Very low frequency of the lactase persistence allele LCT-13910T in the Armenian population.

Primary lactose malabsorption is characterised by a down-regulation of lactase activity after weaning and inability to digest lactose in adulthood. It has been suggested that the historical introduction of dairying led to a positive selection for lactase persistence variants in a regulatory region upstream of the LCT gene. Here, we genotyped 202 Armenian subjects for LCT-13910T, a lactase persistence variant which is widespread in Europeans. The homozygous C/C genotype associated with primary hypolactasia, the heterozygous C/T and the homozygous T/T lactase persistence genotypes were found in 191 (94.6%), 11 (5.4%), and 0 (0.0%) samples, respectively. The frequency for the LCT-13910*T allele was 2.7%. The observed allele frequency of 2.7% for LCT-13910T is even lower than previously reported and supports current phenotypic data about lactose malabsorption in Armenia.

Association between serum amyloid A1 genotype and age of onset restricts to M694 homozygote familial Mediterranean fever patients in Armenia.

OBJECTIVES: Familial Mediterranean fever (FMF) is an autosomal-recessive, inflammatory disorder characterised by short, recurrent attacks of fever, accompanied by pain in the abdomen, chest, or joints and complications of amyloidosis. Recently, we observed a significant association between the serum amyloid A1 (SAA1) ß/ß genotype and a delayed disease onset in 386 M694V homozygous FMF patients. This follow-up study was conducted to additionally analyse MEFV genotypes other than M694V/M694V for a possible influence of the SAA1 genotype on the age of disease onset. METHODS: A total of 700 Armenian patients diagnosed with FMF based on the Tel-Hashomer criteria and carrying two MEFV mutant alleles were included in this study. Patients were divided into three MEFV genotypic subgroups: M694V homozygotes (M694V/M694V), M694V compound heterozygotes (M694V/Other), and patients with genotypes excluding M694V (Other/Other). MEFV and SAA1 analyses were performed by a commercial reverse-hybridisation assay, and resulting genotypes were matched against the demographic and clinical characteristics of the patients. RESULTS: Within the subgroup of M694/M694 homozygotes, SAA1 genotype ß/ß could be identified in 115 (34.43%) and 32 (61.54%) patients with an age of onset <20 and ≥20 years, respectively(p<0.001). However, no such relationship could be observed for MEFV genotypic subgroups M694V/Other (p=0.465) and Other/Other (p=0.697). CONCLUSIONS: Our data suggest, that the influence of SAA1 genotypic variation on the age of disease onset restricts to FMF patients homozygous for MEFV mutation M694V.

Serum amyloid A1 genotype associates with adult-onset familial Mediterranean fever in patients homozygous for mutation M694V.

OBJECTIVES: FMF shows considerable variability in severity and type of clinical manifestations by geographic region, which are attributed to Mediterranean fever (MEFV) gene allelic heterogeneity, additional genetic modifiers and environmental factors. Considering the severe impact of MEFV mutation M694V on the FMF phenotype, this work aimed at investigating a possible disease modifying role of the serum amyloid A1 (SAA1) genotype in a cohort of 386 Armenian FMF patients homozygous for MEFV mutation M694V. METHODS: A cohort of 386 Armenian patients diagnosed with FMF based on the Tel-Hashomer criteria and carrying two MEFV M694V mutant alleles were included in this study. Fifty-two (13.40%) of these patients experienced their first attack at the age of ≥20 years (i.e. adult-onset FMF). MEFV and SAA1 analyses were performed by a commercial reverse-hybridization assay, and resulting genotypes were matched against the patients' clinicodemographic profiles. RESULTS: Genotypic distribution of SAA1 alleles was significantly different between patients with an age of onset <20 and ≥20 years. SAA1 genotypes α/α, α/ß and ß/ß could be identified in 8 (15.38%), 12 (23.08%) and 32 (61.54%) adult-onset patients while this was the case for 47 (14.07%), 172 (51.50%) and 115 (34.43%) patients with a disease onset <20 years, respectively (P < 0.001). Furthermore, adult-onset disease was associated with a less severe FMF phenotype (P < 0.001). CONCLUSION: We have identified a significant relationship between the SAA1ß/ß genotype and the age of disease onset in M694V homozygous FMF patients.

