Surveillance of the source of poultry infections with Enterococcus hirae and Enterococcus cecorum in Slovenia and E. hirae antibiotic resistance patterns.

Enterococcus cecorum and Enterococcus hirae can cause locomotor problems, septicaemia, and endocarditis in broiler chickens. Understanding transmission routes and resistance patterns are essential for effective treatment. The aim of this study was to follow the same animals from the breeder flock to the hatchery and up to 14-day-old broiler chickens on the farm to find the source of E. cecorum and E. hirae. During the production cycle, only faeces and organs of broilers were E. hirae positive in all three sampled farms in which recurrent enterococcal infections were previously confirmed. None of the isolates possessed virulence genes. Based on resistance profiles, a variety of different strains were present in faeces and organs of different broilers' ages. Samples from the breeder flock and hatchery were negative. Faecal shedding on the farm and tolerance of enterococci to the environmental conditions enable persistence of pathogenic enterococci in farm dust; therefore, adequate cleaning and disinfection after depopulation of the farms could prevent disease recurrence in the new cycle. Susceptibility testing of E. hirae isolates showed no resistance to the drugs of choice for the treatment of enterococcal infections in poultry.

Staphylococcus pseudintermedius septicemia in puppies after elective cesarean section: confirmed transmission via dam's milk.

BACKGROUND: In humans, transmission of bacteria causing fatal sepsis in the neonates through mother's milk has been reported. In dogs, it is believed that bacteria from canine milk are not the primary cause of neonatal infections. Staphylococcus pseudintermedius is colonizing the skin and mucocutaneous junctions in adult dogs and can act as an opportunistic pathogen. This bacterium was previously isolated from the canine milk and, although, its transmission from the dam's milk to the newborn puppies causing a neonatal sepsis was suggested, this hypothesis has not been confirmed. CASE PRESENTATION: A 4.5-year-old healthy Boston terrier dam had an elective cesarean section, delivering five normal puppies and one dead runt. Next day, two puppies developed pustules on their legs and around the muzzle. After two more days, strings of blood were noticed in the stool of the biggest puppy that suddenly died later that night. The same day, blood became visible in the feces of all other puppies. Necropsy of the dead puppy revealed a distended abdomen, catarrhal gastroenteritis with lymphadenopathy, dark red and slightly firm lung, mild dilatation of the right heart chamber and congestion of the liver, spleen, pancreas and meninges. The thoracic cavity contained white-yellow slightly opaque exudate, and there was transudate in the abdominal cavity. Histopathology revealed an acute interstitial pneumonia and multifocal myocardial necrosis with mineralization. Bacteriology of the internal organs, body cavity effusions of the dead puppy and dam's milk revealed a diffuse growth of S. pseudintermedius in pure culture. Whole genome sequencing (WGS) revealed that all isolates belonged to the sequence type 241 and differed in 2-5 single nucleotide polymorphisms; thus, the epidemiological link between the outbreak-associated isolates was confirmed. CONCLUSIONS: This is the first report of a confirmed transmission of S. pseudintermedius through dam's milk causing a neonatal sepsis in a puppy after an elective cesarean section. The epidemiological link between S. pseudintermedius isolates obtained from dam's milk and internal organs of the affected puppy was confirmed by WGS. Our findings indicate that milk of healthy dams can serve as a reservoir of bacteria that can cause fatal sepsis in the newborn puppies.

Clostridium difficile in goats and sheep in Slovenia: characterisation of strains and evidence of age-related shedding.

Diversity of Clostridium difficile in different age groups of goats (n = 109) and sheep (n = 105) was investigated. C. difficile was detected in 9.2% of goats and 5.7% of sheep. None of the adult animals were positive. Isolates belonged to four toxinotypes (0, V, XIa, XII), six PCR-ribotypes (010, 014/020, 045, 056, SLO 061, SLO 151) and six pulsotypes. PCR-ribotypes 010, 014/020, 045 and 056 were found previously in other animal species and humans in Slovenia. Additionally, three pulsotypes were indistinguishable from restriction patterns in our PFGE database of animal isolates. All strains were susceptible to metronidazol, vancomycin, moxifloxacin, and with the exception of a single non-toxigenic strain also to clindamycin and erythromycin. While all strains were resistant to ciprofloxacin and levofloxacin, oxacillin-resistance was observed only in strains of PCR-ribotype 045. This first study on C. difficile in small ruminants in Slovenia revealed the evidence of age-related shedding as the highest was demonstrated in neonatal goats and sheep aged up to 16 days.

