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Abstract: Internal dosimetrists are concerned with the development, selection, and calibration of biokinetic models to calculate radiation doses from incorporated radionuclides. This is accomplished using measurements of radionuclides in organs, tissues, and excreta, i.e., bioassay measurements. Each bioassay measurement has a corresponding likelihood function, which represents the relative likelihood of different biokinetic model parameters resulting in the measurement value. In order for a bioassay measurement to be interpreted properly, the correct likelihood function must be determined. Failing to use the correct likelihood function for each bioassay measurement results in improperly weighting certain measurements over other measurements, which in turn leads to incorrect dose estimates. This paper describes the correct likelihood functions to use for a wide variety of bioassay measurements, as well as a description of how to use them. These likelihood functions represent the vast majority of those likely to be needed for interpreting bioassay measurements. Therefore, this paper may serve as a tool kit that can be used by academic and occupational internal dosimetrists., (Copyright © 2025 Health Physics Society.)

Flagellotropic bacteriophages are interesting candidates as therapeutics against pathogenic bacteria dependent on flagellar motility for colonization and causing disease. Yet, phage resistance other than loss of motility has been scarcely studied. Here we developed a soft agar assay to study flagellotropic phage F341 resistance in motile Campylobacter jejuni . We found that phage adsorption was prevented by diverse genetic mutations in the lipooligosaccharides forming the secondary receptor of phage F341. Genome sequencing showed phage F341 belongs to the Fletchervirus genus otherwise comprising capsular-dependent C. jejuni phages. Interestingly, phage F341 encodes a hybrid receptor binding protein (RBP) predicted as a short tail fiber showing partial similarity to RBP1 encoded by capsular-dependent Fletchervirus , but with a receptor binding domain similar to tail fiber protein H of C. jejuni CJIE1 prophages. Thus, C. jejuni prophages may represent a genetic pool from where lytic Fletchervirus phages can acquire new traits like recognition of new receptors., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Ostenfeld, Sørensen, Neve, Vitt, Klumpp and Sørensen.)

Abstract: This paper presents DEPDOSE, an open-source computer application that combines the KDEP respiratory tract deposition fractions for inhaled aerosols with DC_PAK committed equivalent dose coefficients for a unit deposition in each region of the respiratory tract. DEPDOSE allows the user to rapidly produce tables of dose coefficients for workers and members of the public inhaling precisely defined, user-specified aerosols using the ICRP Publication 60 methodology. Combined with a plume dispersion modeling system, such as the Quick Urban & Industrial Complex (QUIC) Dispersion Modeling System, this makes it possible to predict radiation doses downstream from an accidental or intentional release of radioactive materials. For this work, a radioactive plume was calculated to members of the public downstream from a dirty bomb in Chicago. DEPDOSE is published under an open source license, and can be downloaded at https://github.com/lanl/DEPDOSE ., (Copyright © 2023 Health Physics Society.)

The rapid detection and species-level differentiation of bacterial pathogens facilitates antibiotic stewardship and improves disease management. Here, we develop a rapid bacteriophage-based diagnostic assay to detect the most prevalent pathogens causing urinary tract infections: Escherichia coli, Enterococcus spp., and Klebsiella spp. For each uropathogen, two virulent phages were genetically engineered to express a nanoluciferase reporter gene upon host infection. Using 206 patient urine samples, reporter phage-induced bioluminescence was quantified to identify bacteriuria and the assay was benchmarked against conventional urinalysis. Overall, E. coli, Enterococcus spp., and Klebsiella spp. were each detected with high sensitivity (68%, 78%, 87%), specificity (99%, 99%, 99%), and accuracy (90%, 94%, 98%) at a resolution of ≥10 3  CFU/ml within 5 h. We further demonstrate how bioluminescence in urine can be used to predict phage antibacterial activity, demonstrating the future potential of reporter phages as companion diagnostics that guide patient-phage matching prior to therapeutic phage application., (© 2023. The Author(s).)

Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Abstract: In this work, the authors present instantaneous local dose rates from particles of plutonium-239 oxide ( 239 PuO) embedded in various regions of the respiratory tract. For comparison, a small number of simulations were performed in a representative region of the respiratory tract with other chemical compounds including pure metallic 239 Pu, 239 PuO 2 , 239 PuO 3 , 239 Pu 2 O 3 , and 239 Pu(NO 3 ) 4 . A small number of simulations were also performed with 238 PuO, weapons grade Pu, and Pu from a typical radioisotope thermoelectric generator (RTG) source for the same reason. The self-shielding effect is minor for very small particles but gradually becomes more significant as the particle size increases. For particles that are 0.1 μm and larger (excluding Pu nitrate), the calculated dose rate within several microns of the particle may be sufficient to damage lung cells, but the implications of damage to such a small volume of tissue are unclear. However, it is reasonable to assume that clinical effects will be observed if a large enough volume of tissue is damaged, as might happen when large numbers of particles are inhaled. The instantaneous dose rate around a particle may be predictive of deterministic effects, scar tissue formation, and biokinetics., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Health Physics Society.)

Abstract: Accidental inhalation of plutonium at the workplace is a non-negligible risk, even when rigorous safety standards are in place. The intake and retention of plutonium in the human body may be a source of concern. Thus, if there is a suspicion of a significant intake of plutonium, medical countermeasures such as chelation treatment may be administered to the worker. The present work aimed to interpret the bioassay data of a worker involved in an inhalation incident due to a glovebox breach at Los Alamos National Laboratory's plutonium facility. The worker was treated with intravenous injections of calcium salts of diethylenetriaminepentaacetic acid (DTPA) in an attempt to reduce the amount of plutonium from the body and therefore reduce the internal radiation dose. It is well known in the internal dosimetry field that the administration of chelation treatment poses additional challenges to the dose assessment. Hence, a recently developed chelation model was used for the modeling of the bioassay data. The objectives of this work are to describe the incident, model the chelation-affected and non-affected bioassay data, estimate the plutonium intake, and assess the internal radiation dose., (Copyright © 2022 The Author(s). Published by Wolters Kluwer Health, Inc. on behalf of the Health Physics Society.)

