Browsing by Subject "INFECTIONS"

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  • Vultaggio, Alessandra; Agache, Ioana; Akdis, Cezmi A.; Akdis, Mubeccel; Bavbek, Sevim; Bossios, Apostolos; Bousquet, Jean; Boyman, Onur; Chaker, Adam M.; Chan, Susan; Chatzipetrou, Alexia; Feleszko, Wojciech; Firinu, Davide; Jutel, Marek; Kauppi, Paula; Klimek, Ludger; Kolios, Antonios; Kothari, Akash; Kowalski, Marek L.; Matucci, Andrea; Palomares, Oscar; Pfaar, Oliver; Rogala, Barbara; Untersmayr, Eva; Eiwegger, Thomas (2020)
    The outbreak of the SARS-CoV-2-induced coronavirus disease 2019 (COVID-19) pandemic re-shaped doctor-patient interaction and challenged capacities of healthcare systems. It created many issues around the optimal and safest way to treat complex patients with severe allergic disease. A significant number of the patients are on treatment with biologicals, and clinicians face the challenge to provide optimal care during the pandemic. Uncertainty of the potential risks for these patients is related to the fact that the exact sequence of immunological events during SARS-CoV-2 is not known. Severe COVID-19 patients may experience a "cytokine storm" and associated organ damage characterized by an exaggerated release of pro-inflammatory type 1 and type 3 cytokines. These inflammatory responses are potentially counteracted by anti-inflammatory cytokines and type 2 responses. This expert-based EAACI statement aims to provide guidance on the application of biologicals targeting type 2 inflammation in patients with allergic disease. Currently, there is very little evidence for an enhanced risk of patients with allergic diseases to develop severe COVID-19. Studies focusing on severe allergic phenotypes are lacking. At present, noninfected patients on biologicals for the treatment of asthma, atopic dermatitis, chronic rhinosinusitis with nasal polyps, or chronic spontaneous urticaria should continue their biologicals targeting type 2 inflammation via self-application. In case of an active SARS-CoV-2 infection, biological treatment needs to be stopped until clinical recovery and SARS-CoV-2 negativity is established and treatment with biologicals should be re-initiated. Maintenance of add-on therapy and a constant assessment of disease control, apart from acute management, are demanded.
  • Pfaar, O; Klimek, L; Jutel, M; Akdis, C A; Bousquet, J; Breiteneder, H; Chinthrajah, S; Diamant, Z; Eiwegger, T; Fokkens, W J; Fritsch, H W; Nadeau, K C; O'Hehir, R E; O'Mahony, L; Rief, W; Sampath, V; Schedlowski, M; Torres, M; Traidl-Hoffmann, C; Wang, D Y; Zhang, L; Bonini, M; Brehler, R; Brough, H A; Chivato, T; Del Giacco, S; Dramburg, S; Gawlik, R; Gelincik, A; Hoffmann-Sommergruber, K; Hox, V; Knol, E; Lauerma, A; Matricardi, P M; Mortz, C G; Ollert, M; Palomares, O; Riggioni, C; Schwarze, J; Skypala, I; Untersmayr, S; Walusiak-Skorupa, J; Ansotegui, I; Bachert, C; Bedbrook, A; Bosnic-Anticevich, S; Brussino, L; Canonica, G W; Cardona, V; Carreiro-Martins, P; Cruz, A A; Czarlewski, W; Fonseca, J A; Gotua, M; Haahtela, T; Ivancevich, J C; Kuna, P; Kvedariene, V; Larenas-Linnemann, D; Latiff, A; Morais-Almeida, M; Mullol, J; Naclerio, R; Ohta, K; Okamoto, Y; Onorato, G L; Papadopoulos, N G; Patella, V; Regateiro, F S; Samolinski, B; Suppli Ulrik, C; Toppila-Salmi, S; Valiulis, A; Ventura, M T; Yorgancioglu, A; Zuberbier, T; Agache, I (2021)
    BackgroundThe coronavirus disease 2019 (COVID-19) has evolved into a pandemic infectious disease transmitted by the severe acute respiratory syndrome coronavirus (SARS-CoV-2). Allergists and other healthcare providers (HCPs) in the field of allergies and associated airway diseases are on the front line, taking care of patients potentially infected with SARS-CoV-2. Hence, strategies and practices to minimize risks of infection for both HCPs and treated patients have to be developed and followed by allergy clinics. MethodThe scientific information on COVID-19 was analysed by a literature search in MEDLINE, PubMed, the National and International Guidelines from the European Academy of Allergy and Clinical Immunology (EAACI), the Cochrane Library, and the internet. ResultsBased on the diagnostic and treatment standards developed by EAACI, on international information regarding COVID-19, on guidelines of the World Health Organization (WHO) and other international organizations, and on previous experience, a panel of experts including clinicians, psychologists, IT experts, and basic scientists along with EAACI and the "Allergic Rhinitis and its Impact on Asthma (ARIA)" initiative have developed recommendations for the optimal management of allergy clinics during the current COVID-19 pandemic. These recommendations are grouped into nine sections on different relevant aspects for the care of patients with allergies. ConclusionsThis international Position Paper provides recommendations on operational plans and procedures to maintain high standards in the daily clinical care of allergic patients while ensuring the necessary safety measures in the current COVID-19 pandemic.