Antimicrobial Susceptibility and Characterization of Extended-Spectrum ß-Lactamase-Producing Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia.

Antimicrobial resistance of Escherichia coli is a growing problem in both developed and developing countries. This study aimed to investigate the phenotypic antimicrobial resistance of E. coli isolates (n = 260) isolated from the stool specimen of patients attending public health facilities in Addis Ababa and Hossana. This study also aimed to characterize phenotypically confirmed extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates (n = 22) using whole-genome sequencing. Resistance to 18 different antimicrobials was assessed using the disc diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The highest resistance rate among the E. coli isolates was found for ampicillin (52.7%), followed by trimethoprim-sulfamethoxazole (29.6%). Of all isolates, 50 (19.2%) were multidrug-resistant and 22 (8.5%) were ESBL producers. ESBL genes were detected in 94.7% of the sequenced E. coli isolates, and multiple ß-lactamase genes were detected in 57.9% of the isolates. The predominant ESBL gene identified was blaCTX-M-15 (78.9%). The blaTEM-1B gene was detected in combination with other ESBL genes in 57.9% of the isolates, while only one of the sequenced isolates contained the blaTEM-1B gene alone. The blaCTX-M-3 gene was detected in three isolates. The genes blaCTX-M-15 and blaTEM-1B as well as blaCTX-M-15 and blaTEM-169 were confirmed to coexist in 52.6% and 10.5% of the sequenced E. coli isolates, respectively. In addition, blaOXA-1 was identified together with blaCTX-M-15 and blaTEM-1B in one isolate, and in one isolate, blaTEM-169 together with blaCTX-M-15 and blaTEM-1B was found. The results obtained show that measures need to be taken to reduce the spread of drug resistance and ensure the long-term use of available antimicrobials.

Antimicrobial and Antibiofilm Effect of Commonly Used Disinfectants on Salmonella Infantis Isolates.

Salmonella enterica subsp. enterica serovar Infantis is the most prevalent serovar in broilers and broiler meat in the European Union. The aim of our study was to test the biofilm formation and antimicrobial effect of disinfectants on genetically characterized S. Infantis isolates from poultry, food, and humans. For the biofilm formation under various temperature conditions (8 °C, 20 °C, and 28 °C) and incubation times (72 h and 168 h), the crystal violet staining method was used. The evaluation of the in vitro antimicrobial effect of Ecocid® S, ethanol, and hydrogen peroxide was determined using the broth microdilution method. The antibiofilm effect of subinhibitory concentration (1/8 MIC) of disinfectants was then tested on S. Infantis 323/19 strain that had the highest biofilm formation potential. Our results showed that the biofilm formation was strain-specific; however, it was higher at 20 °C and prolonged incubation time. Moreover, strains carrying a pESI plasmid showed higher biofilm formation potential. The antibiofilm potential of disinfectants on S. Infantis 323/19 strain at 20 °C was effective after a shorter incubation time. As shown in our study, more effective precautionary measures should be implemented to ensure biofilm prevention and removal in order to control the S. Infantis occurrence.

Phylogeography of Brucella suis biovar 2 with focus on Slovenian wildlife.

Brucella suis commonly infects swine but occasionally also other animal species and humans. Wild boars are the most important reservoir of B. suis biovar 2, continually infecting susceptible hosts through close contact. Nevertheless, the genetic diversity of B. suis in wildlife remains understudied. Here, we typed 17 Slovenian B. suis biovar 2 isolates obtained in 2017-2019 from wild boars (n = 16) and a hare (n = 1) using whole-genome sequencing (WGS). To assess the global phylogenetic diversity of B. suis, we compared them to 126 publicly available B. suis genomes. All Slovenian isolates fell within the biovar 2 lineage, confirming the previous multiplex PCR typing results. According to MLST-21, the wild boar isolates were of sequence types (STs) ST16 (n = 8) and ST153 (n = 8); the maximum genetic distance between isolates of the same ST was 28 wgMLST alleles. The ST153 isolates were restricted to the Slovenian-Croatian border and clustered together with the Croatian ST153 isolates from swine, indicating cross-border transmission of B. suis ST153 strain. The hare isolate was of ST40 and was genetically distant (≥ 489 alleles) from the wild boar isolates. The genome-wide phylogeny clearly separated different B. suis biovars. The present study is the first report on the population structure of B. suis in wildlife in Slovenia and shows that the Slovenian B. suis population is genetically heterogeneous. At the species level, B. suis biovars are clearly separated in the WGS-based phylogenetic tree and can therefore be reliably predicted using WGS.