Abstract: In addition to a review of theoretical analyses, this work presents an empirical study of nasal swab data from the Los Alamos National Laboratory (LANL) database correlated with intake obtained from plutonium internal dosimetry calculations. As a result of this work, several "intake-versus-nasal-swab" models were derived. We advocate quantitative use of nasal swab measurements in dose assessment calculations and discuss ways that this can be done. The best description of the LANL plutonium internal dose database is arguably intake = A + Bx, where A = 2.7 Bq, B = 3.8, and x = summed nasal swab activity. The geometric standard deviation was found to be 8.2. This relationship, obtained using plutonium data, should apply also for other radionuclides., (Copyright © 2023 Health Physics Society.)

Abstract: A glovebox breach at the plutonium facility at Los Alamos National Laboratory potentially exposed 15 individuals to 238 Pu aerosols. One of the individuals (P0) received two 1-g intravenous DTPA treatments, one on the day of the intake and another the following day. Several urine samples were collected from the individuals involved in the incident. Particle size analysis on the PPE and solubility analysis of the particles on a filter sample were conducted in vitro. The applicability of the results from the in vitro studies for dose assessment was questionable because of the effect of the cloth mask the workers were wearing for COVID-related protection. Based on several considerations, including the effect of cloth masks on the "effective" particle size inhaled and the analysis of fecal-to-urine ratio, the default Type M 1 μm AMAD model was used to estimate intakes and doses. Using the urinary excretion data collected after 100 d post last chelation treatment, the committed effective dose, E(50), for P0 was calculated to be 5.2 mSv. For all others, the bioassay data were consistent with no intakes or very small intakes [corresponding to E(50) less than 0.1 mSv]., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2022 Health Physics Society.)

Abstract: This work presents an alternate analysis of an in vitro solubility study on the lung dissolution rate of 238PuO2 material involved in a recent inhalation incident at Los Alamos National Laboratory (LANL). The original dataset used in this work was retrieved from a recently published report. The present work shows an analysis of the same dataset by modeling the dissolution in separate time intervals rather than modeling the cumulative dissolution., Competing Interests: The authors declare that there are no conflicts of interest., (Copyright © 2022 Health Physics Society.)

Abstract: Anecdotal evidence indicates there may be unpublished physical and psychological events associated with the medical treatment of plutonium intakes. A thorough review was conducted of the medical and bioassay records of current and previous Los Alamos National Laboratory (LANL) employees who had experienced plutonium intakes via wound or inhalation. After finding relatively incomplete information in the medical records, the research team interviewed current LANL employees who had undergone chelation therapy and/or surgical excision. Although the dataset is not large enough to reach statistically significant conclusions, it was observed that adverse events associated with treatment appear to be more frequent and more severe than previously reported., Competing Interests: # The authors declare no conflicts of interest. ( Manuscript accepted 25 May 2022), (Copyright © 2022 Health Physics Society.)

Phages infecting Campylobacter jejuni are considered a promising intervention strategy at broiler farms, yet phage sensitivity of naturally occurring poultry isolates is not well studied. Here, we investigated phage sensitivity and identified resistance mechanisms of C. jejuni strains originating from Danish broilers belonging to the most prevalent MLST (ST) types. Determining plaque formation of 51 phages belonging to Fletchervirus or Firehammervirus showed that 21 out of 31 C. jejuni strains were susceptible to at least one phage. While C. jejuni ST-21 strains encoded the common phase variable O -methyl phosphoramidate (MeO P N) receptor of the Fletchervirus and were only infected by these phages, ST-45 strains did not encode this receptor and were exclusively infected by Firehammervirus phages. To identify internal phage resistance mechanism in ST-21 strains, we performed comparative genomics of two strains, CAMSA2002 sensitive to almost all Fletchervirus phages and CAMSA2038, resistant to all 51 phages. The strains encoded diverse clustered regularly interspaced short palindromic repeats (CRISPR) spacers but none matched the tested phages. Sequence divergence was also observed in a predicted SspE homolog and putative restriction modification systems including a methyl-specific McrBC endonuclease. Furthermore, when mcrB was deleted, CAMSA2038 became sensitive to 17 out of 43 phages, three being Firehammervirus phages that otherwise did not infect any ST-21 strains. Yet, 16 phages demonstrated significantly lower efficiencies of plating on the mcrB mutant suggesting additional resistance mechanism still restricting phage propagation in CAMSA2038. Thus, our work demonstrates that C. jejuni isolates originating from broilers may have acquired several resistance mechanisms to successfully prevent phage infection in their natural habitat., Competing Interests: YG is currently employed by SNIPR Biome. The salary of MS was partially funded by Intralytix, Inc., but the company had no influence on the design of the study nor any impact on the conclusions of the presented work. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Sørensen, Gencay, Fanger, Chichkova, Mazúrová, Klumpp, Nielsen and Brøndsted.)