  • Boenink, Rianne; Stel, Vianda S.; Waldum-Grevbo, Bard E.; Collart, Frederic; Kerschbaum, Julia; Heaf, James G.; de Meester, Johan; Finne, Patrik; Garcia-Marcos, Sergio A.; Evans, Marie; Ambuhl, Patrice M.; Arici, Mustafa; Ayav, Carole; Steenkamp, Retha; Cases, Aleix; Traynor, Jamie P.; Palsson, Runolfur; Zoccali, Carmine; Massy, Ziad A.; Jager, Kitty J.; Kramer, Anneke (2020)
    The objective of this study was to investigate whether the improvement in survival seen in patients on kidney replacement therapy reflects the enhanced survival of the general population. Patient and general population statistics were obtained from the European Renal Association-European Dialysis and Transplant Association (ERA-EDTA) Registry and the World Health Organization databases, respectively. Relative survival models were composed to examine trends over time in all-cause and cause-specific excess mortality, stratified by age and modality of kidney replacement therapy, and adjusted for sex, primary kidney disease and country. In total, 280,075 adult patients started kidney replacement therapy between 2002 and 2015. The excess mortality risk in these patients decreased by 16% per five years (relative excess mortality risk (RER) 0.84; 95% confidence interval 0.83-0.84). This reflected a 14% risk reduction in dialysis patients (RER 0.86; 0.85-0.86), and a 16% increase in kidney transplant recipients (RER 1.16; 1.07-1.26). Patients on dialysis showed a decrease in excess mortality risk of 28% per five years for atheromatous cardiovascular disease as the cause of death (RER 0.72; 0.70-0.74), 10% for non-atheromatous cardiovascular disease (RER 0.90; 0.88-0.92) and 10% for infections (RER 0.90; 0.87-0.92). Kidney transplant recipients showed stable excess mortality risks for most causes of death, although it did worsen in some subgroups. Thus, the increase in survival in patients on kidney replacement therapy is not only due to enhanced survival in the general population, but also due to improved survival in the patient population, primarily in dialysis patients.
  • Friman, Mari Johanna; Eklund, Marjut Hannele; Pitkälä, Anna Helena; Rajala-Schultz, Päivi Johanna; Rantala, Merja Hilma Johanna (2019)
    Background Infection with Serratia spp. have been associated with mastitis outbreaks in dairy cattle herds. Environmental contamination or a point source, like a teat dip product, have often been observed to be potential sources of such outbreaks. We describe two Serratia marcescens associated mastitis outbreaks associated with a contaminated teat dip containing a tertiary alkyl amine, n,n-bis (3-aminopropyl) dodecylamine in two dairy cattle farms in Finland. S. marcescens strains isolated from milk and environmental samples were identified by the MALDI-TOF method. Results Six specimens (n = 19) on Herd 1 and all specimens (n = 9) on Herd 2 were positive for S. marcescens. Positive specimens were from mastitis milk and teat dip liquid and equipment. Bacteria were not isolated from the unopened teat dip canister. The same clone of S. marcescens was isolated from milk samples and teat dip samples within the farms. Pulsed field gel electrophoresis results to the S. marcescens isolates from these two different herds were tested with unweighted pair-group method using arithmetic average clustering analysis. The isolates were not same clone in both herds, because similarity in that test was only 75% when cut-off value to similarity is 85%. Conclusions Our investigation showed that the post milking teat dip and/or temporary containers were contaminated with S. marcescens and these were most likely the sources for new mastitis cases. The negative result from the unopened teat dip canister and positive results from refillable containers demonstrated that the product itself was not contaminated with S. marcescens at the production unit, but became contaminated at the farm level.