Infertility Causes and Pregnancy Outcome in Patients With Familial Mediterranean Fever and Controls.

OBJECTIVE: Recurrent attacks of peritonitis due to familial Mediterranean fever (FMF) may lead to peritoneal adhesions and fallopian tube obstruction. Colchicine, which is the treatment of choice for FMF, may disturb cell division. Secondary amyloidosis, a complication of untreated FMF, may involve the testes and ovaries. Thus, FMF and colchicine may potentially affect fertility and pregnancy in patients with FMF. The aims of the study are to evaluate the causes of infertility and pregnancy outcome in FMF patients and to compare them with 2 groups: non-FMF patients with peritoneal female genital tuberculosis (FGTB) and normal healthy controls. METHODS: This is a retrospective study in which FMF patients with reproductive disorders were recruited from the National Center of Medical Genetics and Primary Health Care in Yerevan, Armenia. The patients with FGTB and the healthy controls with reproductive problems were recruited successively from a large gynecology clinic in Yerevan. Genetic analyses for FMF were performed using ViennaLab StripAssay. RESULTS: The FMF group (211 patients) resembles the FGTB group (127 patients) regarding etiologies of infertility. However, in vitro fertilization (IVF) success rate and pregnancy outcome were comparable between the FMF patients and the control group (162 patients). Infertility in patients with FMF was clearly associated with a more severe disease and a lack of adequate colchicine treatment. CONCLUSIONS: Colchicine medication and controlled FMF disease do not adversely affect the reproductive system and pregnancy outcome. However, a lack of an appropriate colchicine treatment may cause infertility and poor pregnancy outcome.

The FKBP4 Gene, Encoding a Regulator of the Androgen Receptor Signaling Pathway, Is a Novel Candidate Gene for Androgen Insensitivity Syndrome.

Androgen insensitivity syndrome (AIS), manifesting incomplete virilization in 46,XY individuals, is caused mostly by androgen receptor (AR) gene mutations. Therefore, a search for AR mutations is a routine approach in AIS diagnosis. However, some AIS patients lack AR mutations, which complicates the diagnosis. Here, we describe a patient suffering from partial androgen insensitivity syndrome (PAIS) and lacking AR mutations. The whole exome sequencing of the patient and his family members identified a heterozygous FKBP4 gene mutation, c.956T>C (p.Leu319Pro), inherited from the mother. The gene encodes FKBP prolyl isomerase 4, a positive regulator of the AR signaling pathway. This is the first report describing a FKBP4 gene mutation in association with a human disorder of sexual development (DSD). Importantly, the dysfunction of a homologous gene was previously reported in mice, resulting in a phenotype corresponding to PAIS. Moreover, the Leu319Pro amino acid substitution occurred in a highly conserved position of the FKBP4 region, responsible for interaction with other proteins that are crucial for the AR functional heterocomplex formation and therefore the substitution is predicted to cause the disease. We proposed the FKBP4 gene as a candidate AIS gene and suggest screening that gene for the molecular diagnosis of AIS patients lacking AR gene mutations.

Comparing thermal inactivation to a combined process of moderate heat and high pressure: Effect on ascospores in strawberry puree.

High pressure processing is a mild preservation process that inactivates pathogenic and spoilage micro-organisms in food products, but preserves the fresh characteristics of a product. Compared to untreated product, an enhanced shelf life is obtained during refrigerated storage. Knowledge on the use of high pressure pasteurisation aimed for ambient storage is limited. The aim of this research was to investigate if a combination of high pressure and moderate heat could be used to produce a shelf-stable high-acid fruit product. Ascospores of the heat resistant fungi Talaromyces macrosporus and Aspergillus fischeri were added to fresh strawberry puree that served as a model system. The effect of the processing steps and storage at ambient temperature for 2 weeks was studied on viability of the ascospores. A preheating step at 69 °C/2 min resulted in full or partial activation of A. fischeri and T. macrosporus spores, respectively. The pressure build-up by the process without any holding time resulted in additional activation of spores. A combination of moderate heat (maximum 85-90 °C) and high pressure (500-700 MPa) for holding times up to 13 min inactivated these highly resistant spores much faster than a heat treatment alone. At Tmax = 85 °C and 600 MPa the spores of T. macrosporus and A. fischeri were inactivated by 5.0 and 5.5 log10 after 13 and 7 min, respectively. At Tmax = 85 °C the heat treatment alone did not reduce the viability of these spores up to 60 min of treatment. At Tmax = 90 °C the holding time of the combined pressure-heat treatment could be reduced to obtain the same degree of inactivation of the heat resistant fungi. In addition, treated and untreated ascospores in strawberry puree were stored for 14 days at room temperature to evaluate delayed outgrowth of spores. Untreated ascospores of A. fischeri were activated by storage in the puree. However, at conditions combining high pressure ≥ 600 MPa with Tmax ≥ 85 °C for 13 min, heat resistant fungi were successfully inactivated. This research showed that a combination of moderate heat and pressure can drastically improve the effectiveness to inactivate heat-resistant ascospores in a high-acid fruit product compared to a heat treatment, potentially resulting in a better product quality.

