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The interaction between bacteriophages, bacteria and the human host as a tripartite system has recently captured attention. The taxonomic diversity of bacteriophages, as a natural parasite of bacteria, still remains obscure in human body biomes, representing a so-called "viral dark matter." Here, we isolated and characterized coliphages from blood, urine and tracheal aspirates samples collected at a tertiary care hospital in Austria. Phages were more often isolated from blood, followed by urine and tracheal aspirates. Phylogenetic analysis and genome comparisons allowed the identification of phages belonging to the Tunavirinae subfamily, and to the Peduovirus and Tequintavirus genera. Tunavirinae phages cluster together and are found in samples from 14 patients, suggesting their prevalence across a variety of human samples. When compared with other phage genomes, the highest similarity level was at 87.69% average nucleotide identity (ANI), which suggests that these are in fact a newly isolated phage species. Tequintavirus phages share a 95.90% with phage 3_29, challenging the ANI threshold currently accepted to differentiate phage species. The isolated phages appear to be virulent, with the exception of the Peduovirus members, which are integrative and seem to reside as prophages in bacterial genomes. [ABSTRACT FROM AUTHOR]

Antimicrobial resistance is on the rise in certain pathogens that infect pets and their owners. This has raised concerns about the use of antibiotics and the transfer of resistance elements in small animal clinics. We sampled a surgery unit, diagnostic rooms after disinfection, and a dog with chronic urinary tract infection (UTI), in a small animal clinic in Austria, and isolated/characterized phages and Escherichia (E.) coli for antimicrobial resistance, resistance genes and transduction ability. Neither the coliphages nor E. coli were isolated in the 20 samples of the surgery units and diagnostic rooms. From the urinary tract of the dog, we recovered 57 E. coli isolates and 60 coliphages. All of the E. coli isolates were determined as resistant against nalidixic acid, 47 against ampicillin, 34 against sulfonamides, and 33 against streptomycin. No isolate held resistance against tetracycline, trimethoprim, kanamycin, or chloramphenicol. Among the 60 phages, 29 tested positive for one or more resistance gene(s) by PCR, but none was able to transduce it to a laboratory strain or to an E. coli isolated from samples. Nevertheless, six phages out of 60 were able to transduce ampicillin resistance (bla gene) after being grown on a puc19 harboring E. coli strain. [ABSTRACT FROM AUTHOR]

Intensive care units (ICUs) are critical locations for the transmission of pathogenic and opportunistic microorganisms. Bacteria may develop a synergistic relationship with bacteriophages and more effectively resist various stresses, enabling them to persist despite disinfection and antimicrobial treatment. We collected 77 environmental samples from the surroundings of 12 patients with infection/colonizations by Escherichia coli, Staphylococcus aureus or Klebsiella spp. in an ICU in Austria. Surface swabs were tested for lytic phages and bacterial isolates for mitomycin C-inducible prophages. No lytic bacteriophages were detected, but S. aureus was isolated from the surroundings of all patients. About 85% of the colonies isolated from surface samples were resistant to antimicrobials, with 94% of them multidrug resistant. Two inducible temperate bacteriophages—myovirus vB_EcoM_P5 and siphovirus vB_SauS_P9—were recovered from two clinical isolates. Staphylococci phage vB_SauS_P9 lysed S. aureus isolates from the surface swabs collected from the surroundings of three patients. No transductants were obtained on propagation in phage-sensitive antimicrobial-resistant isolates. The two phages were sensitive to 0.25% (v/v) of the disinfectant TPH Protect, which eliminated viable phages after 15 min. Coliphage vB_EcoM_P5 was inactivated at 70 °C and staphylococci phage vB_SauS_P9 at 60 °C after 60 min. [ABSTRACT FROM AUTHOR]

In most European countries human campylobacteriosis is the most important bacterial zoonotic foodborne infection. Chicken meat is considered the main source of infection. Since most strategies assessed so far, in reducing Campylobacter colonization in chickens or in the reduction of human disease, have not been very effective, new knowledge regarding Campylobacter's interaction with the host is needed. In this study we analysed fecal and cecal samples of five chicken flocks of different Austrian farms for the occurrence of Cjejuni and C. coli, and analysed the intestinal microbiota by PCR-SSCP, cultural detection of lactic acid bacteria, Enterococci, Staphylococci, Enterobacteriaceae, E. coli, and total aerobic colony counts. Furthermore ten chicken samples of cecal content of a flock during colonization with Campylobacter spp. was analysed by high throughput sequencing. With all three methods used we could detect a change within the microbiota caused by Cjejuni. Enumeration of different bacteria was significantly lower in fecal samples positive for C. jejuni, pointing out that a higher water content and thus, a preliminary stage of diarrhea might appear during Campylobacter colonization. By PCR-SSCP analysis the microbiota composition differed between colonized and non-colonized chicken fecal samples. This could also be detected in community analysis by high throughput sequencing, but this difference was only a tendency and not statistically significant. It can be concluded that C. jejuni is interacting with the intestinal microflora in their respective hosts and hence, this has to be taken into account when providing new strategies to combat Campylobacter colonization and disease.

Controversy exists on veterinary drug application in food animal production and the relevance for human health of antimicrobial resistant commensals isolated from food. The aim of this study was to analyze antimicrobial resistance in Escherichia coli isolated from retail meat of various animal species (including wild roe deer) in Austria. Our results were analyzed taking into consideration the current practices of Austrian veterinarians with regard to their use of antibiotic drugs during pig, poultry, and beef production. Resistant isolates were found most often in pork (76%) followed by poultry (63%) and beef (40%). On wild deer carcasses purchased from Austrian hunters only one isolate was found to be resistant. The latter indicates that antimicrobial resistance is not yet an environmental problem in animals living in the wild. The common use of tetracyclines in veterinary medication in various animal species is clearly reflected in the incidence of antimicrobial resistant isolates in commensal E. coli. The intensive use of fluoroquinolones in poultry could explain the high numbers of nalidixic acid resistant isolates found on poultry meat. Our findings partly explain the impact of veterinary drug application on the resistance development of E. coli isolated from meat.