Time-calibrated phylogenetic and chromosomal mobilome analyses of Staphylococcus aureus CC398 reveal geographical and host-related evolution.

An international collection of Staphylococcus aureus of clonal complex (CC) 398 from diverse hosts spanning all continents and a 30 year-period is studied based on whole-genome sequencing (WGS) data. The collection consists of publicly available genomic data from 2994 strains and 134 recently sequenced Swiss methicillin-resistant S. aureus (MRSA) CC398 strains. A time-calibrated phylogeny reveals the presence of distinct phylogroups present in Asia, North and South America and Europe. European MRSA diverged from methicillin-susceptible S. aureus (MSSA) at the beginning of the 1950s. Two major European phylogroups (EP4 and EP5), which diverged approximately 1974, are the main drivers of MRSA CC398 spread in Europe. Within EP5, an emergent MRSA lineage spreading among the European horse population (EP5-Leq) diverged approximately 1996 from the pig lineage (EP5-Lpg), and also contains human-related strains. EP5-Leq is characterized by staphylococcal cassette chromosome mec (SCCmec) IVa and spa type t011 (CC398-IVa-t011), and EP5-Lpg by CC398-SCCmecVc-t011. The lineage-specific antibiotic resistance and virulence gene patterns are mostly mediated by the acquisition of mobile genetic elements like SCCmec, S. aureus Genomic Islands (SaGIs), prophages and transposons. Different combinations of virulence factors are present on S. aureus pathogenicity islands (SaPIs), and novel antimicrobial resistance gene containing elements are associated with certain lineages expanding in Europe. This WGS-based analysis reveals the actual evolutionary trajectory and epidemiological trend of the international MRSA CC398 population considering host, temporal, geographical and molecular factors. It provides a baseline for global WGS-based One-Health studies of adaptive evolution of MRSA CC398 as well as for local outbreak investigations.

Azithromycin resistance in Escherichia coli and Salmonella from food-producing animals and meat in Europe.

OBJECTIVES: To characterize the genetic basis of azithromycin resistance in Escherichia coli and Salmonella collected within the EU harmonized antimicrobial resistance (AMR) surveillance programme in 2014-18 and the Danish AMR surveillance programme in 2016-19. METHODS: WGS data of 1007 E. coli [165 azithromycin resistant (MIC > 16 mg/L)] and 269 Salmonella [29 azithromycin resistant (MIC > 16 mg/L)] were screened for acquired macrolide resistance genes and mutations in rplDV, 23S rRNA and acrB genes using ResFinder v4.0, AMRFinder Plus and custom scripts. Genotype-phenotype concordance was determined for all isolates. Transferability of mef(C)-mph(G)-carrying plasmids was assessed by conjugation experiments. RESULTS: mph(A), mph(B), mef(B), erm(B) and mef(C)-mph(G) were detected in E. coli and Salmonella, whereas erm(C), erm(42), ere(A) and mph(E)-msr(E) were detected in E. coli only. The presence of macrolide resistance genes, alone or in combination, was concordant with the azithromycin-resistant phenotype in 69% of isolates. Distinct mph(A) operon structures were observed in azithromycin-susceptible (n = 50) and -resistant (n = 136) isolates. mef(C)-mph(G) were detected in porcine and bovine E. coli and in porcine Salmonella enterica serovar Derby and Salmonella enterica 1,4, [5],12:i:-, flanked downstream by ISCR2 or TnAs1 and associated with IncIγ and IncFII plasmids. CONCLUSIONS: Diverse azithromycin resistance genes were detected in E. coli and Salmonella from food-producing animals and meat in Europe. Azithromycin resistance genes mef(C)-mph(G) and erm(42) appear to be emerging primarily in porcine E. coli isolates. The identification of distinct mph(A) operon structures in susceptible and resistant isolates increases the predictive power of WGS-based methods for in silico detection of azithromycin resistance in Enterobacterales.

Real time detection of pathogenic bacteria in veterinary microbiology using isothermal microcalorimetry - A different approach.

