Prevalence and whole genome-based phylogenetic, virulence and antibiotic -resistance characteristics of nasal -Staphylococcus aureus in healthy Swiss horses.

INTRODUCTION: A total of 100 nasal swabs were collected from healthy horses in Switzerland between January 2020 and August 2020. The samples were taken from horses at 40 different stables in 12 different cantons and screened for both methicillin-resistant (MRSA) and methicillin-susceptible S. aureus (MSSA) using selective agar plates. S. aureus were tested for antibiotic susceptibility by measurement of the minimal inhibitory concentration (MIC) and for virulence factors, antibiotic resistance genes and phylogenetic characteristics using whole genome sequence analysis. Ten horses were found to be positive (10 %, CI: 95 %, 0,0552 - 0,1744) for S. aureus, and four of them harboured MRSA (4 %, CI: 95 %, CI: 1,5 % - 9 %). The MRSA were detected in horses from three different stables in the same region of one canton and MSSA were detected in horses from five different cantons. All the MRSA isolates were genetically related (ST398-t011-IVa), while the MSSA were diverse (ST1-t127/t398/t1508, ST816-t1294, ST133-t1403, ST30-t012). MRSA showed resistance to penicillin (blaZ), cefoxitin (mecA), trimethoprim (dfrK), gentamicin, kanamycin (aac(6')-Ie - aph(2'')-Ia), and tetracycline (tet(M)). MSSA were resistant to either none or one of the antibiotics tested like penicillin (blaZ) and erythromycin (erm(T)). Virulence genes were more abundant in MSSA than in MRSA. This study provides first insight into the prevalence and type of S. aureus in healthy Swiss horses and reveals a source of strains, which may cause infections in both horses and humans.

INTRODUCTION: Au total, 100 écouvillons nasaux ont été prélevés sur des chevaux sains en Suisse entre janvier 2020 et août 2020. Les échantillons ont été prélevés sur des chevaux de 40 écuries différentes dans 12 cantons différents et ont été soumis à un dépistage de S. aureus résistant à la méthicilline (MRSA) et de S. aureus sensible à la méthicilline (MSSA) à l'aide de plaques de gélose sélectives. Les S. aureus ont été testés pour leur sensibilité aux antibiotiques en mesurant la concentration minimale inhibitrice (CMI) et pour les facteurs de virulence, les gènes de résistance aux antibiotiques et les caractéristiques phylogénétiques en analysant la séquence du génome entier. Dix chevaux se sont révélés positifs (10 %, IC: 95 %, 0,0552 ­ 0,1744) pour S. aureus, et quatre d'entre eux étaient porteurs de MRSA (4 %, IC: 95 %, IC: 1,5 % ­ 9 %). Les MRSA ont été détectés chez des chevaux provenant de trois écuries différentes de la même région d'un canton et les MSSA ont été détectés chez des chevaux provenant de cinq cantons différents. Tous les isolats de MRSA étaient génétiquement apparentés (ST398-t011-IVa), tandis que les MSSA étaient divers (ST1-t127/t398/t1508, ST816-t1294, ST133-t1403, ST30-t012). Les MRSA étaient résistants à la pénicilline (blaZ), à la céfoxitine (mecA), au triméthoprime (dfrK), à la gentamicine, à la kanamycine (aac(6')-Ie ­ aph(2")-Ia) et à la tétracycline (tet(M)). Les MSSA étaient résistants à aucun ou à un des antibiotiques testés soit à la pénicilline (blaZ) ou à l'érythromycine (erm(T)). Les gènes de virulence étaient plus abondants chez les MSSA que chez les MRSA. Cette étude donne, pour la première fois, un aperçu de la prévalence et du type de S. aureus chez les chevaux suisses en bonne santé et révèle la présence de souches susceptibles de provoquer des infections chez les chevaux et les humains.

Antimicrobial susceptibility in E. coli and Pasteurellaceae at the beginning and at the end of the fattening process in veal calves: Comparing 'outdoor veal calf' and conventional operations.

Animal husbandry requires practical measures to limit antimicrobial resistance (AMR). Therefore, a novel management and housing concept for veal calf fattening was implemented on 19 intervention farms (IF) and evaluated regarding its effects on AMR in Escherichia (E.) coli, Pasteurella (P.) multocida and Mannheimia (M.) haemolytica in comparison with 19 conventional control farms (CF). Treatment intensity (-80%) and mortality (-50%) were significantly lower in IF than in CF, however, production parameters did not differ significantly between groups. Rectal and nasopharyngeal swabs were taken at the beginning and the end of the fattening period. Susceptibility testing by determination of the minimum inhibitory concentration was performed on 5420 isolates. The presence of AMR was described as prevalence of resistant isolates (%), by calculating the Antimicrobial Resistance Index (ARI: number of resistance of one isolate to single drugs/total number of drugs tested), by the occurrence of pansusceptible isolates (susceptible to all tested drugs, ARI=0), and by calculating the prevalence of multidrug (≥3) resistant isolates (MDR). Before slaughter, odds for carrying pansusceptible E. coli were higher in IF than in CF (+65%, p=0.022), whereas ARI was lower (-16%, p=0.003), and MDR isolates were less prevalent (-65%, p=0.001). For P. multocida, odds for carrying pansusceptible isolates were higher in IF before slaughter compared to CF (+990%, p=0.009). No differences between IF and CF were seen regarding the prevalence of pansuceptible M. haemolytica. These findings indicate that easy-to-implement measures to improve calf management can lead to a limitation of AMR in Swiss veal fattening farms.

