Disentangling outbreaks using whole-genome sequencing: concurrent multistate outbreaks of Salmonella Kottbus in Germany, 2017.

In June 2017, an outbreak of Salmonella Kottbus infection was suspected in Germany. We investigated the outbreak with whole-genome sequencing (WGS) and a case-control study. Forty-six isolates from 69 cases were subtyped. Three WGS clusters were identified: cluster 1 (n = 36), cluster 2 (n = 5) and cluster 3 (n = 3). Compared to controls, cluster 1 cases more frequently consumed raw smoked ham (odds ratio (OR) 10, 95% confidence interval (CI) 1.2-88) bought at supermarket chain X (OR 36, 95% CI 4-356; 9/10 consumed ham Y). All four cluster 2 cases interviewed had consumed quail eggs. Timely WGS was invaluable in distinguishing concurrent outbreaks of a rare Salmonella serotype.

The neonatal intensive parenting unit: an introduction.

This paper describes a paradigm shift occurring in neonatal intensive care. Care teams are moving from a focus limited to healing the baby's medical problems towards a focus that also requires effective partnerships with families. These partnerships encourage extensive participation of mothers and fathers in their baby's care and ongoing bi-directional communication with the care team. The term Newborn Intensive Parenting Unit (NIPU) was derived to capture this concept. One component of the NIPU is family-integrated care, where parents are intimately involved in a baby's care for as many hours a day as possible. We describe six areas of potentially better practices (PBPs) for the NIPU along with descriptions of NIPU physical characteristics, operations, and a relationship-based culture. Research indicates the PBPs should lead to improved outcomes for NIPU babies, better mental health outcomes for their parents, and enhanced well-being of staff.

Two listeria outbreaks caused by smoked fish consumption-using whole-genome sequencing for outbreak investigations.

Listeria monocytogenes may contaminate and persist in food production facilities and cause repeated, seemingly sporadic, illnesses over extended periods of time. We report on the investigation of two such concurrent outbreaks. We compared patient isolates and available isolates from foods and food production facilities by use of whole-genome sequencing and subsequent multilocus sequence type and single nucleotide polymorphism analysis. Outbreak cases shared outbreak strains, defined as Listeria monocytogenes isolates belonging to the same sequence type with fewer than five single nucleotide polymorphism differences. We performed routine food consumption interviews of L. monocytogenes patients and compared outbreak cases with sporadic cases. Two outbreaks were defined, each consisting of ten outbreak cases in the period 2013-15. Seven outbreak cases and a fetus in gestational week 38 died. Listeria monocytogenes isolates from cold smoked or gravad fish products or their two respective production environments were repeatedly found to belong to the outbreak strains. Outbreak cases more often than sporadic cases stated that they consumed the relevant fish products, odds ratio 10.7. Routine collection and typing of food isolates was key to solving the outbreaks. Furthermore, these outbreaks illustrate the value of whole-genome sequencing for outbreak definition and investigation. Whole-genome sequencing combined with epidemiological investigations provided the discriminatory power to recognize low-intensity, extended time-period outbreaks and link them to food products from two different contaminated production facilities with sufficient strength for food authorities to intervene on. Cold smoked and gravad fish constitute risk products and may be responsible for more listeriosis cases than previously recognized.

Recommendations for mental health professionals in the NICU.

This article describes recommended activities of social workers, psychologists and psychiatric staff within the neonatal intensive care unit (NICU). NICU mental health professionals (NMHPs) should interact with all NICU parents in providing emotional support, screening, education, psychotherapy and teleservices for families. NMHPs should also offer educational and emotional support for the NICU health-care staff. NMHPs should function at all levels of layered care delivered to NICU parents. Methods of screening for emotional distress are described, as well as evidence for the benefits of peer-to-peer support and psychotherapy delivered in the NICU. In the ideal NICU, care for the emotional and educational needs of NICU parents are outcomes equal in importance to the health and development of their babies. Whenever possible, NMHPs should be involved with parents from the antepartum period through after discharge.

Measles outbreak spreading from the community to an anthroposophic school, Berlin, 2011.

