Objectives WGS-based antimicrobial susceptibility testing (AST) is as reliable as phenotypic AST for several antimicrobial/bacterial species combinations. However, routine use of WGS-based AST is hindered by the need for bioinformatics skills and knowledge of antimicrobial resistance (AMR) determinants to operate the vast majority of tools developed to date. By leveraging on ResFinder and PointFinder, two freely accessible tools that can also assist users without bioinformatics skills, we aimed at increasing their speed and providing an easily interpretable antibiogram as output. Methods The ResFinder code was re-written to process raw reads and use Kmer-based alignment. The existing ResFinder and PointFinder databases were revised and expanded. Additional databases were developed including a genotype-to-phenotype key associating each AMR determinant with a phenotype at the antimicrobial compound level, and species-specific panels for in silico antibiograms. ResFinder 4.0 was validated using Escherichia coli (n = 584), Salmonella spp. (n = 1081), Campylobacter jejuni (n = 239), Enterococcus faecium (n = 106), Enterococcus faecalis (n = 50) and Staphylococcus aureus (n = 163) exhibiting different AST profiles, and from different human and animal sources and geographical origins. Results Genotype–phenotype concordance was ≥95% for 46/51 and 25/32 of the antimicrobial/species combinations evaluated for Gram-negative and Gram-positive bacteria, respectively. When genotype–phenotype concordance was <95%, discrepancies were mainly linked to criteria for interpretation of phenotypic tests and suboptimal sequence quality, and not to ResFinder 4.0 performance. Conclusions WGS-based AST using ResFinder 4.0 provides in silico antibiograms as reliable as those obtained by phenotypic AST at least for the bacterial species/antimicrobial agents of major public health relevance considered.

Campylobacter jejuni and Campylobacter coli are recognized as the most common causative agents of bacterial gastroenteritis in the world. Humans most often become infected by ingesting contaminated food, especially undercooked chicken, but also other sources of bacteria have been described. Campylobacteriosis is normally a self-limiting disease. Antimicrobial treatment is needed only in patients with more severe disease and in those who are immunologically compromised. The most common antimicrobial agents used in the treatment of Campylobacter infections are macrolides, such as erythromycin, and fluoroquinolones, such as ciprofloxacin. Tetracyclines have been suggested as an alternative choice in the treatment of clinical campylobacteriosis but in practice are not often used. However, during the past few decades an increasing number of resistant Campylobacter isolates have developed resistance to fluoroquinolones and other antimicrobials such as macrolides, aminoglycosides, and beta-lactams. Trends in antimicrobial resistance have shown a clear correlation between use of antibiotics in the veterinary medicine and animal production and resistant isolates of Campylobacter in humans. In this review, the patterns of emerging resistance to the antimicrobial agents useful in treatment of the disease are presented and the mechanisms of resistance to these drugs in Campylobacter are discussed.

The objective of this study was to test the prevalence of virulence-associated markers and antimicrobial resistance in 624 C. jejuni isolated from poultry food chain, i. e., chicken feces (n = 160), poultry carcasses (n = 157), poultry meat (n = 152) and from humans (n = 155). All human strains were positive for 9 out of 13 putative virulence genes responsible for expression of pathogenic factors involved in different stages of the infection. The presence of all markers was also high in strains from chicken feces, carcasses and meat although not all of them were identified in 100% of the isolates. On the other hand, the virB11, wlaN, and iam putative pathogenic genes were detected in only 1.9, 15.2, and 20.5% of strains, respectively. C. jejuni isolates, irrespective of the origin, were highly resistant to ciprofloxacin (92.5% isolates), followed by nalidixic acid (88.9%) and tetracycline (68.4%). In case of ciprofloxacin, significantly more isolates from poultry feces, carcasses and meat were resistant than those obtained from humans and the same relationship was observed for tetracycline where the isolates from chicken feces were more often resistant than C. jejuni of carcasses and meat origin. A low number of strains was resistant to streptomycin (18.4% isolates) and only 5 strains (0.8%) displayed resistance to erythromycin. A relationship between resistance to fluoroquinolones and presence of selected pathogenic markers was observed, e.g., from 83.3% strains with the virB11 to 93.4% with the docA genes were resistant to ciprofloxacin. The isolates that did not possess any of the pathogenic traits were also mainly resistant to this antimicrobial, although the number of such strains was usually low, except virB11 (612 isolates), wlaN (529 strains), and iam (496 isolates). Furthermore, resistance to tetracycline was somehow associated with the presence of the virulence associated genes wlaN and virB11 (56.8 and 75.0% isolates, respectively). The present study shows a high antimicrobial resistance to quinolones and tetracycline of C. jejuni isolated along poultry food chain and from patients with diarrhea, which was closely correlated with the presence of several virulence genes playing a role in the pathogenesis of Campylobacter infection.