Distribution, genetic heterogeneity, and antimicrobial susceptibility of Brachyspira pilosicoli in Swiss pig herds.

Brachyspira (B.) pilosicoli is a bacterium causing porcine intestinal spirochaetosis, a disease characterized by diarrhoea and depressed growth rates especially in nursery and fattening pigs. Knowledge of the epidemiology and antimicrobial susceptibility of this pathogen is limited. Therefore, the aim of this study was to analyse the distribution, genetic heterogeneity, and antimicrobial susceptibility of B. pilosicoli field isolates from Swiss pig farms. Faecal swabs of 693 animals originating from 156 herds were analysed for the presence of Brachyspira spp. using culture and polymerase chain reaction identification. Further characterisation was performed using multilocus sequence typing (MLST) and broth dilution antimicrobial susceptibility testing. With 52.6% positive herds, B. pilosicoli could be frequently isolated from herds with animals suffering from diarrhoea. In herds with animals without clinical signs of diarrhoea, detection was significantly less frequent with only 10.5% positive herds (p 0.001). Among 80 isolates used for typing, genetic heterogeneity was observed with 44 different sequence types (ST) which often differed from herd to herd. No predominant ST was observed. More than 73.0% of the 41 B. pilosicoli isolates analysed, showed minimal inhibitory concentration values above the wild type cut-off values for lincomycin, tylvalosin and/ or tylosin. For tiamulin, valnemulin and doxycycline, this was the case in 48.8%, 43.9% and 36.6%, respectively. In conclusion, a diverse population of B. pilosicoli exhibited decreased susceptibility to antimicrobials used against Brachyspira infections. Monitoring of resistance in Brachyspira spp. is highly recommended to support targeted use of antimicrobials in pigs.

Antibiotic and quaternary ammonium compound resistance in Escherichia coli from calves at the beginning of the -fattening period in Switzerland (2017).

INTRODUCTION: In the Swiss veal calf production, antimicrobials and disinfectants are used to control bacterial infectious diseases, leading to a risk of selecting for a resistant bacterial population. While the prevalence of antibiotic resistance in E. coli from calves has been monitored at slaughterhouses in Switzerland since 2006, the resistance situation of E. coli from young calves entering the fattening period is not known. A total of 100 calves entering the fattening period in 20 geographically distant farms in Switzerland were screened for the presence of E. coli using rectal swabs in 2017. Genetic diversity between isolates was determined using repetitive palindromic Polymerase Chain Reaction (rep-PCR) revealing a genetically diverse E. coli population. Susceptibility to 13 antibiotics and to alkyldimethylbenzylammonium (ADBAC) was determined by the measurement of the minimal inhibitory concentration. Antibiotic and quaternary ammonium compound (QAC) resistance genes were identified using microarray and Polymerase Chain Reaction (PCR). Sixty-four percent of the isolates were resistant to at least one antibiotic, and 52% also exhibited decreased susceptibility to ADBAC. Resistance to more than 3 antibiotics was found in 40% of the isolates. Isolates exhibited resistance to tetracycline (57%) associated with the presence of tet genes (tet(A), (B), (E), (G)), to sulfonamides (61%) (sul1, sul2, sul3), ampicillin (56%) (blaTEM-1), trimethoprim (32%) (dfrA), phenicols (31%) (catA1, cmlA1, floR), gentamicin (27%) (ant(2")-Ia, aac(3)-IVa, aac(3)-VIa), and cefotaxime (2%) (blaCTX-M-14 (ESBL)). Mutations in GyrA (S83L) and ParC (S80I) were found in the fluoroquinolone-resistant isolates (6%). All isolates were susceptible to colistin, tigecycline and meropenem. No association between the presence of decreased susceptibility to ADBAC and qac genes was observed. In conclusion, antibiotic and QAC resistant E. coli are present in the gastrointestinal tract of young calves at the beginning of the fattening period, emphasizing the need for appropriate and reduced use of antibiotics and QAC-containing disinfectants in order to limit further selection of these bacteria during the fattening period.