Between April and July 2011 there was an outbreak of measles virus, genotype D4, in Berlin, Germany. We identified 73 case-patients from the community and among students of an anthroposophic school, who participated in a 4-day school trip, as well as their family and friends. Overall, 27% were aged ≥ 20 years, 57% were female and 15% were hospitalized. Of 39 community case-patients, 38% were aged ≥ 20 years, 67% were female and 63% required hospitalization. Unvaccinated students returning from the school trip were excluded from school, limiting transmission. Within the group of 55 school-trip participants, including 20 measles case-patients, a measles vaccine effectiveness of 97.1% (95% confidence interval 83.4-100) for two doses was estimated using exact Poisson regression. Our findings support school exclusions and the recommendation of one-dose catch-up vaccination for everyone born after 1970 with incomplete or unknown vaccination status, in addition to the two-dose routine childhood immunization recommendation.

A verocytotoxin-producing E. coli outbreak with a surprisingly high risk of haemolytic uraemic syndrome, Denmark, September-October 2012.

Denmark faced an outbreak of verocytotoxin-producing E. coli (VTEC) O157:H7 infections in autumn 2012. Thirteen cases were diagnosed of which eight had haemolytic uraemic syndrome (HUS). Epidemiological investigations suggested ground beef as the vehicle of the outbreak. The outbreak strain had a rare toxin gene subtype profile: eae, vtx1a and vtx2a, and a high proportion of HUS (62%) among cases, a finding previously linked with the outbreak subtype profile. Toxin subtyping can be useful to identify high risk VTEC strains.

Molecular differentiation of Culicoides biting midges (Diptera: Ceratopogonidae) from the subgenus Culicoides Latreille in Denmark.

Identification of Culicoides biting midges to species has attracted attention due to the recent outbreak of bluetongue disease in Northern Europe. Identification of Culicoides to species level has been based on morphological characters and is difficult as several species belonging to species complexes are hard to distinguish. We evaluated the use of the mitochondrial DNA cytochrome oxidase I gene (COI) barcode region in the identification of species within the subgenus Culicoides. COI barcode sequence divergence within species was <1%, whereas it ranged from 12.5% to 19.8% between subgenus Culicoides species. The divergence of subgenus Culicoides species to C. nubeculosus from the subgenus Monoculicoides ranged from 24.4% to 26.1%. Specimens were differentiated into eight unique clusters, including the four common Palaearctic species Culicoides punctatus, Culicoides pulicaris, Culicoides impunctatus, and Culicoides grisescens. Additionally, this study confirms the existence of Culicoides halophilus as a valid taxon and presents the first Culicoides deltus barcode sequences. Three additional groups of specimens were identified: Culicoides dk1 with a COI barcode diverging by 14.3% to 17.2% from other subgenus Culicoides species and Culicoides Kalix and Culicoides dk3, which diverged by 5.9% from each other and showed 12.5% to 17.6% divergence in COI barcode to subgenus Culicoides specimens.

Expression, gene cloning, and characterization of five novel phytases from four basidiomycete fungi: Peniophora lycii, Agrocybe pediades, a Ceriporia sp., and Trametes pubescens.

Phytases catalyze the hydrolysis of phosphomonoester bonds of phytate (myo-inositol hexakisphosphate), thereby creating lower forms of myo-inositol phosphates and inorganic phosphate. In this study, cDNA expression libraries were constructed from four basidiomycete fungi (Peniophora lycii, Agrocybe pediades, a Ceriporia sp., and Trametes pubescens) and screened for phytase activity in yeast. One full-length phytase-encoding cDNA was isolated from each library, except for the Ceriporia sp. library where two different phytase-encoding cDNAs were found. All five phytases were expressed in Aspergillus oryzae, purified, and characterized. The phytases revealed temperature optima between 40 and 60 degrees C and pH optima at 5.0 to 6.0, except for the P. lycii phytase, which has a pH optimum at 4.0 to 5.0. They exhibited specific activities in the range of 400 to 1,200 U. mg, of protein(-1) and were capable of hydrolyzing phytate down to myo-inositol monophosphate. Surprisingly, (1)H nuclear magnetic resonance analysis of the hydrolysis of phytate by all five basidiomycete phytases showed a preference for initial attack at the 6-phosphate group of phytic acid, a characteristic that was believed so far not to be seen with fungal phytases. Accordingly, the basidiomycete phytases described here should be grouped as 6-phytases (EC 3.1.3.26).

Gonadal status in male survivors following childhood brain tumors.