Genomic Insights into Methicillin-Resistant Staphylococci and Mammaliicocci from Bulk Tank Milk of Dairy Farms in Serbia.

The potential risk to human and animal health provides a rationale for research on methicillin-resistant staphylococci (MRS) and mammaliicocci (MRM) in dairy herds. Here, we aimed to estimate their occurrence in the bulk tank milk (BTM) samples collected in 2019-2021 from 283 bovine dairy farms in the Belgrade district. We used whole-genome sequencing to characterize the obtained isolates and assess their genetic relatedness. A total of 70 MRS/MRM were recovered, most frequently Staphylococcus haemolyticus and Mammaliicoccus sciuri. Five clusters of 2-4 genetically related isolates were identified and epidemiological data indicated transmission through, e.g., farm visits by personnel or milk collection trucks. Most MRSA isolates belonged to the typical livestock-associated lineage ST398-t034. One MRSA isolate (ST152-t355) harbored the PVL-encoding genes. Since MRS/MRM isolates obtained in this study frequently harbored genes conferring multidrug resistance (MDR), this argues for their role as reservoirs for the spread of antimicrobial resistance genes. The pipeline milking system and total bacterial count >100,000 CFU/mL were significantly associated with higher occurrences of MRS/MRM. Our study confirms that BTM can be a zoonotic source of MRS, including MDR strains. This highlights the urgent need for good agricultural practices and the continuous monitoring of MRS/MRM in dairy farms.

Coagulase-negative staphylococci from non-mastitic bovine mammary gland: characterization of Staphylococcus chromogenes and Staphylococcus haemolyticus by antibiotic susceptibility testing and pulsed-field gel electrophoresis.

During routine microbiological examination of milk samples from dairy cows without clinical signs of mastitis, quarter milk samples of 231 dairy cows from 12 herds were investigated for the presence of coagulase-negative staphylococci (CNS). The isolates were identified on the basis of colony morphology, Gram staining, catalase and coagulase test and the commercial kit, API Staph. CNS was detected in 29% (67/231) of the cows. A total of seven CNS species were identified with the most prevalent being Staphylococcus (Staph.) chromogenes (30%) and Staph. haemolyticus (28·8%), followed by Staph. simulans (11·2%), Staph. xylosus (11·2%), Staph. epidermidis (7·5%), Staph. hyicus (6·3%) and Staph. sciuri (5%). The predominant species, Staph. chromogenes and Staph. haemolyticus, were further characterized by antibiotic susceptibility testing using the agar disc diffusion method (Kirby-Bauer) and by pulsed-field gel electrophoresis (PFGE). Considerable resistance to ampicillin and penicillin was observed in both species. Isolates with identical or highly similar PFGE profiles were detected at the herd level despite a marked heterogeneity seen for both species. On the basis of somatic cell count, absence of clinical signs of inflammation and heterogeneity of genotypes, we assume that CNS isolated in this study could not be considered as important causative agents of the bovine mammary gland inflammation.

Evidence of Anaplasma phagocytophilum in game animals from Slovenia.

Anaplasma phagocytophilum is a tick-borne rickettsial pathogen responsible for granulocytic anaplasmosis in mammalian hosts including humans. Wild animals may play an important role in the epidemiology of this disease. The aim of this study was to estimate the prevalence of infection with A. phagocytophilum among wildlife in Slovenia. Serum samples (n = 376) from the most important game species [red deer (Cervus elaphus), roe deer (Capreolus capreolus), wild boar (Sus scrofa), chamois (Rupicapra rupicapra) and brown bear (Ursus arctos)] were examined by A. phagocytophilum-specific indirect fluorescent-antibody assay (IFA) and wild boar spleen samples (n = 160) were tested by polymerase chain reaction (PCR). A. phagocytophilum-specific antibodies were found in 72% of sera and A. phagocytophilum DNA was present in 6.2% of spleens. The data indicate that A. phagocytophilum is present and widespread in Slovenian game animals and that game species are involved in the natural life cycle of A. phagocytophilum.