ISSAID/EMQN Best Practice Guidelines for the Genetic Diagnosis of Monogenic Autoinflammatory Diseases in the Next-Generation Sequencing Era.

BACKGROUND: Monogenic autoinflammatory diseases are caused by pathogenic variants in genes that regulate innate immune responses, and are characterized by sterile systemic inflammatory episodes. Since symptoms can overlap within this rapidly expanding disease category, accurate genetic diagnosis is of the utmost importance to initiate early inflammation-targeted treatment and prevent clinically significant or life-threatening complications. Initial recommendations for the genetic diagnosis of autoinflammatory diseases were limited to a gene-by-gene diagnosis strategy based on the Sanger method, and restricted to the 4 prototypic recurrent fevers (MEFV, MVK, TNFRSF1A, and NLRP3 genes). The development of best practices guidelines integrating critical recent discoveries has become essential. METHODS: The preparatory steps included 2 online surveys and pathogenicity annotation of newly recommended genes. The current guidelines were drafted by European Molecular Genetics Quality Network members, then discussed by a panel of experts of the International Society for Systemic Autoinflammatory Diseases during a consensus meeting. RESULTS: In these guidelines, we combine the diagnostic strength of next-generation sequencing and recommendations to 4 more recently identified genes (ADA2, NOD2, PSTPIP1, and TNFAIP3), nonclassical pathogenic genetic alterations, and atypical phenotypes. We present a referral-based decision tree for test scope and method (Sanger versus next-generation sequencing) and recommend on complementary explorations for mosaicism, copy-number variants, and gene dose. A genotype table based on the 5-category variant pathogenicity classification provides the clinical significance of prototypic genotypes per gene and disease. CONCLUSIONS: These guidelines will orient and assist geneticists and health practitioners in providing up-to-date and appropriate diagnosis to their patients.

Inactivation kinetics of Geobacillus stearothermophilus spores by a peracetic acid or hydrogen peroxide fog in comparison to the liquid form.

The aim of this study was to compare the sporicidal effect of the disinfectants peracetic acid (PAA) or hydrogen peroxide (H2O2) applied as a fog or as a liquid. The efficacy of fogging of the disinfectants was tested in a closed isolator cabinet using highly heat and chemical-resistant spores of Geobacillus stearothermophilus. Fogging of a 0.06% solution of PAA resulted in over 5-log reduction of spores in 10 min, whereas for PAA used in liquid form the same reduction was achieved in 4.5 min. The inactivation curves for fog and liquid were fitted using three different models (Linear with shoulder, Weibull, Gauss-Eyring). This showed a shoulder for the fog with an estimated length of 4.1 min, but the D values, calculated for the linear parts of the curves, were not significantly different (1.1 and 0.8 min for the PAA fog and solution, respectively). Similar results were obtained for a 12% H2O2 solution, albeit that H2O2 was less effective compared to PAA, requiring 60 min to reach 3-log reduction when applied as a fog, with an estimated shoulder of 18.5 min. Fogging of a 0.06% peracetic acid solution effectively inactivated G. stearothermophilus spores. Overall, the data show that fogging can be an effective method of applying disinfectants but that a shoulder in the inactivation curves should be considered in process design. This study provides inactivation kinetics for disinfection using PAA or H2O2-based fog, which can aid in selection and validation of process parameters for disinfection of contained areas by fogging.