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Listeria monocytogenes isolates from bovine hides and carcasses (n ‫؍‬ 812) were mainly of serogroup 1/2a. All strains were positive for internalin genes. Several isolates were resistant to oxacillin (72.2%) or clindamycin (37.0%). These findings indicate that L. monocytogenes of beef origin can be considered a public health concern.

ABSTRACT:The study was conducted to investigate the presence of Campylobacter spp. in meat sold to consumers at a retail market in Poland. Antimicrobial resistance and the presence of putative virulence genes of the isolates were also examined. A total of 558 meat samples, including beef (n = 105), pork (n = 85), and poultry (n = 368) were collected over an almost three year study period. It was found that 321 samples, all of them originating from poultry, were contaminated with Campylobacter spp. Most of the obtained isolates were classified as C. coli (189 strains, 58.9%), whereas C. jejuni was identified in 132 (41.1%) samples. All Campylobacter strains were susceptible to gentamicin and all but one C. coli isolate to erythromycin. On the other hand, the highest level of resistance among Campylobacter tested was to ciprofloxacin (91% for C. jejuni and 86.1% for C. coli) and nalidixic acid (89.3% for C. jejuni and 85% for C. coli). Furthermore, resistance to two or more classes of antibiotics was found in the majority (60.9%) of Campylobacter spp. and among them one C. coli strain showed resistance to four different classes of antimicrobials. Identification of virulence genes in the isolated Campylobacter showed that all of them had the flaA and cadF genes. The iam marker was found more often in C. coli strains (88.8%) compared to C. jejuni isolates (53.8%). On the other hand, the virB11 gene was identified only in 4.2% of C. coli and in 6.1% of C. jejuni strains, respectively. Furthermore, the prevalence of the cdtA, cdtB, and cdtC genes among C. jejuni strains was 97.7%, 93.2%, 96.2%, respectively, and was significantly higher than for C. coli regarding the cdtC (66.7%) gene. The obtained results showed that the presence of Campylobacter in retail meat may represent a threat to public health.

is a widespread bacterium in the marine environment and is responsible for gastroenteritis in humans. Foodborne infections are mainly associated with the consumption of contaminated raw or undercooked fish and shellfish. The aim of this study was to determine the antimicrobial resistance, virulence factors, and genetic profiles of isolates from seafood originating from different countries. A total of 104 (17.5%) isolates were recovered from 595 analyzed samples. The isolates were tested for the presence of the and genes, involved in the pathogenesis of infections in humans, and these genes were detected in 3 (2.9%) and 11 (10.6%) isolates, respectively. The -positive isolates also possessed the gene, which is responsible for urease production. Moreover, the activity of protease A was identified in all strains. Antimicrobial resistance revealed that most isolates were resistant to ampicillin (75.0%) and streptomycin (68.3%), whereas all strains were sensitive to chloramphenicol and tetracyclines. Most of the isolates (55.8%) showed resistance against two classes of antimicrobials, mainly to ampicillin and streptomycin (46.2%). Only one isolate displayed a multiresistant pattern. Genotypic analysis of revealed a high degree of diversity among the isolates tested. The pulsed-field gel electrophoresis (PFGE) method distinguished 73 clonal groups, and the most numerous group consisted of 7 strains. Sequencing by the multilocus sequence typing (MLST) method showed 76 sequence types (STs), of which ST481 and ST1361 were most frequently identified. In addition, 51 (67.1%) new sequence types were discovered and added to the PubMLST international database. The presence of in seafood may pose a risk for consumers, especially in countries where shellfish are eaten raw. In recent years, a significant increase of food poisoning caused by these bacteria has been also observed in Europe. Our results highlight the high level of contamination of seafood, along with the isolates being potentially pathogenic for humans. However, the first-line antimicrobials, such as tetracyclines and fluoroquinolones, remained highly effective against The monitoring of antimicrobial resistance of isolates is important to ensure the high efficacy in the treatment of human infections. Most of strains possessed new sequence types (STs), which showed the high genetic diversity of the isolates tested.

In 2015 in the European Union member states listeriosis caused 270 deaths. Food is the route of transmission in 99% of all human infection cases. Several studies from different countries have shown that the presence of Listeria monocytogenes in food can be as high as 58.3%. One of the most important ways to protect food from these microorganisms is to prevent the spread of the bacteria at processing plants at different stages of food production chain. The ability of L. monocytogenes to survive in extreme conditions and to form biofilms on various surfaces is a significant challenge for food safety. Removal of these bacteria from niches in processing plants is difficult and requires the use of sanitisers and precise equipment cleaning. The presence of L. monocytogenes in processing environment at slaughterhouses, deli meat factories or in retail may be a reason of cross-contamination. Proper hygienic systems applied by workers in food preparing places and knowledge about different routes of spreading of these bacteria may effectively decrease the risk of food contamination. Standardised legal regulations and control of meat product manufacture should be a fundamental way to protect food from L. monocytogenes contamination.