  • Masika, Moses Muia; Korhonen, Essi M.; Smura, Teemu; Uusitalo, Ruut; Vapalahti, Katariina; Mwaengo, Dufton; Jääskeläinen, Anne J.; Anzala, Omu; Vapalahti, Olli; Huhtamo, Eili (2020)
    Dengue virus (DENV) has caused recent outbreaks in coastal cities of Kenya, but the epidemiological situation in other areas of Kenya is largely unknown. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. Altogether, 560 patients were sampled in 2016-2017 in rural Taita-Taveta County (n = 327) and urban slums of Kibera, Nairobi (n = 233). The samples were studied for DENV IgM, IgG, NS1 antigen and flaviviral RNA. IgG seroprevalence was found to be higher in Taita-Taveta (14%) than in Nairobi (3%). Five Taita-Taveta patients were positive for flaviviral RNA, all identified as DENV-2, cosmopolitan genotype. Local transmission in Taita-Taveta was suspected in a patient without travel history. The sequence analysis suggested that DENV-2 strains circulating in coastal and southern Kenya likely arose from a single introduction from India. The molecular clock analyses dated the most recent ancestor to the Kenyan strains a year before the large 2013 outbreak in Mombasa. After this, the virus has been detected in Kilifi in 2014, from our patients in Taita-Taveta in 2016, and in an outbreak in Malindi in 2017. The results highlight that silent transmission occurs between epidemics and also affects rural areas. More information is needed to understand the local epidemiological characteristics and future risks of dengue in Kenya. Author summary Dengue virus (DENV) is an emerging mosquito-borne global health threat in the tropics and subtropics. The majority of the world's population live in areas at risk of dengue that can cause a wide variety of symptoms from febrile illness to haemorrhagic fever. Information of DENV in Africa is limited and fragmented. In Kenya, dengue is a recognized disease in coastal cities that have experienced recent outbreaks. We investigated the role of DENV infection as a cause of acute febrile disease in non-epidemic settings in rural and urban study areas in Kenya. We found DENV-2 in five febrile patients from rural Taita-Taveta, where no dengue has been reported before. Genetic analysis of the virus suggests it to be most likely of Indian origin. This Indian origin DENV-2 was detected in the Mombasa outbreak in 2013, in Kilifi in 2014, in Taita-Taveta in 2016 (our study samples) and again in the Malindi outbreak in 2017. The results suggest that dengue is unrecognized in rural Kenya and more studies are needed for local risk assessment. Our findings of virus transmission between epidemics contribute to better understanding of the epidemiological situation and origins of DENV in Kenya.
  • Mauramo, Matti; Rohde, Luzius; Ramseier, Adrian M.; Rovo, Alicia; Waltimo, Tuomas (2017)
    The aetiology of hyposalivation in haematopoietic stem cell transplantation (HSCT) recipients is not fully understood. This study examined the effects of treatment-related aetiological factors, particularly medications, on stimulated salivary flow in HSCT recipients. Adult HSCT recipients (N = 118, 66 males, 27 autologous and 91 allogeneic transplants) were examined. Stimulated whole salivary flow rates (SWSFR) were measured before HSCT and at 6 and 12 months post-HSCT. Linear regression models were used to analyse the associations of medications and transplant-related factors with salivary flow rates, which were compared to salivary flow rates of generally healthy controls (N = 247). The SWSFR of recipients were lower pre-HSCT (mean +/- standard deviation, 0.88 +/- 0.56 ml/min; P <0.001), 6 months post-HSCT (0.84 +/- 0.61; P <0.001) and 12 months post-HSCT (1.08 +/- 0.67; P = 0.005) than the SWSFR of controls (1.31 +/- 0.65). In addition, hyposalivation (<0.7 ml/min) was more frequent among HSCT recipients pre-HSCT (P <0.001), 6 months post-HSCT (P <0.001) and 12 months post-HSCT (P = 0.01) than among controls. The SWSFR was observed to improve over time being significantly higher 12 months post-HSCT compared to pre-HSCT (P <0.001). The observed decrease of salivary flow could not be explained by the examined transplant-related factors and medications. Decreased stimulated salivary flow rates could not be explained by the examined factors alone; these findings indicate that hyposalivation in HSCT recipients exhibits a multifactorial aetiology. All HSCT recipients should be considered to be at high risk of hyposalivation and consequent oral diseases, and they should be treated accordingly.