Clonal Spread of pESI-Positive Multidrug-Resistant ST32 Salmonella enterica Serovar Infantis Isolates among Broilers and Humans in Slovenia.

Salmonella enterica subsp. enterica serovar Infantis is the most prevalent serovar found in broilers and broiler meat and is among the top five serovars responsible for human infections in Europe. In 2008, a multidrug-resistant S. Infantis isolate emerged in Israel with a mosaic megaplasmid named pESI, associated with increased virulence, biofilm formation, and multidrug resistance. Since then, S. Infantis clones with pESI-like plasmids have been reported worldwide, replacing pESI-free clones. Here, we typed 161 S. Infantis isolates of poultry (n = 133) and human clinical (n = 28) origin using whole-genome sequencing. The isolates were collected between 2007 and 2021. In addition, we performed PacBio/Illumina sequencing for two representative pESI-like plasmids and compared them with publicly available sequences. All isolates belonged to sequence type 32 (ST32), except for one isolate that represented a novel single-locus variant of ST32. Core genome MLST (cgMLST) analysis revealed 14 clusters of genetically closely related isolates, of which four suggested broiler-to-human transmission of S. Infantis. pESI-like plasmids were present in 148/161 (91.9%) isolates; all were highly similar to the publicly available pESI-like sequences but lacked extended-spectrum beta-lactamase (ESBL) genes. PacBio/Illumina hybrid assembly allowed the reconstruction of two novel complete pESI variants. The present study revealed that the multidrug-resistant, pESI-positive S. Infantis clone became the predominant S. Infantis clone in Slovenian broilers and humans during the last decade. Continued surveillance of resistant S. Infantis clones along the food chain is needed to guide public health efforts. IMPORTANCE Salmonella Infantis clones with pESI-like plasmids harboring several virulence and resistance genes have been reported worldwide. In the present study, we compared the population structure of 161 Salmonella Infantis isolates obtained from humans and broilers in Slovenia from 2007 to 2021. Whole-genome sequencing showed that most human isolates clustered apart from broiler isolates, suggesting an alternative source of infection. Most isolates were multidrug resistant due to the presence of pESI-like plasmids, of which two variants (pS89 and pS19) were fully reconstructed using long-read sequencing. Both exhibited high similarity with the original Israeli pESI plasmid and German p2747 plasmid. The prototype plasmid pS89 harbored the typical pESI-associated resistance genes aadA1, qacEΔ1, sul1, and tet(A), which were absent in the truncated plasmid pS19.

Antimicrobial Resistance and Molecular Characterization of Methicillin-Resistant Staphylococcus aureus from Two Pig Farms: Longitudinal Study of LA-MRSA.

Pigs were identified as the most important reservoir of livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA), mostly belonging to the emergent zoonotic clonal complex (CC) 398. Here, we investigated the presence of MRSA in sows and piglets over a period of several months in two pig farms (intensive farm A and family-run farm B). Isolates underwent antimicrobial susceptibility testing, PCR characterization and spa typing. We collected 280 samples, namely 206 nasal swabs from pigs and 74 environmental samples from pig housings at 12 consecutive time points. A total of 120/161 (74.5%) and 75/119 (63.0%) samples were MRSA-positive in farms A and B, respectively. All isolates harbored mecA but lacked mecC and PVL-encoding genes. The identified spa types (t571, t034, t1250 and t898 in farm A, t1451 and t011 in farm B) were indicative of CC398. Antimicrobial resistance patterns (all multidrug resistant in farm A, 57.2% in farm B) depended on the farm, suggesting the impact of farm size and management practices on the prevalence and characteristics of MRSA. Due to the intermittent colonization of pigs and the high contamination of their immediate environment, MRSA status should be determined at the farm level when considering preventive measures or animal trade between farms.