The effect of radiotherapy (RT) and chemotherapy (CT) on gonadal function was assessed in males treated for a childhood brain tumor not directly involving the hypothalamus/pituitary (HP) axis in a population-based study with a long follow-up time. All males <15 yr at the time of diagnosis (median: 9.0 yr, range: 0.8 to 14.9 yr) and diagnosed from January 1970 through February 1997 in the eastern part of Denmark and [gte]18 yr at the time of follow-up (median: 25.8 yr, range:18.5 to 39.3 yr) were included. Thirty males fulfilled the criteria. The median age at time of RT was 9.0 yr (range: 0.8 to 14.9 yr) and the median length of follow-up was 18 yr (range: 2.0 to 28.0 yr). The biological effective dose of RT was determined to the HP region and to the spine and expressed in gray because the biological effective dose gives a means of expressing the biological effect on normal tissue of different dosage schedules in a uniform way. Levels of serum FSH, luteinizing hormone (LH), sexual hormone-binding globulin, testosterone, and inhibin B were measured and compared with healthy age-matched male controls (n = 347), and the patients had a GnRH stimulation test performed with determination of peak FSH and LH. Patients treated with RT + CT (n = 13), compared with patients treated with RT only (n = 17), had significantly higher median peak FSH (8.33 vs. 3.79 IU/L, P = 0.03) and median peak LH (20.0 vs. 12.8 IU/L, P = 0.03), and significantly lower median inhibin B (86.0 vs. 270 pg/ml, P = 0.03), and median inhibin B/FSH ratio (12.8 vs. 107.9, P = 0.04), which indicates gonadal damage. Inhibin B and inhibin B/FSH ratio were also significantly lower in the RT + CT group, compared with controls (median: 86.0 vs. 215 pg/ml, P = 0.02), (median:12.8 vs. 67; P = 0.01), respectively. We found a significantly inverse correlation between basal FSH and inhibin B and FSH and total testicular volume (r(s) = -0.83; P < 0.0001), (r(s) = -0.67; P < 0.0001), respectively, and a significant correlation between inhibin B and total testicular volume (r(s) = 0.63; P < 0.0001). Stepwise backward multiple linear regression analysis showed the best-fit model to predict inhibin B levels included total testicular volume (P = 0.002) and CT (P = 0.09). Median basal LH in the RT-only group was significantly lower, compared with controls (3.44 vs. 2.45 IU/L; P = 0.0001) indicating secondary hypogonadism, and in both the RT + CT group and the RT-only group, levels of testosterone were significantly lower, compared with our reference population (12.8 vs. 21.9 nmol/L; P = 0.001, and 14.7 vs. 21.9 nmol/L; P = 0.0003), respectively. In conclusion these data suggest that cranial irradiation for a childhood brain tumor may affect the HP axis, and adjuvant CT can reduce inhibin B indicating primary gonadal damage. Thus, such patients may have normal or even low levels of FSH despite damage to the seminiferous epithelium, and because the fertility status by a semen analysis for psychological reasons can be difficult to obtain in this group of patients, we suggest inhibin B as the most useful direct serum marker of spermatogenesis in the follow-up of individuals who have received both cranial irradiation and gonadotoxic chemotherapy. However, because the number of patients with RT + CT and RT only are small, these data must be confirmed in further studies.

Humicola insolens cellobiose dehydrogenase: cloning, redox chemistry, and "logic gate"-like dual functionality.

1Cellobiose dehydrogenase is a hemoflavoenzyme that catalyzes the sequential electron-transfer from an electron-donating substrate (e.g. cellobiose) to a flavin center, then to an electron-accepting substrate (e.g. quinone) either directly or via a heme center after an internal electron-transfer from the flavin to heme. We cloned the dehydrogenase from Humicola insolens, which encodes a protein of 761 amino acid residues containing an N-terminal heme domain and a C-terminal flavin domain, and studied how the catalyzed electron transfers are regulated. Based on the correlation between the rate and redox potential, we demonstrated that with a reduced flavin center, the enzyme, as a reductase, could export electron from its heme center by a "outer-sphere" mechanism. With the "resting" flavin center, however, the enzyme could have a peroxidase-like function and import electron to its heme center after a peroxidative activation. The dual functionality of its heme center makes the enzyme a molecular "logic gate", in which the electron flow through the heme center can be switched in direction by the redox state of the coupled flavin center.

Cranial radiotherapy of childhood brain tumours: growth hormone deficiency and its relation to the biological effective dose of irradiation in a large population based study.