Abstract: Recently, a glovebox breach led to the potential exposure of 15 Los Alamos National Laboratory employees to 238Pu. Given what is known about the material involved in the incident, the possibility of an intake with a ceramic-type component must be considered. Incidents in which intakes of ceramic solubility-type material is suspected represent a challenge for internal dose assessment via urine bioassay because even relatively large doses cannot be detected in urine until many months after the intake. Ideally, in these situations fecal samples should be collected to assess the intake, but in this case fecal sampling was delayed. This paper presents a method to calculate the maximum possible doses for all individuals involved in an incident using only early time-decreasing urine bioassay measurements., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Health Physics Society.)

Abstract: This work considers the implications of cloth masks due to the COVID-19 pandemic on suspected plutonium inhalations and dose assessment. In a plutonium inhalation scenario, the greater filtration efficiency for large particles exhibited by cloth masks can reduce early fecal excretion without a corresponding reduction in dose. For plutonium incidents in which cloth masks are worn, urinary excretion should be the preferred method of inferring dose immediately after the inhalation, and fecal excretion should be considered unreliable for up to 10 days., Competing Interests: The authors declare no conflicts of interest., (Copyright © 2021 Health Physics Society.)

Phase variation is a common mechanism for creating phenotypic heterogeneity of surface structures in bacteria important for niche adaptation. In Campylobacter, phase variation occurs by random variation in hypermutable homonucleotide 7-11 G (polyG) tracts. To elucidate how phages adapt to phase-variable hosts, we study Fletchervirus phages infecting Campylobacter dependent on a phase-variable receptor. Our data demonstrate that Fletcherviruses mimic their host and encode hypermutable polyG tracts, leading to phase-variable expression of two of four receptor-binding proteins. This creates phenotypically diverse phage populations, including a sub-population that infects the bacterial host when the phase-variable receptor is not expressed. Such population dynamics of both phage and host promote co-existence in a shared niche. Strikingly, we identify polyG tracts in more than 100 phage genera, infecting more than 70 bacterial species. Future experimental work may confirm phase variation as a widespread strategy for creating phenotypically diverse phage populations., Competing Interests: Declaration of interests The authors declare no competing interests. The salary of M.C.H.S was partially funded by Intralytix, Inc., which had no influence on the design or conclusions of the present work., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Introduction: Because of the clinical relevance of Mycobacteria , and from a therapeutic perspective, there is an increasing interest to study phages that infect bacteria belonging to this genus. Materials and Methods: A phage was isolated from a soil sample, using Mycobacterium smegmatis as host. Its characterization included sequencing, annotation, and analysis of the genome, host range determination, and electron microscopy imaging. Results: Mycobacterium phage vB_MsmS_Celfi is a temperate phage able to infect Mycobacterium tuberculosis with high efficiency. From electron microscopy images, Celfi belongs to the Siphoviridae family. Genome analysis classified phage Celfi into cluster L, subcluster L2 of Actinobacteriophage clusters. Mycobacterium phage Celfi exhibits a Lysin B distant to those present in other members of the subcluster and other mycobacteriophages. Conclusions: The discovery of new phages that infect M. tuberculosis could contribute to the development of novel tools for detection systems and future treatment of the disease., Competing Interests: The authors declare that no competing financial interests exist., (Copyright 2021, Mary Ann Liebert, Inc., publishers.)

Introduction: Only a few Lactobacillus casei phages have so far been characterized. As several L. casei strains are part of probiotic formulations, bacteriophage outbreaks targeting these strains can lead to critical losses within the dairy industry. Materials and Methods: A new L. casei phage was isolated from raw milk obtained from a milking yard from the province of Buenos Aires. The phage genome was sequenced, annotated, and analyzed. Morphology was determined by electron microscopy and the host range was established. Results: Lactobacillus phage vB_LcaM_Lbab1 is a member of the Herelleviridae family and features a host range including L. casei/Lactobacillus paracasei and Lactobacillus kefiri strains. We further analyzed the baseplate proteins in silico and found putative carbohydrate binding modules that are responsible for host recognition in other Lactobacillus phages. Conclusions: A new Lactobacillus phage was isolated and characterized. The focus was made on its host recognition mechanism, pointing toward the development of future strategies to avoid deleterious infections in the dairy industry., Competing Interests: The authors declare that no competing financial interests exist., (Copyright 2021, Mary Ann Liebert, Inc., publishers.)

Listeria monocytogenes is an important food-borne pathogen and its bacteriophages are promising tools for its control in food and surfaces. Listeria bacteriophages belonging to the genus Pecentumvirus of the family Herelleviridae are strictly lytic, have a contractile tail and a large double stranded DNA genome (mean of 135.4 kb). We report the isolation and genome sequences of two new Pecentumvirus bacteriophages: vB_Lino_VEfB7 and vB_Liva_VAfA18. Twenty-one bacteriophages of this genus have been described and their genomes were used for the study of Pecentumvirus evolution. Analyses showed collinear genomes and gene gain and loss propensity and recombination events were distinctly found in two regions. A large potential recombination event (≈20 kB) was detected in P100 and vB_Liva_VAfA18. Phylogenetic analyses of multi-gene alignments showed that diversification events formed two groups of species distantly related., (Copyright © 2020 Elsevier Inc. All rights reserved.)

The three principal pathways for intakes of plutonium are ingestion, inhalation, and contaminated wounds. In August 2018, a glovebox worker at Los Alamos National Laboratory (LANL) sustained a puncture from a thread of a braided steel cable contaminated with Pu. The puncture produced no pain, no blood, and little or no visible mark. As a result, the potential for a contaminated wound was not immediately recognized, and a wound count was not conducted until elevated urine bioassay results were received 12 d after the incident. This paper discusses the circumstances of the incident, along with the medical response and dose assessment, and a discussion of the risks and benefits of the medical interventions.