  • Elf, Sonja; Auvinen, Pauliina; Jahn, Lisa; Liikonen, Karoliina; Sjöblom, Solveig; Saavalainen, Päivi; Mäki, Minna; Eboigbodin, Kevin E. (2018)
    Isothermal nucleic acid amplification methods can potentially shorten the amount of time required to diagnose influenza. We developed and evaluated a novel isothermal nucleic acid amplification method, RT-SIBA to rapidly detect and differentiate between influenza A and B viruses in a single reaction tube. The performance of the RT-SIBA Influenza assay was compared with two established RT-PCR methods. The sensitivities of the RT-SIBA, RealStar RT-PCR, and CDC RT-PCR assays for the detection of influenza A and B viruses in the clinical specimens were 98.8%, 100%, and 89.3%, respectively. All three assays demonstrated a specificity of 100%. The average time to positive result was significantly shorter with the RT-SIBA Influenza assay (90 min). The method can be run using battery-operated, portable devices with a small footprint and therefore has potential applications in both laboratory and near-patient settings. (C) 2018 Elsevier Inc. All rights reserved.
  • Pietilä, Jukka-Pekka; Meri, Taru; Siikamäki, Heli; Tyyni, Elisabet; Kerttula, Anne-Marie; Pakarinen, Laura; Jokiranta, T. Sakari; Kantele, Anu (2019)
    Despite the global distribution of the intestinal protozoan Dientamoeba fragilis, its clinical picture remains unclear. This results from underdiagnosis: microscopic screening methods either lack sensitivity (wet preparation) or fail to reveal Dientamoeba (formalin-fixed sample). Aim: In a retrospective study setting, we characterised the clinical picture of dientamoebiasis and compared it with giardiasis. In addition, we evaluated an improved approach to formalin-fixed samples for suitability in Dientamoeba diagnostics. Methods: This study comprised four parts: (i) a descriptive part scrutinising rates of Dientamoeba findings; (ii) a methodological part analysing an approach to detect Dientamoebalike structures in formalin samples; (iii) a clinical part corn paring demographics and symptoms between patients with dientamoebiasis (n = 352) and giardiasis (n = 272), and (iv) a therapeutic part (n = 89 patients) investigating correlation between faecal eradication and clinical improvement. Results: The rate of Dientamoeba findings increased 20-fold after introducing criteria for Dientamoeba-like structures in formalin-fixed samples (88.9% sensitivity and 83.3% specificity). A further increase was seen after implementing faecal PCR. Compared with patients with giardiasis, the symptoms in the Dientamoeba group lasted longer and more often included abdominal pain, cramping, faecal urgency and loose rather than watery stools. Resolved symptoms correlated with successful faecal eradication (p<0.001). Conclusions: Previously underdiagnosed, Dientamoeba has become the most frequently recorded pathogenic enteroparasite in Finland. This presumably results from improved diagnostics with either PCR or detection of Dientamoeba-like structures in formalin-fixed samples, an approach applicable also in resource-poor settings. Symptoms of dientamoebiasis differ slightly from those of giardiasis; patients with distressing symptoms require treatment.
  • Jokelainen, P.; Murat, J-B.; Nielsen, H. V. (2018)
    Genetic variation within Toxoplasma gondii can have both clinical and epidemiological significance, while the genotypes circulating in many parts of the world, including the Nordic country Denmark, are still unknown. We genetically characterized T. gondii strains that had been detected in human clinical samples in Denmark in 2011-2016. Samples that had tested positive for T. gondii DNA and had a quantification cycle value <33 were included in this study and subjected to direct genetic characterization of T. gondii based on length-polymorphism of 15 microsatellite markers. A total of 23 DNA samples from 22 individual patients were analyzed. The results were consistent with genotype II with 15/15 markers amplified from seven samples from the central nervous system (CNS) including two samples from one patient, four ocular samples, and one unspecified sample; with genotype III with 15/15 markers amplified from two ocular samples; with genotype Africa 1 with 15/15 markers amplified from one amniotic fluid sample and from one CNS-sample; with atypical genotype with 15/15 markers amplified from one CNS-sample and with 11/15 markers amplified from one CNS-sample; and with HG12-like genotype with 9/15 markers amplified from one CNS-sample. Genotype II, which is endemic in Europe, was predominant, but more than a third of the successfully genotyped strains were non-type-II. The possibility that clinical toxoplasmosis is caused by a strain that is not considered endemic to the region is definitely not negligible.