INTRODUCTION: Dans la production de veaux en Suisses, des antimicrobiens et des désinfectants sont utilisés pour contrôler les maladies infectieuses bactériennes, ce qui entraîne un risque de sélection d'une population bactérienne résistante. Si la prévalence de la résistance de E. coli aux antibiotiques chez les veaux est surveillée dans les abattoirs suisses depuis 2006, la situation de la résistance de E. coli chez les jeunes veaux au début de la période d'engraissement n'est pas connue. Un total de 100 veaux entrant dans la période d'engraissement dans 20 exploitations géographiquement éloignées de Suisse ont été testés en 2017 pour détecter la présence de E. Coli à l'aide de prélèvements rectaux. La diversité génétique entre les isolats a été déterminée à l'aide de la réaction de polymérase en chaîne répétitive palindrome (rep-PCR) révélant une population de E.coli génétiquement diversifié. La sensibilité à 13 antibiotiques et au chlorure d'alkyldiméthylbenzylammonium (ADBAC) a été déterminée par la mesure de la concentration inhibitrice minimale. Les gènes de résistance aux antibiotiques et aux composés d'ammonium quaternaire (QAC) ont été identifiés à l'aide d'une puce à ADN et de la réaction de polymérase en chaîne (PCR). Soixante-quatre pour cent des isolats étaient résistants à au moins un antibiotique et 52% présentaient également une diminution de la sensibilité à l'ADBAC. Une résistance à plus de 3 antibiotiques a été trouvée dans 40% des isolats. Les isolats présentaient une résistance à la tétracycline (57%) associée à la présence de gènes tet (tet (A), (B), (E), (G)), aux sulfonamides (61%) (sul1, sul2, sul3), à l'ampicilline (56%) (blaTEM-1), au triméthoprime (32%) (dfrA), aux phénicols (31%) (catA1, cmlA1, floR), à la gentamicine (27%) (ant(2'')-Ia, aac (3) -IVa, aac (3) -VIa) et à la céfotaxime (2%) (blaCTX-M-14 (BLSE)). Les isolats résistants aux fluoroquinolones (6%) présentaient des mutations dans GyrA (S83L) et ParC (S80I). Tous les isolats étaient sensibles à la colistine, à la tigécycline et au méropénème. Aucune association entre la présence d'une sensibilité diminuée à l'ADBAC et les gènes qac n'a été observée. En conclusion, des E. coli résistants aux antibiotiques et aux QAC sont présents dans le tractus gastro-intestinal des jeunes veaux au début de la période d'engraissement, ce qui souligne la nécessité d'un usage approprié et réduit d'antibiotiques et de désinfectants contenant un QAC afin de limiter la sélection ultérieure de ces bactéries au cours de la période d'engraissement.

Nasal carriage of methicillin-resistant Staphylococcus aureus (MRSA) among Swiss veterinary health care providers: detection of livestock- and healthcare-associated clones.

We screened a total of 340 veterinarians (including general practitioners, small animal practitioners, large animal practitioners, veterinarians working in different veterinary services or industry), and 29 veterinary assistants for nasal carriage of methicillin-resistant Staphylococcus aureus (MRSA) and Staphylococcus pseudintermedius (MRSP) at the 2012 Swiss veterinary annual meeting. MRSA isolates (n = 14) were detected in 3.8 % (95 % CI 2.1 - 6.3 %) of the participants whereas MRSP was not detected. Large animal practitioners were carriers of livestock-associated MRSA (LA-MRSA) ST398-t011-V (n = 2), ST398-t011-IV (n = 4), and ST398-t034-V (n = 1). On the other hand, participants working with small animals harbored human healthcare-associated MRSA (HCA-MRSA) which belonged to epidemic lineages ST225-t003-II (n = 2), ST225-t014-II (n = 1), ST5-t002-II (n = 2), ST5-t283-IV (n = 1), and ST88-t186-IV (n = 1). HCA-MRSA harbored virulence factors such as enterotoxins, ß-hemolysin converting phage and leukocidins. None of the MRSA isolates carried Panton-Valentine leukocidin (PVL). In addition to the methicillin resistance gene mecA, LA-MRSA ST398 isolates generally contained additional antibiotic resistance genes conferring resistance to tetracycline [tet(M) and tet(K)], trimethoprim [dfrK, dfrG], and the aminoglycosides gentamicin and kanamycin [aac(6')-Ie - aph(2')-Ia]. On the other hand, HCA-MRSA ST5 and ST225 mainly contained genes conferring resistance to the macrolide, lincosamide and streptogramin B antibiotics [erm(A)], to spectinomycin [ant(9)-Ia], amikacin and tobramycin [ant(4')-Ia], and to fluoroquinolones [amino acid substitutions in GrlA (S84L) and GyrA (S80F and S81P)]. MRSA carriage may represent an occupational risk and veterinarians should be aware of possible MRSA colonization and potential for developing infection or for transmitting these strains. Professional exposure to animals should be reported upon hospitalization and before medical intervention to allow for preventive measures. Infection prevention measures are also indicated in veterinary medicine to avoid MRSA transmission between humans and animals, and to limit the spread of MRSA both in the community, and to animal and human hospitals.