With today's challenges regarding antibiotic resistance and the importance of the implementation of prudent use of antibiotics, fast and reliable diagnostic tools for bacterial infections and subsequent antimicrobial susceptibility testing are of utmost relevance. Isothermal microcalorimetry (IMC) is a broadly applicable method, with which metabolic heat flow in reproducing bacteria can be measured in real time. To the best of the authors' knowledge, this is the first report on examination of 124 urine samples from feline and canine urinary tract infection with an IMC-based prototype instrument. A concentration-dependent time of peak heat flow by dilution series with Escherichia coli and Enterococcus faecalis reference strains demonstrated the general good performance of the prototype for detection of these bacteria. With diagnostic culture being set as a gold standard, the diagnostic sensitivity of IMC compared to bacteriological culture was 80 %, the diagnostic specificity was 97 %. With a Cohens' kappa value (κ) of 0.80, the two methods show good concordance. The results from our study demonstrate that the IMC technology is suitable to allow reliable, but much faster detection of bacteria than conventional culture, especially for Escherichia coli. Thus, implementing IMC technology could markedly speed up the bacteriological diagnostic process in veterinary medicine.

Pilot testing the EARS-Vet surveillance network for antibiotic resistance in bacterial pathogens from animals in the EU/EEA.

Introduction: As part of the EU Joint Action on Antimicrobial Resistance (AMR) and Healthcare-Associated Infections, an initiative has been launched to build the European AMR Surveillance network in veterinary medicine (EARS-Vet). So far, activities included mapping national systems for AMR surveillance in animal bacterial pathogens, and defining the EARS-Vet objectives, scope, and standards. Drawing on these milestones, this study aimed to pilot test EARS-Vet surveillance, namely to (i) assess available data, (ii) perform cross-country analyses, and (iii) identify potential challenges and develop recommendations to improve future data collection and analysis. Methods: Eleven partners from nine EU/EEA countries participated and shared available data for the period 2016-2020, representing a total of 140,110 bacterial isolates and 1,302,389 entries (isolate-antibiotic agent combinations). Results: Collected data were highly diverse and fragmented. Using a standardized approach and interpretation with epidemiological cut-offs, we were able to jointly analyze AMR trends of 53 combinations of animal host-bacteria-antibiotic categories of interest to EARS-Vet. This work demonstrated substantial variations of resistance levels, both among and within countries (e.g., between animal host species). Discussion: Key issues at this stage include the lack of harmonization of antimicrobial susceptibility testing methods used in European surveillance systems and veterinary diagnostic laboratories, the absence of interpretation criteria for many bacteria-antibiotic combinations of interest, and the lack of data from a lot of EU/EEA countries where little or even surveillance currently exists. Still, this pilot study provides a proof-of-concept of what EARS-Vet can achieve. Results form an important basis to shape future systematic data collection and analysis.

Surgical site infection after 769 Tibial Plateau Leveling Osteotomies.

Objective: To report surgical site infections (SSI) after Tibial Plateau Leveling Osteotomy (TPLO), treatment course, associated risk factors, bacterial isolates and antimicrobial resistance. Study design: Retrospective clinical cohort study. Study population: Six hundred and twenty seven dogs and 769 TPLO procedures. Methods: Data from electronic medical records of dogs undergoing TPLO between 2005 and 2015 at a single institution have been retrospectively reviewed. A generalized mixed logistic regression was used to determine possible risk factors. The Chi-Square test of independence was used to examine the relationship between the isolation of multidrug-resistant (MDR) bacteria and the development of major infections undergoing additional surgical treatment. To assess the correlation between number of SSI and number MDR isolate per year, Pearson's correlation coefficient was calculated. Results: The overall complication rate was 19.3% (n = 149). SSI was most frequent with 8.5% (n = 65). Major SSI occurred in 6.8% (n = 52) TPLO (80.0% SSI). Staphylococcus (S.) pseudintermedius (n = 37) and S. aureus (n = 10) were most frequently isolated. Multidrug-resistant bacteria were identified in 2.7% (n = 21) TPLO (32.3% SSI) but were not associated with major SSI (p = 0.426). There was a strong positive correlation between number of MDR isolates per year and number of SSI per year [r (9) = 0.79, p = 0.004]. Factors associated with SSI were previous TPLO in the contralateral stifle (p = 0.02, OR = 2.01, 95% CI = 1.11-3.64) and German Shepherd dogs (p = 0.035, OR = 4.41, 95% CI = 1.11-17.54). The use of non-locking implants was found to be protective (p = 0.02, OR = 0.179, 95% CI = 0.18-0.77). Clinical significance: Infection with multidrug-resistant bacteria is an emerging problem in veterinary practice and treatment is challenging. The incidence of major SSI was found to be high but was not associated with the isolation of MDR bacteria.