Clinical and genetic heterogeneity in a large cohort of Armenian patients with late-onset familial Mediterranean fever.

PURPOSE: This work aimed at investigating demographic, clinical, and genetic characteristics of individuals experiencing their first familial Mediterranean fever (FMF) attack at age ≥40 years in a very large cohort of Armenian FMF patients. METHODS: In total, 10,370 Armenian patients diagnosed with FMF based on the Tel Hashomer criteria and carrying at least one MEFV mutant allele were included in this study. RESULTS: A total of 354 (3.40%) patients had late-onset FMF. Of these, 194 (54.80%) were female and 160 (45.20%) were male. The following genotypes were significantly associated with the late-onset variant: M680I/E148Q (P = 0.004), M694V/E148Q (P < 0.001), and V726A/V726A (P< 0.001). Of note, 12/354 (3.40%) patients were found to be homozygous for the M694V mutation. Individuals with late-onset FMF had a milder disease phenotype presenting significantly less frequent fever, skin manifestation, and chest pain compared to individuals with a disease onset before 40 years of age. Abdominal pain was found more often in the late-onset FMF group, whereas arthritis, proteinuria, and amyloidosis did not differ significantly between the two groups. CONCLUSION: Our data suggest that late-onset FMF is more prevalent in women and is of greater clinical as well as genetic heterogeneity than previously reported.

Comprehensive analysis of mutations in the MEFV gene reveal that the location and not the substitution type determines symptom severity in FMF.

BACKGROUND: Familial Mediterranean Fever (FMF) is an autoinflammatory disorder caused by mutations in the MEFV gene. These mutations appear in different populations with different frequencies and their caused symptom severities vary from mild to moderate to severe depending on the mutation type. METHODS: In this study, we analyzed the mutations that have been reported in the MEFV gene from symptomatic FMF patients and compared their frequencies in different populations from the 1000 Genome and the Exome databases, using statistical clustering. We also analyzed the nucleotide and amino acid substitution patterns across the MEFV gene. RESULTS: We found 16 (8%) nonsynonymous mutations outside exon 10 that did not cluster with known disease-causing mutations (DCMs), due to their high frequencies in other populations. We also studied the substitution patterns for nucleotides and amino acids to determine the conserved and variable regions in the MEFV gene. In general more nonsynonymous substitutions were reported in exons 2, 3, and 10 from the FMF database (symptomatic FMF patients) compared to the 1000 Genome and the Exome databases. The same was true for amino acid (AA) substitutions where there were 1.5 times more radical (RAD) to conservative (CON) changes. However, when it came to AA substitutions exon 10 was quite conserved with a RAD/CON ratio of 0.9. In fact, we report that the most severe FMF symptoms are caused by conservative mutations in two highly conserved exon 10 regions. CONCLUSION: We found presumptive FMF-causing mutations that did not cluster with DCMs based on their allele frequencies. We also observed that the type of mutation is less likely to determine the severity of the FMF symptoms; rather it was the location of the mutations that was the determining factor.

MEFV and SAA1 genotype associations with clinical features of familial Mediterranean fever and amyloidosis in Armenia.

OBJECTIVES: Familial Mediterranean fever (FMF) is a hereditary periodic disease characterised by recurrent attacks of fever and serositis. The most devastating complication of FMF is amyloidosis (AA) affecting mainly the kidneys. Aim of the study is to search for correlations between the MEFV genotype and the SAA polymorphisms with the clinical manifestations of FMF and the occurrence of amyloidosis in a large cohort of Armenian patients. METHODS: Information about the MEFV mutations, SAA polymorphisms and FMF clinical features, were obtained for 1017 FMF patients, from the database of the Center of Medical Genetics in Yerevan. For identifying probable correlation between the MEFV and SAA genotype and clinical features of FMF, regression logistic analyses were conducted between the genotype and phenotype of the patients. RESULTS: Patients homozygous for M694V were highly associated with all the clinical features of FMF and its complications - proteinuria and amyloidosis. None of the SAA1 polymorphisms had any correlation with FMF clinical features. However, homozygosis for SAA1 α/α polymorphism was associated with proteinuria and amyloidosis whereas carrying the ß/ß polymorphism was found to be protective for amyloidosis. CONCLUSIONS: The SAA1 α allele is strongly associated with amyloidosis in FMF patients. This observation is valid in inflammatory diseases other than FMF too. SAA1 polymorphism has no effect on the clinical features of FMF. M694V homozygosis is highly associated withal typical features of FMF and with amyloidosis. FMF course in Armenia is similar to that in Middle Eastern countries where FMF disease is common.