Salmonella is one of the most common agents of foodborne disease worldwide. As natural alternatives to traditional antimicrobial agents, bacteriophages (phages) are emerging as highly effective biocontrol agents against Salmonella and other foodborne bacteria. Due to the high diversity within the Salmonella genus and emergence of drug resistant strains, improved efforts are necessary to find broad range and strictly lytic Salmonella phages for use in food biocontrol. Here, we describe the isolation and characterization of two Salmonella phages: ST-W77 isolated on S. Typhimurium and SE-W109 isolated on S. Enteritidis with extraordinary Salmonella specificity. Whole genome sequencing identified ST-W77 as a Myovirus within the Viunalikevirus genus and SE-W109 as a Siphovirus within the Jerseylikevirus genus. Infectivity studies using a panel of S. Typhimurium cell wall mutants revealed both phages require the lipopolysaccharide O-antigen, with SE-W109 also recognizing the flagella, during infection of Salmonella. A combination of both phages was capable of prolonged (one-week) antibacterial activity when added to milk or chicken meat contaminated with Salmonella. Due to their broad host ranges, strictly lytic lifestyles and lack of lysogeny-related genes or virulence genes in their genomes, ST-W77 and SE-W109 are ideal phages for further development as Salmonella biocontrol agents for food production., (Copyright © 2020 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Based on $n$ replicate measurements that require known normalization factors and assuming an underlying normal distribution for individual measurements but with unknown standard deviation, a combined likelihood function is derived that takes the form of a Student's $t$-distribution with $\nu = n-1$ degrees of freedom and $t=(\psi -\overline{Y})/s$, where $\psi $ is the true value of the measurement quantity calculated from the forward model, and $\overline{Y}$ and $s$ are average and standard error of the mean obtained from the $n$ measurements defined with weighting proportional to the inverse of the normalization factor squared. Assuming an underlying triangle distribution rather than a normal distribution does not produce a large change for six replicates. Examples of replicate data from an animal study and sequential occupational urine and fecal monitoring are given. The use of the empirical likelihood function in data modeling is discussed., (© The Author(s) 2020. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Bacterial urinary tract infections (UTIs) are very frequent, especially in patients with neurogenic lower urinary tract dysfunction (NLUTD). The steady increase in antibiotic resistance among causative bacteria prompts the search for highly effective therapeutic alternatives with little or no side effects. Bacteriophages - obligate intracellular viruses that solely infect and kill bacteria - are promising tools for treating bacterial infections and have been used for this purpose for almost a century. Recent clinical studies using bacteriophage therapy for UTIs showed encouraging results. In particular, patients with recurrent UTIs, such as individuals with NLUTD who rely on assisted bladder emptying, might benefit from this treatment method. However, bacteriophages are not yet a panacea. More high-quality basic and clinical research on bacteriophage therapy is needed to answer questions on the use of this therapeutic option and its potential to provide a solution to the global threat of multidrug-resistant bacteria. PATIENT SUMMARY: Urinary tract infections are very common, especially in patients with neurogenic lower urinary tract dysfunction. In this review we discuss the potential of bacteriophage therapy as an alternative to antibiotics for treating patients with bladder infections., (Copyright © 2019. Published by Elsevier B.V.)

This article is a summary of the activities of the ICTV's Bacterial and Archaeal Viruses Subcommittee for the years 2018 and 2019. Highlights include the creation of a new order, 10 families, 22 subfamilies, 424 genera and 964 species. Some of our concerns about the ICTV's ability to adjust to and incorporate new DNA- and protein-based taxonomic tools are discussed.

Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order., (© The Author(s) 2019. Published by Oxford University Press on behalf of the Society of Systematic Biologists.)

Background: Several serious vegetable-associated outbreaks of enterohemorrhagic Escherichia coli (EHEC) infections have occurred during the last decades. In this context, vegetables have been suggested to function as secondary reservoirs for EHEC strains. Increased knowledge about the interaction of EHEC with plants including gene expression patterns in response to plant-derived compounds is required. In the current study, EHEC O157:H7 strain Sakai, EHEC O157:H - strain 3072/96, and the EHEC/enteroaggregative E. coli (EAEC) hybrid O104:H4 strain C227-11φcu were grown in lamb's lettuce medium and in M9 minimal medium to study the differential transcriptional response of these strains to plant-derived compounds with RNA-Seq technology., Results: Many genes involved in carbohydrate degradation and peptide utilization were similarly upregulated in all three strains, suggesting that the lamb's lettuce medium provides sufficient nutrients for proliferation. In particular, the genes galET and rbsAC involved in galactose metabolism and D-ribose catabolism, respectively, were uniformly upregulated in the investigated strains. The most prominent differences in shared genome transcript levels were observed for genes involved in the expression of flagella. Transcripts of all three classes of the flagellar hierarchy were highly abundant in strain C227-11φcu. Strain Sakai expressed only genes encoding the basal flagellar structure. In addition, both strains showed increased motility in presence of lamb's lettuce extract. Moreover, strain 3072/96 showed increased transcription activity for genes encoding the type III secretion system (T3SS) including effectors, and was identified as a powerful biofilm-producer in M9 minimal medium., Conclusion: The current study provides clear evidence that EHEC and EHEC/EAEC strains are able to adjust their gene expression patterns towards metabolization of plant-derived compounds, demonstrating that they may proliferate well in a plant-associated environment. Moreover, we propose that flagella and other surface structures play a fundamental role in the interaction of EHEC and EHEC/EAEC with plants.