Genomic Characterization and Antimicrobial Susceptibility of Dromedary-Associated Staphylococcaceae from the Horn of Africa.

Members of the Staphylococcaceae family, particularly those of the genus Staphylococcus, encompass important human and animal pathogens. We collected and characterized Staphylococcaceae strains from apparently healthy and diseased camels (n = 84) and cattle (n = 7) in Somalia and Kenya. We phenotypically characterized the strains, including their antimicrobial inhibitory concentrations. Then, we sequenced their genomes using long-read sequencing, closed their genomes, and subsequently compared and mapped their virulence- and resistance-associated gene pools. Genome-based phylogenetics revealed 13 known Staphylococcaceae and at least two novel species. East African strains of different species encompassed novel sequence types and phylogenetically distant clades. About one-third of the strains had non-wild-type MICs. They were resistant to at least one of the following antimicrobials: tetracycline, benzylpenicillin, oxacillin, erythromycin, clindamycin, trimethoprim, gentamicin, or streptomycin, encoded by tet(K), blaZ/blaARL, mecA/mecA1, msrA/mphC, salA, dfrG, aacA-aphD, and str, respectively. We identified the first methicillin- and multidrug-resistant camel S. epidermidis strain of sequence type (ST) 1136 in East Africa. The pool of virulence-encoding genes was largest in the S. aureus strains, as expected, although other rather commensal strains contained distinct virulence-encoding genes. We identified toxin-antitoxin (TA) systems such as the hicA/hicB and abiEii/abiEi families, reported here for the first time for certain species of Staphylococcaceae. All strains contained at least one intact prophage sequence, mainly belonging to the Siphoviridae family. We pinpointed potential horizontal gene transfers between camel and cattle strains and also across distinct Staphylococcaceae clades and species. IMPORTANCE Camels are a high value and crucial livestock species in arid and semiarid regions of Africa and gain importance giving the impact of climate change on traditional livestock species. Our current knowledge with respect to Staphylococcaceae infecting camels is very limited compared to that for other livestock species. Better knowledge will foster the development of specific diagnostic assays, guide promising antimicrobial treatment options, and inform about potential zoonotic risks. We characterized 84 Staphylococcaceae strains isolated from camels with respect to their antimicrobial resistance and virulence traits. We detected potentially novel Staphylococcus species, resistances to different classes of antimicrobials, and the first camel multidrug-resistant S. epidermidis strain of sequence type 1136.

Prevalence and antimicrobial resistance of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) in Swiss sheep flocks.

Salmonella (S.) enterica subspecies diarizonae (IIIb) serovar 61:k:1,5,(7) (S. IIIb 61:k:1,5,(7)) is considered to be sheep-associated, as it can be found in the intestine, tonsils and nose of clinically healthy sheep, but it has also been described in separate clinical disorders in sheep. In particular, S. IIIb 61:k:1,5,(7) is described as the causative agent of chronic proliferative rhinitis (CPR) in sheep. In Switzerland, CPR in sheep due to S. IIIb 61:k:1,5,(7) was first described in 2017 in a flock of Texel sheep. Therefore, we assessed the prevalence of S. IIIb 61:k:1,5,(7) within the Swiss sheep population using a representative sampling strategy. From May 2017 to June 2018 a total of 681 nasal swabs from individual clinically healthy sheep of 141 different flocks throughout Switzerland were taken. Swabs were analysed by selective enrichment for the presence of S. IIIb 61:k:1,5,(7). Additionally, antimicrobial resistance of the isolates was determined by broth microdilution. A total of 146 out of 681 nasal swabs tested positive for S. IIIb 61:k:1,5,(7), which corresponds to a prevalence on animal level of 21% (95%CI 18%-25%). In 73 out of 141 flocks tested, at least one sheep tested positive for S. IIIb 61:k:1.5,(7), resulting in a minimal prevalence on flock level of 52% (95%CI 43%-60%). Positive flocks were found in all cantons except the canton of Jura. Adults were significantly more affected than sheep under one year/lambs and positive sheep were found in several breeds. No microbiologically resistant isolates were detected, except for one isolate showing resistance against ampicillin. Because of its widespread occurrence in the Swiss sheep population, further research should focus on the pathogenic impact of S. IIIb 61:k:1,5,(7) on the health status of sheep.