Genomic insights into the emergence and spread of methicillin-resistant Staphylococcus pseudintermedius in veterinary clinics.

Staphylococcus pseudintermedius is a common cause of skin and soft tissue infections in dogs but can also cause infections in cats and humans. The frequency of methicillin-resistant S. pseudintermedius (MRSP) strains is increasing worldwide. Here, we obtained 43 MRSP isolates from dogs (n = 41), one cat (n = 1) and the small animal clinic environment (n = 1) in Slovenia from the period 2008-2018, which underwent whole-genome sequencing (WGS) and antimicrobial susceptibility testing. Five sequence types (STs) were identified, with ST71 (32/43) and ST551 (8/43) being the predominant. In Slovenia, ST551 was first detected in 2016, whereas a decrease in the frequency of ST71 was observed after 2015. All isolates were multidrug-resistant and most antimicrobial-resistant phenotypes could be linked to acquisition of the corresponding resistance genes or gene mutations. Core-genome multilocus sequence typing (cgMLST) revealed several potential MRSP transmission routes: (i) between two veterinary clinics by a single MRSP-positive dog, (ii) between the environment of a veterinary clinic and a dog, and (iii) between a canine and a feline patient through the contaminated environment of a veterinary clinic. Of the six dogs that were additionally sampled from 14 days to five months after the initial sampling, each harbored the same MRSP strain, suggesting a limited within-host diversity of MRSP in symptomatic dogs. The present results highlight the importance of MRSP-positive dogs in the spread of veterinary care-associated MRSP infections and call for the implementation of strict control measures to reduce MRSP contamination in veterinary clinic environments originating from animal-contact surfaces.

Genomic insights into Salmonella Choleraesuis var. Kunzendorf outbreak reveal possible interspecies transmission.

Salmonella enterica serovar Choleraesuis is a host-adapted serovar that causes serious infections in domestic pigs and wild boars. Here, we investigated an outbreak of salmonellosis in domestic pigs in Slovenia, 2018-2019. To assess the outbreak, 18 isolates from domestic pigs, wild boars, wild boar meat and a human patient underwent whole-genome sequencing (WGS). All isolates were of sequence type (ST) 145 and harbored no antimicrobial resistance genes or AMR-associated mutations. A single transmission cluster (≤ 6 alleles) of spatially (< 100 km) and temporally linked isolates was observed, comprising isolates of pig (n = 9), wild boar (n = 2) and human (n = 1) origin, and suggesting possible interspecies transmission. In all outbreak-related animal cases, septicemic salmonellosis was observed, accompanied in some cases by enteric symptoms. All pig isolates were linked to a single intensive breeding farm that distributed growers to small family farms. The same transport vehicles were used to distribute growers to family farms and also to transport livestock between neighboring countries. Both isolates that originated from the imported wild boar meat were genetically distant (≥ 122 alleles) from the outbreak cluster. The present results indicate the importance of screening domestic pigs and proper disinfection of transport vehicles to control the spread of S. Choleraesuis.

Feline Otitis Externa Caused by Methicillin-Resistant Staphylococcus aureus with Mixed Hemolytic Phenotype and Overview of Possible Genetic Backgrounds.

Methicillin-resistant Staphylococcus aureus (MRSA) is an important cause of nosocomial infections in humans, but its importance in small animal practice is increasing. Here, we present a case of feline otitis externa (OE) caused by MRSA; both hemolytic and nonhemolytic variants with a stable phenotype were recovered from the external auditory canal after infection was detected by routine otoscopy. One isolate per variant underwent antimicrobial susceptibility testing (AST) by broth microdilution method, conventional spa typing and whole-genome sequencing (WGS). The results showed that both variants were genetically related and were of sequence type (ST) 1327, SCCmec type IV and spa type t005. AST and WGS showed that both isolates were resistant to ß-lactams and sensitive to all tested non-ß-lactam antibiotics. Both isolates were pvl-negative, but encoded several other virulence genes (aur, hlgABC, sak, scn, seg, sei, sem, sen, seo and seu). Genetic background of the mixed hemolytic phenotype was not identified; no differences in the agr locus or other regulatory regions were detected. Three single-nucleotide polymorphisms were identified but could not be associated with hemolysis. This well-documented case of MRSA infection in companion animals adds to the reports of MRSA infections with a mixed hemolytic phenotype.