  • Pietikainen, Risto; Nordling, Stig; Jokiranta, Sakari; Saari, Seppo; Heikkinen, Petra; Gardiner, Chris; Kerttula, Anne-Marie; Kantanen, Tiina; Nikanorova, Anna; Laaksonen, Sauli; Lavikainen, Antti; Oksanen, Antti (2017)
    Background: The spread of vector-borne diseases to new regions has become a global threat due to climate change, increasing traffic, and movement of people and animals. Dirofilaria repens, the canine subcutaneous filarioid nematode, has expanded its distribution range northward during the last decades. The northernmost European locations, where the parasite life-cycle has been confirmed, are Estonia and the Novgorod Region in Russia. Results: Herein, we describe an autochthonous D. repens infection in a Finnish woman. We also present two cases of D. repens infection in imported dogs indicating the life-cycle in the Russian Vyborg and St Petersburg areas, close to the Finnish border. Conclusions: The most obvious limiting factor of the northern distribution of D. repens is the summer temperature, due to the temperature-dependent development of larvae in vectors. With continuing climate change, further spread of D. repens in Fennoscandia can be expected.
  • Ristagno, Giuseppe; Masson, Serge; Tiainen, Marjaana; Bendel, Stepani; Bernasconi, Roberto; Varpula, Tero M; Milani, Valentina; Vaahersalo, Jukka; Magnoli, Michela; Spanuth, Eberhard; Barlera, Simona; Latini, Roberto; Hoppu, Sanna; Pettila, Ville; Skrifvars, Markus; FINNRESUSCI Study Grp (2016)
    Background: An intense systemic inflammatory response is observed following reperfusion after cardiac arrest. Heparin-binding protein (HBP) is a granule protein released by neutrophils that intervenes in endothelial permeability regulation. In the present study, we investigated plasma levels of HBP in a large population of patients resuscitated from out-of-hospital cardiac arrest. We hypothesized that high circulating levels of HBP are associated with severity of post-cardiac arrest syndrome and poor outcome. Methods: Plasma was obtained from 278 patients enrolled in a prospective multicenter observational study in 21 intensive care units (ICU) in Finland. HBP was assayed at ICU admission and 48 h later. Multiple organ dysfunction syndrome (MODS) was defined as the 24 h Sequential Organ Failure Assessment (SOFA) score >= 12. ICU death and 12-month Cerebral Performance Category (CPC) were evaluated. Multiple linear and logistic regression tests and receiver operating characteristic curves with area under the curve (AUC) were performed. Results: Eighty-two percent of patients (229 of 278) survived to ICU discharge and 48 % (133 of 276) to 1 year with a favorable neurological outcome (CPC 1 or 2). At ICU admission, median plasma levels of HBP were markedly elevated, 15.4 [9.6-31.3] ng/mL, and persisted high 48 h later, 14.8 [9.8-31.1] ng/mL. Admission levels of HBP were higher in patients who had higher 24 h SOFA and cardiovascular SOFA score (p <0.0001) and in those who developed MODS compared to those who did not (29.3 [13.7-60.1] ng/mL vs. 13.6 [9.1-26.2] ng/mL, p <0.0001; AUC = 0.70 +/- 0.04, p = 0.0001). Admission levels of HBP were also higher in patients who died in ICU (31.0 [17.7-78.2] ng/mL) compared to those who survived (13.5 [9.1-25.5] ng/mL, p <0.0001) and in those with an unfavorable 12-month neurological outcome compared to those with a favorable one (18.9 [11.3-44.3] ng/mL vs. 12.8 [8.6-30.4] ng/mL, p <0.0001). Admission levels of HBP predicted early ICU death with an AUC of 0.74 +/- 0. 04 (p <0.0001) and were independently associated with ICU death (OR [95 %CI] 1.607 [1.076-2.399], p = 0.020), but not with unfavorable 12-month neurological outcome (OR [95 %CI] 1.154 [0.834-1.596], p = 0.387). Conclusions: Elevated plasma levels of HBP at ICU admission were independently associated with early death in ICU.