Seroprevalence of Mycoplasma hyopneumoniae in sows fifteen years after implementation of a control programme for enzootic pneumonia in Switzerland.

Mycoplasma hyopneumoniae is the etiological agent of enzootic pneumonia (EP), an economically important chronic respiratory disease in pigs. M. hyopneumoniae impacts the mucociliary clearance system by disrupting the cilia and modulates the immune response, resulting in intermittent dry non-productive cough. For progressive control of EP in Switzerland, a corresponding programme was fully implemented in 2004. It is based on total depopulation strategies of affected fattening farms as well as partial depopulation in breeding farms. Surveillance of EP status in Switzerland is mainly based on real-time PCR of nasal swabs from coughing animals or suspicious lungs and thereby sporadic cases are still observed every year. In order to obtain information on the seroprevalence, serum samples of 5021 sows from 968 farms collected in 2018 at eight different slaughterhouses were analyzed for the presence of M. hyopneumoniae-specific antibodies using a commercial ELISA kit. The overall seroprevalence was low with 0.98% of sows testing positive and these seropositive animals could be allocated to 3.92% of farms tested. Most seropositive farms presented weakly positive singleton reactors and only one farm showed several strongly seropositive animals. In conclusion, the serological status mirrors the successful progressive control of M. hyopneumoniae in the Swiss domestic pig population over the years. The current study underlines the added value of serological testing in the surveillance of EP in a country with low prevalence and confirms the sustained benefit of strategic control programmes.

Macrococcus armenti sp. nov., a novel bacterium isolated from the skin and nasal cavities of healthy pigs and calves.

Gram-positive coccoid bacteria were isolated from the nasal cavities of pigs and calves as well as from axillar and inguinal skin regions of pigs. Phylogenetic analysis of seven strains based on complete genome, 16S rRNA, hsp60, dnaJ, rpoB and sodA gene sequences and MALDI-TOF MS profiles revealed that they belonged to the genus Macrococcus with the closest relatedness to Macrococcus canis, Macrococcus caseolyticus subsp. caseolyticus and Macrococcus caseolyticus subsp. hominis. DNA relatedness of the type strain JEK37T with the type strains of M. canis, M. caseolyticus subsp. caseolyticus and M. caseolyticus subsp. hominis was 23.4, 23.1 and 23.0 % by digital DNA-DNA hybridization and 80.39, 80.45 and 80.87 % by average nucleotide identity (ANI) calculations, confirming that they do not belong to the same species. The DNA G+C content of JEK37T was 35.65 mol%. The novel strains can be differentiated from M. canis KM 45013T by the ability to fermentate d-ribose and by the absence of DNAase production and haemolysis, from M. caseolyticus subsp. caseolyticus CCUG 15606T by the ability to fermentate sucrose and from both species by the inability to grow in 9 and 12% NaCl. They differ from M. caseolyiticus subsp. hominis by the presence of α-glucosidase. The most common fatty acids of JEK37T were C14 : 0, C18 : 1 ω9c and C18 : 0. Known polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, aminolipid, aminoglycolipid, aminophospholipid, glycolipid and phospholipid. Cell-wall peptidoglycan of JEK37T was of type A3α l-Lys-Gly2-L-Ser-Gly (similar to A11.3) and the respiratory quinolone was menaquinone 6. Based on their genotypic and chemotaxonomic characteristics, these strains represent a novel species of the genus Macrococcus, for which we propose the name Macrococcus armenti sp. nov. The type strain is JEK37T (=DSM 112712T=CCOS 1982T).

Feedborne Salmonella enterica Serovar Jerusalem Outbreak in Different Organic Poultry Flocks in Switzerland and Italy Linked to Soya Expeller.