Despite a wealth of knowledge on Salmonella phages worldwide, little is known about poultry-associated Salmonella phages from Thailand. Here, we isolated 108 phages from Thai poultry farms that infect Salmonella enterica serovar Typhimurium. Phages STm101 and STm118 were identified as temperate Siphoviridae phages. Genome sequencing and analyses revealed these phages share approximately 96% nucleotide sequence similarity to phage SPN19, a member of the Chi-like virus genus. PCR amplification of the gene encoding capsid protein E of the Chi-like phage was positive for 50% of phage isolates, suggesting a predominance of this phage type among the sampled poultry farms. In addition to the flagella, two phages required the lipopolysaccharide to infect and lyse Salmonella. Furthermore, phylogenomic analysis demonstrated that phages STm101 and STm118 formed a monophyletic clade with phages isolated from Western countries, but not from closer isolated phages from Korea. However, further investigation and more phage isolates are required to investigate possible causes for this geographic distribution., Competing Interests: The authors declare that they have no competing interests.

Bacteriophages represent a promising alternative for controlling pathogenic bacteria. They are ubiquitous in the environment, and their isolation is usually simple and fast. However, not every phage is suitable for biocontrol applications. It must be virulent (i.e., strictly lytic), non-transducing, and safe. We have developed a method for identifying selected types of virulent phages at an early stage of the isolation process to simplify the search for suitable candidates. Using the major capsid protein (MCP) as a phylogenetic marker, we designed degenerate primers for the identification of Felix O1-, GJ1-, N4-, SP6-, T4-, T7-, and Vi1-like phages in multiplex PCR setups with single phage plaques as templates. Performance of the MCP PCR assay was evaluated with a set of 26 well-characterized phages. Neither false-positive nor false-negative results were obtained. In addition, 154 phages from enrichment cultures from various environmental samples were subjected to MCP PCR analysis. Eight of them, specific for Salmonella enterica, Escherichia coli, or Erwinia amylovora, belonged to one of the selected phage types. Their PCR-based identification was successfully confirmed by pulsed-field gel electrophoresis of the phage genomes, electron microscopy, and sequencing of the amplified mcp gene fragment. The MCP PCR assay was shown to be a simple method for preliminary assignment of new phages to a certain group and thus to identify candidates for biocontrol immediately after their isolation. Given that sufficient sequence data are available, this method can be extended to any phage group of interest.

Bacillus cytotoxicus is a member of the Bacillus cereus group linked to fatal cases of diarrheal disease. Information on B. cytotoxicus is very limited; in particular comprehensive genomic data is lacking. Thus, we applied a genomic approach to characterize B. cytotoxicus and decipher its population structure. To this end, complete genomes of ten B. cytotoxicus were sequenced and compared to the four publicly available full B. cytotoxicus genomes and genomes of other B. cereus group members. Average nucleotide identity, core genome, and pan genome clustering resulted in clear distinction of B. cytotoxicus strains from other strains of the B. cereus group. Genomic content analyses showed that a hydroxyphenylalanine operon is present in B. cytotoxicus, but absent in all other members of the B. cereus group. It enables degradation of aromatic compounds to succinate and pyruvate and was likely acquired from another Bacillus species. It allows for utilization of tyrosine and might have given a B. cytotoxicus ancestor an evolutionary advantage resulting in species differentiation. Plasmid content showed that B. cytotoxicus is flexible in exchanging genes, allowing for quick adaptation to the environment. Genome-based phylogenetic analyses divided the B. cytotoxicus strains into four clades that also differed in virulence gene content.

Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of Listeria bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion., (© 2019 The Authors.)

The ability of phages to infect specific bacteria has led to their exploitation as bio-tools for bacterial remediation and detection. Many phages recognize bacterial hosts via adhesin tips of their long tail fibers (LTFs). Adhesin sequence plasticity modulates receptor specificity, and thus primarily defines a phage's host range. Here we present the crystal structure of an adhesin (gp38) attached to a trimeric β-helical tip (gp37) from the Salmonella phage S16 LTF. Gp38 contains rare polyglycine type II helices folded into a packed lattice, herein designated "PG II sandwich." Sequence variability within the domain is limited to surface-exposed helices and distal loops that form putative receptor-binding sites. In silico analyses revealed a prevalence of the adhesin architecture among T-even phages, excluding the archetypal T4 phage. Overall, S16 LTF provides a valuable model for understanding binding mechanisms of phage adhesins, and for engineering of phage adhesins with expandable or modulated host ranges., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

The rise of antibiotic resistance in pathogenic bacteria is endangering the efficacy of antibiotics, which consequently results in greater use of silver as a biocide. Chromosomal mapping of the Cus system or plasmid encoded Sil system and their relationship with silver resistance was studied for several gram-negative bacteria. However, only few reports investigated silver detoxification mediated by the Sil system integrated in Escherichia coli chromosome. Accordingly, this work aimed to study the Sil system in E. coli ATCC 8739 and to produce evidence for its role in silver resistance development. Silver resistance was induced in E. coli ATCC 8739 by stepwise passage in culture media containing increasing concentrations of AgNO 3 . The published genome of E. coli ATCC 8739 contains a region showing strong homology to the Sil system genes. The role of this region in E. coli ATCC 8739 was assessed by monitoring the expression of silC upon silver stress, which resulted in a 350-fold increased expression. De novo sequencing of the whole genome of a silver resistant strain derived from E. coli ATCC 8739 revealed mutations in ORFs putative for SilR and CusR. The silver resistant strain (E. coli AgNO 3 R) showed constitutive expression of silC which posed a cost of fitness resulting in retarded growth. Furthermore, E. coli AgNO 3 R exhibited cross-resistance to ciprofloxacin and a slightly increased tolerance to ampicillin. This study demonstrates that E. coli is able to develop resistance to silver, which may pose a threat towards an effective use of silver compounds as antiseptics.