OBJECTIVE: The study was to determine the incidence of GH deficiency (GHD) following cranial radiotherapy (RT) for a childhood brain tumour in a large population based study and analyse the biological effective dose (BED) to the hypothalamus/pituitary (HP) region as a risk factor. DESIGN: BED was assessed by use of the linear-quadratic (LQ) model, which gives a means of expressing the biological effect of various treatment schedules in a uniform way. In patients aged >/= 18 years (n = 53) GH status was assessed by an insulin-tolerance test (ITT) (n = 34), however, in patients with seizure disorders (n = 19), and in 20 children aged < 18 years GH status was assessed by an arginine test. Cut-off levels for GHD, indicating GH substitution, were defined by a peak GH response of < 9 mU/l and < 15 mU/l for patients >/= 18 and < 18 years, respectively. PATIENTS: Ninety-one children aged < 15 years eligible for the study, diagnosed between 1970 and 1997 in the Eastern part of Denmark, the Faroe Islands and Greenland, with a primary brain tumour not directly involving the HP axis. 84% (n = 76) agreed to participate. Three patients were excluded due to hypothyroidism detected at time of testing. MEASUREMENTS: Serum GH and levels of serum insulin-like growth factor-I (s-IGF-I) and serum insulin-like growth factor binding protein-3 (s-IGFBP-3) were measured. BED was assessed to the HP region. RESULTS: The median age at the time of RT was 8.7 years (range: 0.8-14.9 years) and the median time of follow-up was 15 years (range: 2-28 years). Fifty-eight patients (80%) had GHD and they had received a median BED of 77.5 Gy to the HP region, whereas the median BED was 54.5 Gy for 15 patients without GHD (P = 0.002). Peak GH and BED were correlated (rs = -0.53, P < 0001). Median IGF-I SDS and IGFBP-3 SDS were -2.5 (-5.2-0.7 SDS) and -1.7 (-5.8-0.9 SDS), respectively, and IGF-I SDS was correlated to peak GH (rs = 0.45, P < 0.001). Peak GH and length of follow-up were related (rs = -0.28, P = 0.018). Stepwise backward multiple linear regression analysis showed that the best-fit model to predict the peak GH release following ITT/arginine stimulation included BED (P < 0.0001) and length of follow-up (P = 0.05). CONCLUSIONS: The data of this study suggest that the majority of long-term survivors of brain tumours develop GH deficiency following radiotherapy in childhood and that the adverse effects of radiotherapy may be directly related to the biologically effective dose. With longer follow-up fewer patients might respond normally to GH stimulation tests.

The consensus concept for thermostability engineering of proteins.

Previously, sequence comparisons between a mesophilic enzyme and a more thermostable homologue were shown to be a feasible approach to successfully predict thermostabilizing amino acid substitutions. The 'consensus approach' described in the present paper shows that even a set of amino acid sequences of homologous, mesophilic enzymes contains sufficient information to allow rapid design of a thermostabilized, fully functional variant of this family of enzymes. A sequence alignment of homologous fungal phytases was used to calculate a consensus phytase amino acid sequence. Upon construction of the synthetic gene, recombinant expression and purification, the first phytase obtained, termed consensus phytase-1, displayed an unfolding temperature (T(m)) of 78.0 degrees C which is 15-22 degrees C higher than the T(m) values of all parent phytases used in its design. Refinement of the approach, combined with site-directed mutagenesis experiments, yielded optimized consensus phytases with T(m) values of up to 90.4 degrees C. These increases in T(m) are due to the combination of multiple amino acid exchanges which are distributed over the entire sequence of the protein and mainly affect surface-exposed residues; each individual substitution has a rather small thermostabilizing effect only. Remarkably, in spite of the pronounced increase in thermostability, catalytic activity at 37 degrees C is not compromised. Thus, the design of consensus proteins is a potentially powerful and novel alternative to directed evolution and to a series of rational approaches for thermostability engineering of enzymes and other proteins.

Growth hormone response to a growth hormone-releasing hormone stimulation test in a population-based study following cranial irradiation of childhood brain tumors.