Poultry feed is a leading source of Salmonella infection in poultry. In Switzerland, heat-treated feed is used to reduce Salmonella incursions into flocks in conventional poultry production. By contrast, organic feed is only treated with organic acids. In 2019, the Swiss National Reference Center for Enteropathogenic Bacteria identified the rare serovar S. Jerusalem from samples of organic soya feed. Further, in July 2020, the European Union's Rapid Alert System for Food and Feed published a notification of the detection of S. Jerusalem in soya expeller from Italy. During 2020, seven S. Jerusalem isolates from seven different poultry productions distributed over six cantons in Switzerland were reported, providing further evidence of a possible outbreak. Using whole-genome sequencing (WGS), S. Jerusalem isolates from feed and from animals in Switzerland were further characterized and compared to S. Jerusalem from organic poultry farm environments in Italy. WGS results showed that feed isolates and isolates from Swiss and Italian poultry flocks belonged to the sequence type (ST)1028, grouped in a very tight cluster, and were closely related. This outbreak highlights the risk of spreading Salmonella by feed and emphasizes the need for a heat-treatment process for feed, also in organic poultry production.

Complete Genome Sequences of the Methicillin-Resistant Strain Staphylococcus aureus 17Gst354 and Its Prophage Staphylococcus Phage vB_StaphS-IVBph354.

We report the complete 2,783,931-bp circular genome sequence of the human methicillin-resistant strain Staphylococcus aureus 17Gst354, isolated from a nasal swab. The strain possessed an additional 4,397-bp plasmid. Moreover, we induced and sequenced its temperate phage Staphylococcus phage vB_StaphS-IVBph354, which has a circular genome of 41,970 bp.

Dynamics of extended-spectrum cephalosporin-resistant Escherichia coli in pig farms: A longitudinal study.

OBJECTIVES: Point prevalence estimates of extended-spectrum cephalosporin-resistant Escherichia coli (ESC-R-Ec) are important surveillance measures but may not uncover the ESC-R-Ec dynamics within pig farms. A longitudinal study was therefore performed by sampling individual pigs, pig farmers and the environment. METHODS: On average, 30 (range 10-46) piglets of 31 Swiss farms were sampled during the suckling, weaning and fattening stages (n= 2437 samples). In addition, stool from pig farmers and environmental samples were obtained and metadata collected by questionnaires. ESC-R-Ec was identified by routine culture, and clonal relationships and resistance genes were derived from whole genome sequencing data. RESULTS: Working on pig farms was not associated with an increased prevalence of ESC-R-Ec in humans. ESC-R-Ec prevalence significantly decreased from 6.2% to 3.9% and 1.8% for the suckling, weaned and fattening pigs, respectively (P < 0.001). Within the 57 ESC-R-positive suckling piglets, persisting carriage was detected in 25 animals at two consecutive time points and one animal at three consecutive time points. Clonal spread (n=7 farms, 22.6%) and horizontal gene transfer (n=1 farm, 3%) within pigs but not between humans and animals was detected. Liquid manure (n=10 samples, 16.7%) was identified as the major environmental reservoir of ESC-R-Ec in the pig farm environment. CONCLUSIONS: Pig farming practices like all-in-all-out systems, but not antimicrobial usage, were associated with reduced risk of ESC-R-Ec at the farm level. As carriage duration is normally short within the individual pigs, the risk of recolonisation and clonal spread of ESC-R-Ec might be reduced by applying appropriate decontamination strategies.

Evaluation of oral fluids for surveillance of foodborne and zoonotic pathogens in pig farms.

The use of oral fluid (OF) to detect zoonotic pathogens in pigs has been only scarcely assessed. We evaluated OF as a potential specimen for detection by culture of methicillin-resistant Staphylococcus aureus (MRSA) and Yersinia enterocolitica, and the detection of antibodies against Salmonella spp. and hepatitis E virus (HEV) using commercial ELISAs. Samples from 33 pig farms were collected at the beginning and end of the fattening period. Results of the OF samples were compared with the results of serum samples and nasal swabs from individual pigs and pen floor fecal samples, using the Cohen kappa (κ) and the McNemar test. For Salmonella spp. antibodies, OF samples were negative, although the corresponding serum samples were positive. The detection of HEV antibodies in sera and OF had agreement at the first sampling, and poor and significant agreement at the second sampling (κ = 0.185, McNemar p = 0.238; κ = 0.088, McNemar p < 0.001). At both sampling times, the detection of MRSA in nasal swabs and OF showed agreement (κ = 0.466, McNemar p = 0.077; κ = 0.603, McNemar p = 1); agreement was seen for the detection of Y. enterocolitica in fecal and OF samples (κ = 0.012, McNemar p = 0.868; κ = 0.082, McNemar p = 0.061, respectively). According to the McNemar test, the use of pen-based OFs is more feasible for the detection of MRSA and Y. enterocolitica by culture than is detection of antibodies by commercial ELISA.

