroquinolone resistance in Atlantic Canada.

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