The inherent ability of bacteriophages (phages) to infect specific bacterial hosts makes them ideal candidates to develop into antimicrobial agents for pathogen-specific remediation in food processing, biotechnology, and medicine (e.g., phage therapy). Conversely, phage contaminations of fermentation processes are a major concern to dairy and bioprocessing industries. The first stage of any successful phage infection is adsorption to a bacterial host cell, mediated by receptor-binding proteins (RBPs). As the first point of contact, the binding specificity of phage RBPs is the primary determinant of bacterial host range, and thus defines the remediative potential of a phage for a given bacterium. Co-evolution of RBPs and their bacterial receptors has forced endless adaptation cycles of phage-host interactions, which in turn has created a diverse array of phage adsorption mechanisms utilizing an assortment of RBPs. Over the last decade, these intricate mechanisms have been studied intensely using electron microscopy and X-ray crystallography, providing atomic-level details of this fundamental stage in the phage infection cycle. This review summarizes current knowledge surrounding the molecular basis of host interaction for various socioeconomically important Gram-positive targeting phage RBPs to their protein- and saccharide-based receptors. Special attention is paid to the abundant and best-characterized Siphoviridae family of tailed phages. Unravelling these complex phage-host dynamics is essential to harness the full potential of phage-based technologies, or for generating novel strategies to combat industrial phage contaminations.

CRISPR-Cas systems provide bacteria with adaptive immunity against invading DNA elements including bacteriophages and plasmids. While CRISPR technology has revolutionized eukaryotic genome engineering, its application to prokaryotes and their viruses remains less well established. Here we report the first functional CRISPR-Cas system from the genus Listeria and demonstrate its native role in phage defense. LivCRISPR-1 is a type II-A system from the genome of L. ivanovii subspecies londoniensis that uses a small, 1078 amino acid Cas9 variant and a unique NNACAC protospacer adjacent motif. We transferred LivCRISPR-1 cas9 and trans-activating crRNA into Listeria monocytogenes. Along with crRNA encoding plasmids, this programmable interference system enables efficient cleavage of bacterial DNA and incoming phage genomes. We used LivCRISPR-1 to develop an effective engineering platform for large, non-integrating Listeria phages based on allelic replacement and CRISPR-Cas-mediated counterselection. The broad host-range Listeria phage A511 was engineered to encode and express lysostaphin, a cell wall hydrolase that specifically targets Staphylococcus peptidoglycan. In bacterial co-culture, the armed phages not only killed Listeria hosts but also lysed Staphylococcus cells by enzymatic collateral damage. Simultaneous killing of unrelated bacteria by a single phage demonstrates the potential of CRISPR-Cas-assisted phage engineering, beyond single pathogen control.

Enterohemorrhagic E. coli (EHEC) are serious bacterial pathogens which are able to cause a hemorrhagic colitis or the life-threatening hemolytic-uremic syndrome (HUS) in humans. EHEC strains can carry different numbers of phage-borne nanS-p alleles that are responsible for acetic acid release from mucin from bovine submaxillary gland and 5-N-acetyl-9-O-acetyl neuraminic acid (Neu5,9Ac 2 ), a carbohydrate present in mucin. Thus, Neu5,9Ac 2 can be transformed to 5-N-acetyl neuraminic acid, an energy source used by E. coli strains. We hypothesize that these NanS-p proteins are involved in competitive growth of EHEC in the gastrointestinal tract of humans and animals. The aim of the current study was to demonstrate and characterize the nanS-p alleles of the 2011 E. coli O104:H4 outbreak strain LB226692 and analyze whether the presence of multiple nanS-p alleles in the LB226692 genome causes a competitive growth advantage over a commensal E. coli strain. We detected and characterized five heterogeneous phage-borne nanS-p alleles in the genome of E. coli O104:H4 outbreak strain LB226692 by in silico analysis of its genome. Furthermore, successive deletion of all nanS-p alleles, subsequent complementation with recombinant NanS-p13-His, and in vitro co-culturing experiments with the commensal E. coli strain AMC 198 were conducted. We could show that nanS-p genes of E. coli O104:H4 are responsible for growth inhibition of strain AMC 198, when Neu5,9Ac 2 was used as sole carbon source in co-culture. The results of this study let us suggest that multiple nanS-p alleles may confer a growth advantage by outcompeting other E. coli strains in Neu5,9Ac 2 rich environments, such as mucus in animal and human gut., (Copyright © 2018 Elsevier GmbH. All rights reserved.)

Engineered bacteriophages provide powerful tools for biotechnology, diagnostics, pathogen control, and therapy. However, current techniques for phage editing are experimentally challenging and limited to few phages and host organisms. Viruses that target Gram-positive bacteria are particularly difficult to modify. Here, we present a platform technology that enables rapid, accurate, and selection-free construction of synthetic, tailor-made phages that infect Gram-positive bacteria. To this end, custom-designed, synthetic phage genomes were assembled in vitro from smaller DNA fragments. We show that replicating, cell wall-deficient Listeria monocytogenes L-form bacteria can reboot synthetic phage genomes upon transfection, i.e., produce virus particles from naked, synthetic DNA. Surprisingly, Listeria L-form cells not only support rebooting of native and synthetic Listeria phage genomes but also enable cross-genus reactivation of Bacillus and Staphylococcus phages from their DNA, thereby broadening the approach to phages that infect other important Gram-positive pathogens. We then used this platform to generate virulent phages by targeted modification of temperate phage genomes and demonstrated their superior killing efficacy. These synthetic, virulent phages were further armed by incorporation of enzybiotics into their genomes as a genetic payload, which allowed targeting of phage-resistant bystander cells. In conclusion, this straightforward and robust synthetic biology approach redefines the possibilities for the development of improved and completely new phage applications, including phage therapy., Competing Interests: Conflict of interest statement: The technology described in this manuscript is a pending patent.