ERIC and WGS Typing of Paenibacillus larvae in Slovenia: Investigation of ERIC I Outbreaks.

Paenibacillus larvae is the causative agent of American foulbrood (AFB), a fatal disease of honeybee brood. Here, we obtained 506 P. larvae isolates originating from honey or brood samples and from different geographic regions of Slovenia in the period 2017-2019. In the first part of the study, we conducted ERIC-PCR typing to assess the frequency of ERIC types in Slovenia. Capillary electrophoresis was used for the analysis of ERIC patterns, revealing good separation efficiency and enabling easy lane-to-lane comparisons. ERIC II was the predominant type (70.2%), followed by ERIC I (29.8%); two slightly altered ERIC I banding patterns were observed but were not considered relevant for the discrimination of ERIC types. No evident spatiotemporal clustering of ERIC types was observed. To assess the clonality of the outbreak-related P. larvae ERIC I isolates, 59 isolates of this type underwent whole-genome sequencing (WGS). Whole-genome multilocus sequence typing (wgMLST) revealed seven ERIC I-ST2 outbreak clusters (≤35 allele differences) with the median intra-outbreak diversity ranging from 7 to 27 allele differences. In all seven clusters, the transmission of P. larvae outbreak clone within a 3-km radius (AFB zone) was observed, which could be explained by the activity of honeybees. In three clusters, the transmission of the outbreak clone between geographically distant apiaries was revealed, which could be explained by the activities of beekeepers such as migratory beekeeping and trading of bee colonies. The present findings reinforce the importance of beekeeping activities in the transmission of P. larvae. WGS should be used as a reference typing method for the detection of P. larvae transmission clusters.

Novel TaqMan PCR Assay for the Quantification of Paenibacillus larvae Spores in Bee-Related Samples.

Paenibacillus larvae is the causative agent of American foulbrood (AFB), a devastating disease of honeybees. P. larvae spore counts in bee-related samples correlate with the presence of AFB symptoms and may, therefore, be used to identify at-risk colonies. Here, we constructed a TaqMan-based real-time PCR (qPCR) assay targeting a single-copy chromosomal metalloproteinase gene for reliable quantification of P. larvae. The assay was calibrated using digital PCR (dPCR) to allow absolute quantification of P. larvae spores in honey and hive debris samples. The limits of detection and quantification were 8 and 58 spores/g for honey and 188 and 707 spores/mL for hive debris, respectively. To assess the association between AFB clinical symptoms and spore counts, we quantified spores in honey and hive debris samples originating from honeybee colonies with known severity of clinical symptoms. Spore counts in AFB-positive colonies were significantly higher than those in asymptomatic colonies but did not differ significantly with regard to the severity of clinical symptoms. For honey, the average spore germination rate was 0.52% (range = 0.04-6.05%), indicating poor and inconsistent in vitro germination. The newly developed qPCR assay allows reliable detection and quantification of P. larvae in honey and hive debris samples but can also be extended to other sample types.

A Suggested Diagnostic Approach for Sporadic Anthrax in Cattle to Protect Public Health.

The repeated occurrence of anthrax in grazing animals should be a reminder of a widespread presence of Bacillus anthracis spores in the environment. Its rapid diagnosis is critical to protect public health. Here, we report a case of anthrax in cattle that was investigated using conventional and molecular methods. In 2015, six cows suddenly died within three days and the number of dead animals increased to a total of 12 within two weeks. At necropsy, anthrax was suspected. Therefore, spleen tissue samples were collected (from 6/12 animals) and laboratory tests (microscopy, cultivation, and real-time PCR) performed. The results of tissue staining for microscopy and cultivation were in congruence, while B. anthracis real-time PCR outperformed both. Spleen tissues from all six animals were real-time PCR-positive, while B. anthracis was successfully cultivated and detected by microscopy from the spleen of only three animals. Additionally, the ear tissue from another (1/12) cow tested positive by real-time PCR, supporting the suitability of ear clippings for molecular confirmation of B. anthracis. Genotyping of the isolates using multiple-locus variable-number tandem repeat analysis (MLVA) revealed a common source of infection as all three typed isolates had an indistinguishable MLVA genotype, which has not been observed previously in Europe. The results indicate that molecular testing should be selected as the first-line tool for confirming anthrax outbreaks in animals to ensure timely protection of public health.