  • Vuori-Holopainen, Elina; Salo, Eeva; Saxen, Harri; Hedman, Klaus; Hyypiä, Timo; Lahdenperä, Raija; Leinonen, Maija; Tarkka, Eveliina; Vaara, Martti; Peltola, Heikki (2002)
    Childhood pneumonia is usually treated without determining its etiology. The causative organism can be isolated from specimens of blood, empyema fluid, or lung aspirate, but this is rarely done. The potential of transthoracic needle aspiration for identification of causative agents was tested with use of modern microbiological methods. Aspiration was performed for 34 children who had radiological signs compatible with community-acquired pneumonia and had alveolar consolidation. In addition to bacterial and viral cultures and viral antigen detection, nucleic acid detection for common respiratory pathogens was performed on aspirate specimens. Aspiration disclosed the etiology in 20 (59%) of 34 cases overall and in 18 (69%) of 26 patients from whom a representative specimen was obtained. Aspiration's advantages are high microbiological yield and a relatively low risk of a clinically significant adverse event. Aspiration should be used if identification of the causative agent outweighs the modest risk of the procedure.
  • Poelman, Randy; Schuffenecker, Isabelle; Van Leer-Buter, Coretta; Josset, Laurence; Niesters, Hubert G. M.; Lina, Bruno; Vuorinen, Tytti; ESCV-ECDC EV-D68 Study Grp; Lappalainen, Maija; Jääskeläinen, Anne; Smura, Teemu (2015)
    Background: In August and September 2014, unexpected clusters of enterovirus-D68 (EV-D68) infections associated with severe respiratory disease emerged from North-America. In September, the European Centre for Disease Prevention and Control (ECDC) asked European countries to strengthen respiratory sample screening for enterovirus detection and typing in cases with severe respiratory presentations. Objectives: To provide a detailed picture of EV-D68 epidemiology in Europe by conducting a retrospective and prospective laboratory analysis of clinical specimens. Study design: An initiative supported by the European Society for Clinical Virology (ESCV) and ECDC was launched to screen for EV-D68 in respiratory specimens between July 1st and December 1st 2014 in Europe and to sequence the VP1 region of detected viruses for phylogenetic analytic purposes. Results: Forty-two institutes, representing 51 laboratories from 17 European countries, analyzed 17,248 specimens yielding 389 EV-D68 positive samples (2.26%) in 14 countries. The proportion of positive samples ranged between 0 and 25% per country. These infections resulted primarily in mild respiratory disease, mainly detected in young children presenting with wheezing and in immuno-compromised adults. The viruses detected in Europe are genetically very similar to those of the North-American epidemic and the majority (83%) could be assigned to clade B. Except for 3 acute flaccid paralysis (AFP) cases, one death and limited ICU admissions, no severe cases were reported. Conclusions: The European study showed that EV-D68 circulated in Europe during summer and fall of 2014 with a moderate disease burden and different pathogenic profile compared to the North-American epidemic. (C) 2015 The Authors. Published by Elsevier B.V.
  • Luukinen, Bruno Vincent; Vuento, Risto; Hirvonen, Jari Juhani (2020)
    In areas of low tuberculosis (TB) prevalence, laboratory diagnosis of TB may essentially cover non-tuberculous mycobacteria (NTM) in addition to Mycobacterium tuberculosis (MTB). In this study, a semi-automated PCR workflow distinguishing MTB and NTM (Anyplex (TM) MTB/NTMe, Seegene) and subsequently detecting MTB isoniazid/rifampicin resistance (Allplex (TM) MTB/MDRe, Seegene) was evaluated for replacing smear microscopy of acid-fast bacilli as the rapid screening method for TB. With 279 clinical samples, 47 cultures positive for MTB and 76 for NTM, the Anyplex (TM) MTB/NTMe assay and smear microscopy showed equal sensitivities (49.6% vs 50.8%, respectively) but Anyplex (TM) MTB/NTMe was more sensitive for MTB (63.8% vs 25.6%) than for NTM (40.8% vs 64.5%). Allplex (TM) MTB/MDRe showed a slightly higher sensitivity of 68.1% for MTB (32/47 positive, n = 222). Antibiotic resistance profiles were correctly identified for all MTB isolates (one MDR isolate). Specificity was 100% for both assays. Anyplex (TM) MTB/NTMe detected all the 18 NTM species present in the study. The analytical performance of the evaluated high-throughput workflow was relatively weak compared to culture but potentially adequate as a rapid screening method analogous to smear microscopy with additional differentiation between TB, MDR-TB, and NTM.