Children with brain tumors are at high risk of developing growth hormone deficiency (GHD) after cranial irradiation (CI) if the hypothalamus/pituitary (HP) axis falls within the fields of irradiation. The biological effective dose (BED) of irradiation to the HP region was determined, since BED gives a means of expressing the biological effect of various irradiation treatment schedules in a uniform way. Hypothalamic versus pituitary damage as cause of GHD was distinguished in 62 patients by comparing the growth hormone (GH) peak response to an insulin tolerance test (ITT)/arginine stimulation test and the GH response to a growth hormone-releasing hormone (GHRH) stimulation test. Peak GH response to a GHRH test was significantly higher (median 7.3 mU/l; range: 0.5--79.0 mU/l) than that of an ITT/arginine test (median 4.7 mU/l; range: 0.01--75.0 mU/l) (p = 0.017). Peak GH after a GHRH test was significantly inversely correlated to follow-up time (r(s) = -0.46, p < 0.0001) and to BED (R(s) = -0.28, p = 0.03), and both were found to be of significance in a multivariante regression analysis. We speculate that a significant number of patients developed hypothalamic radiation-induced damage to the GHRH secreting neurons, and secondary to this the pituitary gland developed decreased responsiveness to GHRH following CI in childhood.

Dosimetry and growth hormone deficiency following cranial irradiation of childhood brain tumors.

BACKGROUND: Dosimetry of the hypothalamus-pituitary (HP) region could allow prediction of the risk of growth hormone deficiency (GHD) following cranial irradiation. PROCEDURE: Nineteen children (15 boys) with a median age of 6.3 years (range 1.7-16.5) at the time of irradiation of a brain tumor not involving the HP axis were followed for 1.2-6.3 years (median 3.4) from radiotherapy (RT). The dose to a standardized anatomical model including the HP region was calculated from dose-volume histograms of 10% to 100% in steps of 10% of the HP model based on data from a computer-based treatment planning system. If GHD was suspected from insulin-like growth factor-I, serum insulin-like growth factor binding protein-3, and/or height velocity measurements, an arginine stimulation test was performed. GHD was defined by a peak GH <15mU/liter. RESULTS: Ten patients developed GHD 10-26 months from irradiation. Cox regression analysis identified the 90% dose-volume of the HP box as the strongest predictor of development of GHD (P = 0.03). The median dose to the 90% dose-volume of the HP region was 37.5 Gy (range 2. 3-55.3). The cumulated risk of GHD 2.5 years after radiotherapy for children receiving more than and less than 37.5 Gy to the HP region was 87% and 33%, respectively (P = 0.036). CONCLUSIONS: Dosimetry of a defined HP volume provides the opportunity to 1) calculate the exact dose delivered to this region, 2) predict the risk of GHD and, 3) in the future revise the treatment planning and thus reduce the risk of endocrine adverse effects.

Flow cytometric detection of wild yeast in lager breweries.

A flow cytometric method for detection of wild yeast infections in breweries is reported. It is based on selective enrichment in Malt extract Yeast extract Glucose Peptone broth (MYGP) at 37 degrees C and in MYGP with 200 ppm CuSO4 at 25 degrees C, staining with a fluorochrome precursor and flow cytometry. In experiments with several types of wild yeast isolated from breweries and two different strains of lager yeast it has been possible to detect one wild yeast per 10(6) culture yeast after 48-72 h of incubation and, in some cases, after 24 h.

Tandem translation of Bacillus subtilis initiation factor IF2 in E. coli. Over-expression of infBB.su in E. coli and purification of alpha- and beta-forms of IF2B.su.

The protein synthesis initiation factor, IF2, in Bacillus subtilis has previously been characterized as being present in two forms, alpha and beta, of molecular mass 79 and 68 kDa, respectively, on the basis of their cross-reaction with anti-E. coli IF2 antibodies and by the DNA sequence of the gene for IF2, infBB.su. In this work we have cloned infBB.su in E. coli cells. Two proteins of molecular mass identical to the B. subtilis IF2 alpha and -beta were over-expressed and purified using a new three-step ion-exchange chromatography procedure. The N-terminal amino acid sequence of the two proteins was determined and the results confirmed that the two forms were IF2 alpha and -beta, both encoded by the infB gene. The N-terminal amino acid sequence determined for IF2 beta is Met94-Gln-Asn-Asn-Gln-Phe. The presence of methionine at position 94 shows that this form is, in fact, the result of a second translational initiation in infBB.su mRNA, since the codon at amino acid position 94 is GUG, which is the normal codon for valine, but also known to be an initiator codon. This is a new example of the unusual tandem translation in E. coli of an open mRNA reading frame.