Infectious Abortions in Small Ruminants: Challenges for Diagnosis and Public Health.

In this study, we report an abortion outbreak in a ruminant herd consisting of goats, sheep, and cows, with scenarios in two consecutive years. In early 2017, abortions occurred in ∼70% of goats and 66% tested positive for Coxiella burnetii (C. burnetii) and 40% of goats were positive for Chlamydophila abortus (C. abortus). In February 2018, the same herd reported an abortion rate of 75%, with 55% positive for C. burnetii, 36% for C. abortus, and 22% for Toxoplasma gondii. Six goat milk samples were positive for C. burnetii by molecular analysis. Three family members were positive for C. burnetii. C. burnetii could be considered as the main cause of abortions in the first and second year. Animals that undergo an infection and abortion are prone to secondary infections. Vaccination or other rapid interventions should be initiated to protect animals and humans.

Livestock-associated methicillin-resistant Staphylococcus aureus: Establishing links between animals and humans on livestock holdings.

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) represents a concern in both human and veterinary medicine. The aim of this study was to investigate potential LA-MRSA transmission between animals and humans in rural settings. To this aim, a study was designed to include 14 farms in Slovenia, which were selected on the basis of a farmer (initial patient) with confirmed LA-MRSA infection and regular animal contacts. On all farms, the initial patients, their household members, animals and barn environment were analysed for the presence of LA-MRSA. In addition, the epidemiologically linked hospital-related LA-MRSA isolates were included to investigate possible nosocomial transmissions. On five farms, LA-MRSA was discovered both in animals and in humans. In total, 49 LA-MRSA isolates of different origins underwent whole-genome sequencing, antimicrobial susceptibility testing and spa typing. All 49 isolates belonged to the sequence type 398 (ST398), spa types t011 and t034, and harboured staphylococcal chromosomal cassette mec Vc. High levels of concordance between resistance phenotypes and genotypes were observed. No transmission pairs between animals and initial patients were discovered. However, several isolates originating from farm animals and other household members formed clusters with pairwise distances of ≤14 single nucleotide polymorphisms (SNPs), indicating recent transmission events. In addition, three closely related isolates (0 SNP) form hospitalized patients were observed, indicating a possible nosocomial transmission. Two hospital-related isolates harboured the immune evasion cluster genes, which are associated with adaptation to the human host; however, these two isolates differed in >30 SNPs from the remaining isolates. Characteristics of LA-MRSA from Slovenia reflect those observed previously in other European studies. Immune evasion cluster-positive LA-MRSA ST398 suggests its re-adaptation to the human host and calls for a closer monitoring of such emerging LA-MRSA lineages, in addition to monitoring and preventing the introduction of LA-MRSA from farms to hospitals where transmission is highly plausible.

A pulsed-field gel electrophoresis study of the genetic diversity of Campylobacter jejuni and Campylobacter coli in poultry flocks in Slovenia.

Campylobacter jejuni and C. coli have recently become the most frequent cause of bacterial foodborne enteric infection in most industrialised countries. Consumption and handling of undercooked contaminated poultry meat was identified as an important risk factor for human campylobacteriosis. The aim of this study was to ascertain the genetic diversity of C. jejuni and C. coli strains isolated from poultry in Slovenia. A total of 68 isolates (42 C. jejuni , 26 C. coli ) from faeces (n = 48), meat (n = 15) and skin/carcasses (n = 5) of chicken (n = 60) and turkey samples (n = 5) were analysed by pulsed-field gel electrophoresis. Sma I macrorestriction discriminated between C. jejuni and C. coli isolates. C. jejuni isolates exhibited a higher degree of diversity compared to C. coli isolates. In the C. jejuni group, a number of small clusters were apparent, while C. coli strains formed less but larger clusters. Additional Kpn I digestion of selected isolates resulted in poor subtyping. Strains with identical or very similar profiles were found on different farms, either in the same or different regions and time periods. Some of the clones indicated possible cross-contamination at slaughterhouses.