The aim of this study is to present several approaches that have been used to model the behavior of radioactive materials (specifically Pu) in contaminated wounds. We also review some attempts by the health physics community to validate and revise the National Council on Radiation Protection and Measurements (NCRP) 156 biokinetic model for wounds, and present some general recommendations based on the review. Modeling of intake via the wound pathway is complicated because of a large array of wound characteristics (e.g. solubility and chemistry of the material, type and depth of the tissue injury, anatomical location of injury). Moreover, because a majority of the documented wound cases in humans are medically treated (excised or treated with chelation), the data to develop biokinetic models for unperturbed wound exposures are limited. Since the NCRP wound model was largely developed from animal data, it is important to continue to validate and improve the model using human data whenever plausible., (© The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.)

Complying with regulations for bioassay monitoring of radionuclide intakes is significantly more complex for mixtures than it is for pure radionuclides. Different constituents will naturally have different dose coefficients, be detectable at significantly different levels, and may require very different amounts of effort to bioassay. The ability to use certain constituents as surrogates for others will depend on how well characterized the mixture is, as well as whether the employee is also working with other radionuclides. This is further compounded by the fact that the composition of a mixture (or even of a pure radionuclide) is likely to change over time. Internal dosimetrists must decide how best to monitor employees who work with radionuclide mixtures. In particular, they must decide which constituents should be monitored routinely, which constituents only need to be monitored in the case of an intake, and how to estimate doses based on intakes of monitored and unmonitored constituents.

Background: Mcr-1 -harboring Enterobacteriaceae are reported worldwide since their first discovery in 2015. However, a limited number of studies are available that compared full-length plasmid sequences of human and animal origins., Methods: In this study, mcr-1 -bearing plasmids from seven Escherichia coli isolates recovered from patients (n = 3), poultry meat (n = 2) and turkey meat (n = 2) in Switzerland were further analyzed and compared. Isolates were characterized by multilocus sequence typing (MLST). The mcr-1 -bearing plasmids were transferred by transformation into reference strain E. coli DH5α and MCR-1-producing transformants were selected on LB-agar supplemented with 2 mg/L colistin. Purified plasmids were then sequenced and compared., Results: MLST revealed six distinct STs, illustrating the high clonal diversity among mcr-1- positive E. coli isolates of different origins. Two different mcr-1 -positive plasmids were identified from a single E. coli ST48 human isolate. All other isolates possessed a single mcr-1 harboring plasmid. Transferable IncI2 (size ca. 60-61 kb) and IncX4 (size ca. 33-35 kb) type plasmids each bearing mcr-1 were found associated with human and food isolates. None of the mcr-1 -positive IncI2 and IncX4 plasmids possessed any additional resistance determinants. Surprisingly, all but one of the sequenced mcr-1 -positive plasmids lacked the IS Apl1 element, which is a key element mediating acquisition of mcr-1 into various plasmid backbones., Conclusions: There is strong evidence that the food chain may be an important transmission route for mcr-1 -bearing plasmids. Our data suggest that some "epidemic" plasmids rather than specific E. coli clones might be responsible for the spread of the mcr-1 gene along the food chain.

We present the complete genome sequence of Escherichia coli ABWA45, a 16S rRNA methyltransferase-producing wastewater isolate. Assembly and annotation resulted in a 5,094,639-bp circular chromosome and four closed plasmids of 145,220 bp, 113,793 bp, 57,232 bp, and 47,900 bp in size. Furthermore, a small open plasmid (7,537 bp in size) was assembled., (Copyright © 2017 Zurfluh et al.)

We present the genome sequence of Citrobacter freundii 705SK3, a wastewater isolate harboring an IncL OXA-48-encoding plasmid. Assembly of the genome resulted in a 5,242,839-bp circular chromosome (GC content, 52%) and two closed plasmids of 296,175 bp and 63, 458 bp in size., (Copyright © 2017 Zurfluh et al.)

The Swiss wastewater isolate Klebsiella pneumoniae 704SK6, encoding OXA-48 and CTX-M-15 β-lactamases, was fully sequenced. The assembly resulted in an open chromosome of 5,208,104 bp in size (G+C content, 57.6%) and four closed plasmid sequences of 209,651, 197,670, 65,998, and 63,605 bp in size., (Copyright © 2017 Marti et al.)

Here we present the complete genome sequence of Enterobacter cloacae 704SK10, a Swiss wastewater isolate encoding an OXA-48 carbapenemase. Assembly resulted in closed sequences of the 4,876,946-bp chromosome, a 111,184-bp IncF plasmid, and an OXA-48-encoding IncL plasmid (63,458 bp) nearly identical to the previously described plasmid pOXA-48., (Copyright © 2017 Marti et al.)

The thermophilic spore-forming bacterium Anoxybacillus flavithermus is responsible for powdered milk product spoilage, and its presence in dairy processing environments is a concern. Here, the complete genome sequence of the A. flavithermus strain 52-1A isolated from a heat-processed powdered milk product concentrate in Switzerland is presented., (Copyright © 2017 Tasara et al.)