Influence of pig farming on human Gut Microbiota: role of airborne microbial communities.

It has been hypothesized that both genetics and diet influence the composition of the human cecal microbiota. However, it remains unclear whether and how occupational exposure to microbes impacts the microbial communities in human guts. Using a One Health approach, we visited pig farms (n = 26) and collected stool specimens from pig workers (n = 59), pig barn air samples (n = 19), and rectal swabs from pigs at three different growth stages (n = 144). Stool samples from cattle workers were included as a control group (n = 22). Each sample's microbiota was characterized using 16S rRNA gene sequencing and the DADA2 pipeline.We obtained a significantly different clustering of the microbial compositions of pig and cattle workers by permutational multivariate analysis of variance (PERMANOVA; P < .001). Workers primarily exposed to pigs had higher relative abundances of Prevotellaceae and less Bacteroidaceae than workers exposed to cattle. We also found that the microbial compositions of pig workers' stool samples shared extensive fractions with the samples from their pigs. We also identified amplicon sequencing variants (ASVs) in the airborne microbiota which were likely involved in zoonotic transmission events.We hypothesize that ASVs originating from pig feces are aerosolized and, through breathing, get trapped in the pig farm workers' upper respiratory tract from where they can get swallowed. Consequently, some of the animal associated ASVs are transferred into the gastrointestinal tracts (GITs) which leads to changes in the composition of the human gut microbiota. The importance of this finding for human health must be investigated further.

The influence of clinical severity and topical antimicrobial treatment on bacteriological culture and the microbiota of equine pastern dermatitis.

BACKGROUND: Equine pastern dermatitis (EPD) is a common dermatological problem in horses, yet its aetiology and pathogenesis are poorly understood. OBJECTIVES: This study aimed to investigate the effects of lesion severity and topical antimicrobial treatment on bacterial flora of EPD-affected skin. ANIMALS: Sixteen horses with EPD were investigated. METHODS AND MATERIALS: An observational study was conducted by assigning a clinical severity score ranging from 0 (macroscopically nonlesional) to 21 (severe), and sampling the most and least severely affected limbs of 16 horses (32 limbs) for bacteriological culture and 16S rRNA sequencing. Topical antimicrobial treatment in the month before sampling was recorded. The limbs were allocated to a nonlesional or mildly affected group (Group A, score 0-3) and a moderate to severely affected group (Group B, score 4-21). RESULTS: The most commonly cultured bacterial species was Staphylococcus aureus (one of 15 Group A versus nine of 17 Group B). Within Group B, S. aureus was found in three of six limbs treated with topical antimicrobials and in six of 11 untreated limbs. ß-haemolytic streptococci (three of 32) and Trueperella pyogenes (two of 32) also were cultured exclusively in the untreated limbs of Group B. Staphylococci and streptococci were found more often by 16S rRNA sequencing than in culture. Limbs with higher lesion severity and topical antimicrobial treatment appeared to have a lower alpha diversity and different beta diversity compared to milder and untreated lesions. CONCLUSIONS AND CLINICAL IMPORTANCE: Observed differences in microbiota of equine skin are likely to be linked to the presence and severity of EPD and topical antimicrobial treatment. Further research is needed to establish causal bacteria.

Driving Laboratory Standardization of Bacterial Culture and Antimicrobial Susceptibility Testing in Veterinary Clinical Microbiology in Europe and Beyond.