  • Gray, Penelope; Palmroth, Johanna; Luostarinen, Tapio; Apter, Dan; Dubin, Gary; Garnett, Geoff; Eriksson, Tiina; Natunen, Kari; Merikukka, Marko; Pimenoff, Ville; Soderlund-Strand, Anna; Vanska, Simopekka; Paavonen, Jorma; Pukkala, Eero; Dillner, Joakim; Lehtinen, Matti (2018)
    Efficacy of human papillomavirus (HPV) vaccines promises to control HPV infections. However, HPV vaccination programs may lay bare an ecological niche for non-vaccine HPV types. We evaluated type-replacement by HPV type and vaccination strategy in a community-randomized trial executed in HPV vaccination naive population. Thirty-three communities were randomized to gender-neutral vaccination with AS04-adjuvanted HPV16/18 vaccine (Arm A), HPV vaccination of girls and hepatitis B-virus (HBV) vaccination of boys (Arm B) and gender-neutral HBV vaccination (Arm C). Resident 1992-95 born boys (40,852) and girls (39,420) were invited. 11,662 boys and 20,513 girls were vaccinated with 20-30% and 45-48% coverage, respectively. HPV typing of 11,396 cervicovaginal samples was performed by high throughput PCR. Prevalence ratios (PR) between arms and ranked order of HPV types and odds ratio (OR) for having multiple HPV types in HPV16 or 18/45 positive individuals were calculated. The ranked order of HPV types did not significantly differ between arms or birth cohorts. For the non-HPV vaccinated 1992-1993 birth cohorts increased PR, between the gender-neutral intervention versus control arms for HPV39 (PRA 1.84, 95% CI 1.12-3.02) and HPV51 (PRA 1.56, 95% CI 1.11-2.19) were observed. In the gender-neutral arm, increased clustering between HPV39 and the vaccine-covered HPV types 16 or 18/45 (ORA16 = 5.1, ORA18/45 = 11.4) was observed in the non-HPV vaccinated 1994-1995 birth cohorts. Comparable clustering was seen between HPV51 and HPV16 or HPV18/45 (ORB16 = 4.7, ORB18/45 = 4.3), in the girls-only arm. In conclusion, definitively consistent postvaccination patterns of HPV type-replacement were not observed. Future occurrence of HPV39 and HPV51 warrant investigation.
  • Niskanen, Silja; Jääskeläinen, Anne; Vapalahti, Olli; Sironen, Tarja (2019)
    Puumala virus (PUUV) is the most common cause of hantavirus infection in Europe, with thousands of cases occurring particularly in Northern, Central and Eastern Europe and Russia. It causes a mild form of hemorrhagic fever with renal syndrome also known as nephropathia epidemica (NE) with clinical picture ranging from mild to severe. Currently, the laboratory diagnosis of NE is mainly based on serology. Here, we evaluated a real-time one-step qRT-PCR (PUUV-qRT-PCR) for detection of PUUV with 238 consecutive diagnostic serum samples from patients with suspected PUUV infection. The PUUV-qRT-PCR was both specific and sensitive for PUUV RNA. The analytical sensitivity (limit of detection) was estimated to be four copies of PUUV per reaction. Altogether 28 out of 30 (93%) PUUV IgM positive samples were positive also for PUUV RNA. No false positives were detected and the specificity was thus 100%. Interestingly, one sample was found positive in PUUV-qRT-PCR prior to subsequent IgM and IgG seroconversion. PUUV-qRT-PCR could be used for diagnostics in the early phase of NE infection and might be helpful especially in the rare severe cases when the patient's condition may deteriorate rapidly.
  • Hussain, Nazar; Tariq, Muhammad; Saris, Per Erik Joakim; Zaidi, Arsalan (2021)
    Introduction: Probiotic and postbiotic potential of thirty-two strains of lactic acid bacteria (LAB), obtained earlier from artisanal dairy sources in Pakistan, have been investigated against major multi-drug resistant (MDR) and food borne pathogenic bacteria. Methodology: LAB strains were identified by 16S rRNA gene sequencing and their antibacterial activity was assessed by the microdilution method. Four LAB isolates, Weissella confusa PL6, Enterococcus faecium PL7, and Lactobacillus delbrueckii PL11 and PL13 were shortlisted. Their ability to degrade lactose and safety for human consumption in terms of hemolysis and antibiotic susceptibility were assessed in vitro. The antibacterial components in the cell-free supernatants (CFSs) of isolate cultures were characterized biochemically by HPLC. Results: Acid neutralization but not protease treatment abolished the antibacterial activity of CFSs. Lactic, acetic and propionic acids were the main acids in the CFSs, and acid production peaked in the stationary phase of growth. The antibacterial activity of the LAB cultures resulted from secretion of organic acids that lowered the pH. The strains exhibited variable ability to degrade lactose and were non-hemolytic and susceptible to the most common antibiotics. Conclusions: These LAB strains are probiotic candidates for further investigation of their postbiotic role in naturally preserving processed foods and for attenuation of lactose intolerance.