To enable specific and tightly controlled gene expression both in vitro and during the intracellular lifecycle of the pathogen Listeria monocytogenes, a TetR-dependent genetic induction system was developed. Highest concentration of cytoplasmic TetR and best repression of tetO-controlled genes was obtained by tetR expression from the synthetic promoter Pt 17 . Anhydrotetracycline (ATc) as inducer permitted concentration-dependent, fine-tuned expression of genes under control of the tetO operator and a suitable promoter. The actin-polymerizing ActA protein represents a major virulence factor of L. monocytogenes, required for actin-based motility and cell-to-cell spread in infected host cells. To be able to observe its spatial and temporal distribution on intracellular L. monocytogenes cells, conditional mutants featuring actA placed under TetR control were used to infect PtK2 epithelial cells. Following induction at different time intervals, the subsequent recruitment of actin by L. monocytogenes could be monitored. We found that cells displayed functional ActA after approximately 15 min, while formation of polarized actin tail was complete after 90-120 min. At this point, intracellular motility of the induced mutants was indistinguishable from wild-type bacteria. Interestingly, de novo ActA synthesis in intracellular Listeria also demonstrated the temporal, asymmetric redistribution of the membrane-anchored proteins from the lateral walls toward the cell poles., (© 2017 John Wiley & Sons Ltd.)

This paper presents KDEP, an open-source implementation of the ICRP lung deposition model developed by the authors. KDEP, which is freely available to the public, can be used to calculate lung deposition values under a variety of different conditions using the ICRP methodology. The paper describes how KDEP implements this model and discusses some key points of the implementation. The published lung deposition values for intakes by workers were reproduced, and new deposition values were calculated for intakes by members of the public. KDEP can be obtained for free at github.com or by emailing the authors directly.

The foodborne pathogen Listeria monocytogenes causes severe disease mainly in the vulnerable populations of the young, old, pregnant, and immunocompromised. Here, we present the genome sequence of L. monocytogenes H34, a serotype 1/2b, lineage I, sequence type 489 (ST489) strain, isolated from a neonatal sepsis case in Uruguay., (Copyright © 2017 Muchaamba et al.)

Bacteriophage-based assays and biosensors rival traditional antibody-based immunoassays for detection of low-level Salmonella contaminations. In this study, we harnessed the binding specificity of the long tail fiber (LTF) from bacteriophage S16 as an affinity molecule for the immobilization, enrichment, and detection of Salmonella We demonstrate that paramagnetic beads (MBs) coated with recombinant gp37-gp38 LTF complexes (LTF-MBs) are highly effective tools for rapid affinity magnetic separation and enrichment of Salmonella Within 45 min, the LTF-MBs consistently captured over 95% of Salmonella enterica serovar Typhimurium cells from suspensions containing from 10 to 10 5 CFU · ml -1 , and they yielded equivalent recovery rates (93% ± 5%, n = 10) for other Salmonella strains tested. LTF-MBs also captured Salmonella cells from various food sample preenrichments, allowing the detection of initial contaminations of 1 to 10 CFU per 25 g or ml. While plating of bead-captured cells allowed ultrasensitive but time-consuming detection, the integration of LTF-based enrichment into a sandwich assay with horseradish peroxidase-conjugated LTF (HRP-LTF) as a detection probe produced a rapid and easy-to-use Salmonella detection assay. The novel enzyme-linked LTF assay (ELLTA) uses HRP-LTF to label bead-captured Salmonella cells for subsequent identification by HRP-catalyzed conversion of chromogenic 3,3',5,5'-tetramethylbenzidine substrate. The color development was proportional for Salmonella concentrations between 10 2 and 10 7 CFU · ml -1 as determined by spectrophotometric quantification. The ELLTA assay took 2 h to complete and detected as few as 10 2 CFU · ml -1 S Typhimurium cells. It positively identified 21 different Salmonella strains, with no cross-reactivity for other bacteria. In conclusion, the phage-based ELLTA represents a rapid, sensitive, and specific diagnostic assay that appears to be superior to other currently available tests. IMPORTANCE The incidence of foodborne diseases has increased over the years, resulting in major global public health issues. Conventional methods for pathogen detection can be laborious and expensive, and they require lengthy preenrichment steps. Rapid enrichment-based diagnostic assays, such as immunomagnetic separation, can reduce detection times while also remaining sensitive and specific. A critical component in these tests is implementing affinity molecules that retain the ability to specifically capture target pathogens over a wide range of in situ applications. The protein complex that forms the distal tip of the bacteriophage S16 long tail fiber is shown here to represent a highly sensitive affinity molecule for the specific enrichment and detection of Salmonella Phage-encoded long tail fibers have huge potential for development as novel affinity molecules for robust and specific diagnostics of a vast spectrum of bacteria., (Copyright © 2017 American Society for Microbiology.)

We recently described the 4.5-year time course of the enteric bacterial microbiota and virome of a patient cured from recurrent Clostridium difficile infection (rCDI) by fecal microbiota transplantation (FMT). Here, we extended the virome analyses and found the patient's phage population to exhibit highly donor-similar characteristics following FMT, which remained stable for the whole period tested (up to 7 months). Moreover, the detected viral populations of donor and patient exhibited comparable diversity and richness. These findings were unexpected since enteric viromes are normally highly variable, assumed to influence the bacterial host community and change with environmental conditions. In contrast to the virome, the bacterial microbiota varied indeed for more than 7 months with ongoing dysbiosis before it reached donor similarity. Our findings that are based on sequence information and protein domain analysis seem to suggest that stable phage properties correlate with successful FMT better than the changing bacterial communities. We speculate that we here preferentially detected a stable core virome, which dominated over a variable flexible virome that may have been too heterogeneous for experimental detection or was underrepresented in the databases. It will be interesting to analyze whether the enteric virome allows predictions for the clinical outcome of FMT for rCDI and other diseases such as inflammatory bowel disease or obesity.