Globally, antimicrobial resistance is one of the most important public health challenges in which the clinical microbiology laboratory plays a critical role by providing guidance for antimicrobial treatment. Despite the recognition of its importance, there is still a real need for the standardized training of clinical microbiologists and harmonization of diagnostic procedures. This is particularly true for veterinary clinical microbiology, where additional challenges exist when microbiologists are trying to fulfill a professional role very similar to that of their colleagues working in human microbiology laboratories. The specific points that need addressing to improve the outputs of veterinary microbiology laboratories discussed here include (i) harmonization of methodologies used by veterinary laboratories for antimicrobial susceptibility testing (AST); (ii) specific guidelines for interpretation and reporting of AST results for animal pathogens; (iii) guidelines for detection of antimicrobial resistance mechanisms in animal isolates; (iv) standardization of diagnostic procedures for animal clinical specimens; and (v) the need to train more veterinary clinical microbiology specialists. However, there is now a plan to address these issues, led by the European Network for Optimization of Veterinary Antimicrobial Treatment (ENOVAT), which is bringing together experts in veterinary microbiology, pharmacology, epidemiology, and antimicrobial stewardship from Europe and wider afield. ENOVAT is aiming to work with project partners toward standardization and harmonization of laboratory methodologies and optimization of veterinary antimicrobial treatment. Ultimately, the project may provide a mechanism for standardization and harmonization of veterinary clinical microbiology methodologies that could then be used as a template for implementation at a wider international level.

Complete Genome Sequences of Four Brucella suis Strains Isolated from Swiss Wild Boars.

We present the complete genomes of four Brucella suis biovar 2 isolates that were obtained from wild boars in Switzerland in 2008 and 2009. Genomes were sequenced with PacBio technology, contained two chromosomes each, had a genome size of 3.3 Mbp, and contained more than 3,225 genes per genome.

Assessing Campylobacter Colonization of Broiler Herds Ante Mortem and Monitoring Campylobacter Contamination Post Mortem by qPCR.

Human campylobacteriosis is the most prevalent zoonosis, with chicken meat contributing substantially to the number of cases. Measures to avoid or at least reduce exposure by meat contaminated with Campylobacter (C.) spp. are needed. With regard to the process hygiene criterion introduced in 2018 for Campylobacter spp. on broiler carcasses, we evaluated the performance of a recently developed quantitative real-time PCR (qPCR) for C. jejuni/coli on random caecal samples and chicken meat. With the qPCR on pooled caecal samples not only C. jejuni/coli positive (69.6%) versus negative broiler herds (30.4%) were identified, but herds highly colonized with C. jejuni/coli (39.4%) could also be identified. From the chicken meat samples, 8.0% were positive for C. jejuni/coli by qPCR and 0.7% by enumeration (>10 cfu/g) compared to 58.3% using cultural enrichment. Given the higher sensitivity, the qPCR method could replace the currently used enumeration method to assess the process hygiene criterion for Campylobacter spp. on broiler carcasses. Moreover, with the qPCR, a reliable identification of C. jejuni/coli colonized incoming broiler herds a few days before slaughter is feasible, which provides important information to optimize slaughter processes. Finally, identifying and monitoring herds with high C. jejuni/coli colonization rates could help to individually improve biosecurity measures at farm level, eventually reducing the C. jejuni/coli load on chicken meat.

Campylobacter jejuni from Canine and Bovine Cases of Campylobacteriosis Express High Antimicrobial Resistance Rates against (Fluoro)quinolones and Tetracyclines.

Campylobacter (C.) spp. from poultry is the main source of foodborne human campylobacteriosis, but diseased pets and cattle shedding Campylobacter spp. may contribute sporadically as a source of human infection. As fluoroquinolones are one of the drugs of choice for the treatment of severe human campylobacteriosis, the resistance rates of C. jejuni and C. coli from poultry against antibiotics, including fluoroquinolones, are monitored within the European program on antimicrobial resistance (AMR) in livestock. However, much less is published on the AMR rates of C.jejuni and C. coli from pets and cattle. Therefore, C. jejuni and C. coli isolated from diseased animals were tested phenotypically for AMR, and associated AMR genes or mutations were identified by whole genome sequencing. High rates of resistance to (fluoro)quinolones (41%) and tetracyclines (61.1%) were found in C. jejuni (n = 29/66). (Fluoro)quinolone resistance was associated with the known point mutation in the quinolone resistance-determining region (QRDR) of gyrA, and tetracycline resistance was mostly caused by the tet(O) gene. These high rates of resistance, especially to critically important antibiotics in C. jejuni and C. coli, are worrisome not only in veterinary medicine. Efforts to preserve the efficacy of important antimicrobial treatment options in human and veterinary medicine have to be strengthened in the future.