Comparative Genomics of Iron-Transporting Systems in Bacillus cereus Strains and Impact of Iron Sources on Growth and Biofilm Formation.

Iron is an important element for bacterial viability, however it is not readily available in most environments. We studied the ability of 20 undomesticated food isolates of Bacillus cereus and two reference strains for capacity to use different (complex) iron sources for growth and biofilm formation. Studies were performed in media containing the iron scavenger 2,2-Bipyridine. Transcriptome analysis using B. cereus ATCC 10987 indeed showed upregulation of predicted iron transporters in the presence of 2,2-Bipyridine, confirming that iron was depleted upon its addition. Next, the impact of iron sources on growth performance of the 22 strains was assessed and correlations between growth stimulation and presence of putative iron transporter systems in the genome sequences were analyzed. All 22 strains effectively used Fe citrate and FeCl3 for growth, and possessed genes for biosynthesis of the siderophore bacillibactin, whereas seven strains lacked genes for synthesis of petrobactin. Hemoglobin could be used by all strains with the exception of one strain that lacked functional petrobactin and IlsA systems. Hemin could be used by the majority of the tested strains (19 of 22). Notably, transferrin, ferritin, and lactoferrin were not commonly used by B. cereus for growth, as these iron sources could be used by 6, 3, and 2 strains, respectively. Furthermore, biofilm formation was found to be affected by the type of iron source used, including stimulation of biofilms at liquid-air interphase (FeCl3 and Fe citrate) and formation of submerged type biofilms (hemin and lactoferrin). Our results show strain variability in the genome-encoded repertoire of iron-transporting systems and differences in efficacy to use complex iron sources for growth and biofilm formation. These features may affect B. cereus survival and persistence in specific niches.

Draft Whole-Genome Sequences of 11 Bacillus cereus Food Isolates.

Bacillus cereus is a foodborne pathogen causing emetic and diarrheal-type syndromes. Here, we report the whole-genome sequences of 11 B. cereus food isolates.

Bacillus cereus ATCC 14579 RpoN (Sigma 54) Is a Pleiotropic Regulator of Growth, Carbohydrate Metabolism, Motility, Biofilm Formation and Toxin Production.

Sigma 54 is a transcriptional regulator predicted to play a role in physical interaction of bacteria with their environment, including virulence and biofilm formation. In order to study the role of Sigma 54 in Bacillus cereus, a comparative transcriptome and phenotypic study was performed using B. cereus ATCC 14579 WT, a markerless rpoN deletion mutant, and its complemented strain. The mutant was impaired in many different cellular functions including low temperature and anaerobic growth, carbohydrate metabolism, sporulation and toxin production. Additionally, the mutant showed lack of motility and biofilm formation at air-liquid interphase, and this correlated with absence of flagella, as flagella staining showed only WT and complemented strain to be highly flagellated. Comparative transcriptome analysis of cells harvested at selected time points during growth in aerated and static conditions in BHI revealed large differences in gene expression associated with loss of phenotypes, including significant down regulation of genes in the mutant encoding enzymes involved in degradation of branched chain amino acids, carbohydrate transport and metabolism, flagella synthesis and virulence factors. Our study provides evidence for a pleiotropic role of Sigma 54 in B. cereus supporting its adaptive response and survival in a range of conditions and environments.

Comparative analysis of biofilm formation by Bacillus cereus reference strains and undomesticated food isolates and the effect of free iron.