  • Kuukka-Anttila, Hanna; Peuhkuri, Nina; Kolari, Irma; Kause, Antti (2020)
    Parasite infectivity, virulence and host resistance have been in the centre of the scientific interest when it comes to host-parasite relationships. In addition to resistance, hosts may also vary in their tolerance against parasites. This is important to notice because resistance and tolerance have different consequences in host-parasite co-evolution. Here, we show that families of farmed rainbow trout (Oncorhynchus mykiss) show both host defence strategies, resistance, and tolerance, against infectivity and virulence ofDiplostomumsp. (Trematoda) parasites. Both strategies have moderate genetic variation and are genetically independent of each other. It is also shown that the families having the highest performance measured as higher weight, better condition factor and lower mortality in absence of the parasites suffer the most when parasitism increases. For practical breeding programmes, this means that both resistance and tolerance can be improved by selection without compromising one of the strategies. These results give new insight into defence strategies against parasites in fish and into processes of fish-parasite co-evolution.
  • Dhaygude, Kishor Uttam; Johansson, Helena; Kulmuni, Jonna Katharina; Sundström, Liselotte (2019)
    We present the genome organization and molecular characterization of the three Formica exsecta viruses, along with ORF predictions, and functional annotation of genes. The Formica exsecta virus-4 (FeV4; GenBank ID: MF287670) is a newly discovered negative-sense single-stranded RNA virus representing the first identified member of order Mononegavirales in ants, whereas the Formica exsecta virus-1 (FeV1; GenBank ID: KF500001), and the Formica exsecta virus-2 (FeV2; GenBank ID: KF500002) are positive single-stranded RNA viruses initially identified (but not characterized) in our earlier study. The new virus FeV4 was found by re-analyzing data from a study published earlier. The Formica exsecta virus-4 genome is 9,866 bp in size, with an overall G + C content of 44.92%, and containing five predicted open reading frames (ORFs). Our bioinformatics analysis indicates that gaps are absent and the ORFs are complete, which based on our comparative genomics analysis suggests that the genomes are complete. Following the characterization, we validate virus infection for FeV1, FeV2 and FeV4 for the first time in field-collected worker ants. Some colonies were infected by multiple viruses, and the viruses were observed to infect all castes, and multiple life stages of workers and queens. Finally, highly similar viruses were expressed in adult workers and queens of six other Formica species: F. fusca, F. pressilabris, F. pratensis, F. aquilonia, F. truncorum and F. cinerea. This research indicates that viruses can be shared between ant species, but further studies on viral transmission are needed to understand viral infection pathways.
  • Savijoki, Kirsi; Miettinen, Ilkka; Nyman, Tuula; Kortesoja, Maarit; Hanski, Leena; Varmanen, Pekka; Fallarero, Adyary (2020)
    The present study investigated Staphylococcus aureus ATCC25923 surfaceomes (cell surface proteins) during prolonged growth by subjecting planktonic and biofilm cultures (initiated from exponential or stationary cells) to label-free quantitative surfaceomics and phenotypic confirmations. The abundance of adhesion, autolytic, hemolytic, and lipolytic proteins decreased over time in both growth modes, while an opposite trend was detected for many tricarboxylic acid (TCA) cycle, reactive oxygen species (ROS) scavenging, Fe-S repair, and peptidolytic moonlighters. In planktonic cells, these changes were accompanied by decreasing and increasing adherence to hydrophobic surface and fibronectin, respectively. Specific RNA/DNA binding (cold-shock protein CspD and ribosomal proteins) and the immune evasion (SpA, ClfA, and IsaB) proteins were notably more abundant on fully mature biofilms initiated with stationary-phase cells (SDBF) compared to biofilms derived from exponential cells (EDBF) or equivalent planktonic cells. The fully matured SDBF cells demonstrated higher viability in THP-1 monocyte/macrophage cells compared to the EDBF cells. Peptidoglycan strengthening, specific urea-cycle, and detoxification enzymes were more abundant on planktonic than biofilm cells, indicating the activation of growth-mode specific pathways during prolonged cultivation. Thus, we show that S. aureus shapes its surfaceome in a growth mode-dependent manner to reach high levofloxacin tolerance (>200-times the minimum biofilm inhibitory concentration). This study also demonstrates that the phenotypic state of the cells prior to biofilm formation affects the immune-evasion and persistence-related traits of S. aureus.