Biofilm formation of Bacillus cereus reference strains ATCC 14579 and ATCC 10987 and 21 undomesticated food isolates was studied on polystyrene and stainless steel as contact surfaces. For all strains, the biofilm forming capacity was significantly enhanced when in contact with stainless steel (SS) as a surface as compared to polystyrene (PS). For a selection of strains, the total CFU and spore counts in biofilms were determined and showed a good correlation between CFU counts and total biomass of these biofilms. Sporulation was favoured in the biofilm over the planktonic state. To substantiate whether iron availability could affect B. cereus biofilm formation, the free iron availability was varied in BHI by either the addition of FeCl3 or by depletion of iron with the scavenger 2,2-Bipyridine. Addition of iron resulted in increased air-liquid interface biofilm on polystyrene but not on SS for strain ATCC 10987, while the presence of Bipyridine reduced biofilm formation for both materials. Biofilm formation was restored when excess FeCl3 was added in combination with the scavenger. Further validation of the iron effect for all 23 strains in microtiter plate showed that fourteen strains (including ATCC10987) formed a biofilm on PS. For eight of these strains biofilm formation was enhanced in the presence of added iron and for eleven strains it was reduced when free iron was scavenged. Our results show that stainless steel as a contact material provides more favourable conditions for B. cereus biofilm formation and maturation compared to polystyrene. This effect could possibly be linked to iron availability as we show that free iron availability affects B. cereus biofilm formation.

Patient management and the association of less common familial Mediterranean fever symptoms with other disorders.

PURPOSE: In this study, we present clinical data from 16,000 familial Mediterranean fever patients. We also discuss the clinical manifestation of a subset of these patients and their potential symptom associations with other disorders. METHODS: Familial Mediterranean fever patients were confirmed using Tel-Hashomer criteria and were tested for the 12 most common mutations using the familial Mediterranean fever StripAssay. A total of 100 samples were selected, and their MEFV gene exons and intron junctions were completely sequenced. RESULTS: We observed that in children severe phenotypes with polyserositis, erysipelas-like erythema, splenomegaly, and vasculitis are associated with high penetrance of exon 10 mutations, particularly M694V. Several forms of arthritis were associated with familial Mediterranean fever, including acute mono/oligoarthritis in the lower extremities, destructive arthritis, ankylosing spondylitis, sacroiliitis, arthritis of the hip joint, and juvenile chronic arthritis. Severe life-threatening complications, such as adhesive intestinal obstruction, renal amyloidosis, and uncommon/rare symptoms were sometimes the only form of familial Mediterranean fever manifestation. CONCLUSION: We suggest performing familial Mediterranean fever genetic testing for patients presenting with rare/uncommon symptoms also common in other disorders, to prevent misdiagnosis or delayed diagnosis. In our experience, the most effective patient management for familial Mediterranean fever was its rapid diagnosis through genetic testing, initiation of colchicine therapy, and promotion of attack prevention through counseling.

Identification and functional consequences of a recurrent NLRP12 missense mutation in periodic fever syndromes.

OBJECTIVE: To gain insight into the molecular bases of genetically unexplained periodic fever syndromes (PFS) by screening NLRP12, a gene in which only a nonsense and a splice site mutation have so far been identified, and to assess the functional consequences of the identified missense variation. METHODS: NLRP12 was screened for mutations by direct sequencing. Functional assays were performed in HEK 293T cells stably expressing the proapoptotic protein ASC and procaspase 1, in order to determine the effects of normal and mutated NLRP12 proteins on speck formation, caspase 1 signaling, and NF-κB activation. RESULTS: A heterozygous NLRP12 missense mutation involving a CpG site (c.1054C>T; p.Arg352Cys) was identified in exon 3, which encodes the nucleotide-binding site (NBS) of the protein, in 2 patients from different countries and carrying different NLRP12 haplotypes. The mutation, which does not alter the inhibitory effect of NLRP12 on NF-κB activation, increases speck formation and activates caspase 1 signaling. To define this new class of PFS, we propose the term NLRP12-associated disorders (NLRP12AD). CONCLUSION: Given the rarity of known NLRP12-associated disorders, the identification of this NLRP12 molecular defect contributes to the delineation of the clinical spectrum associated with mutations in this gene and highlights the importance of screening NLRP12 in patients presenting with unexplained PFS. This study also demonstrates, by means of functional assays, the deleterious effect of this recurrent missense mutation; the gain of function for speck formation and caspase 1 signaling associated with this NBS mutation is consistent with the inflammatory phenotype of PFS.