Types Of Methods Research Articles

SaLTy: a novel Staphylococcus aureus Lineage Typer.

Staphylococcus aureus asymptomatically colonises 30 % of humans but can also cause a range of diseases, which can be fatal. In 2017 S. aureus was associated with 20 000 deaths in the USA alone. Dividing S. aureus isolates into smaller sub-groups can reveal the emergence of distinct sub-populations with varying potential to cause infections. Despite multiple molecular typing methods categorising such sub-groups, they do not take full advantage of S. aureus genome sequences when describing the fundamental population structure of the species. In this study, we developed Staphylococcus aureus Lineage Typing (SaLTy), which rapidly divides the species into 61 phylogenetically congruent lineages. Alleles of three core genes were identified that uniquely define the 61 lineages and were used for SaLTy typing. SaLTy was validated on 5000 genomes and 99.12 % (4956/5000) of isolates were assigned the correct lineage. We compared SaLTy lineages to previously calculated clonal complexes (CCs) from BIGSdb (n=21 173). SALTy improves on CCs by grouping isolates congruently with phylogenetic structure. SaLTy lineages were further used to describe the carriage of Staphylococcal chromosomal cassette containing mecA (SCCmec) which is carried by methicillin-resistant S. aureus (MRSA). Most lineages had isolates lacking SCCmec and the four largest lineages varied in SCCmec over time. Classifying isolates into SaLTy lineages, which were further SCCmec typed, allowed SaLTy to describe high-level MRSA epidemiology. We provide SaLTy as a simple typing method that defines phylogenetic lineages (https://github.com/LanLab/SaLTy). SaLTy is highly accurate and can quickly analyse large amounts of S. aureus genome data. SaLTy will aid the characterisation of S. aureus populations and ongoing surveillance of sub-groups that threaten human health.

Polymorphisms of HLA genes and hypersensitivity to penicillin among patients in a Taiwanese population.

Penicillin allergy is a potentially life-threatening condition that is common among patients. However, the genetic associations with penicillin allergy are not yet recognized for prevention or diagnosis, particularly in East Asian populations. We conducted a retrospective case-control study using data from the Taiwan Precision Medicine Initiative and analysing DNA samples to identify eight major MHC Class I and Class II loci. We employed imputation methods for accurate HLA typing and enrolled 17,827 individuals who received penicillin. Logistic regression analyses were utilized to explore associations between HLA genotypes, comorbidities and allergy risk, while simultaneously conducting a subgroup analysis to explore the association between HLA genotypes, comorbidities and the severity of allergic reactions. Our study assigned 496 cases to the penicillin allergy group and 4960 controls to a matched group. The risk of penicillin allergy was significantly higher with HLA-DPB1*05:01 (OR=1.36, p=.004) and HLA-DQB1*05:01 (OR=1.54, p=.03), with adjusted p-values of.032 and.24, respectively. Urticaria was identified as a separate risk factor (OR=1.73, p<.001). However, neither the HLA alleles nor the comorbidities had a significant relationship with the risk of severe penicillin-induced allergy. HLA-DPB1*05:01 was found to be significantly associated with penicillin allergy reactions among the Taiwanese population.

Crop type rather than production method determines functional trait composition of insect communities on arable land in boreal agricultural landscapes

Abstract To understand the potential consequences of arable land use changes for insect conservation and ecosystem functioning, it is fundamental to know how insect species with different functional traits respond to crop choice and production method. This study examined the effects of crop type and production method on functional traits of butterfly, bumblebee and carabid beetle communities using species abundance data from 78 fields in Southern Finland. Surrounding landscape composition was also accounted for. The studied traits were associated with dispersal capacity, habitat or diet specialization and phenology—the key determinants modifying species responses to agricultural disturbances and land use changes. Butterfly habitat breadth was narrowest and wingspan shortest in long‐term fallows. Fallows also supported the highest share of butterflies overwintering in early development stages and bumblebees with late‐emerging queens. The tongue length of bumblebees was longest in organic oat fields, probably due to flowering weeds with long corolla. For carabid beetles, the proportion of poor flyers and carnivores was highest in perennial crops and fallows. Carabid beetles overwintering as adults were relatively more abundant in organic than in conventional production, probably due to more intensive tillage in organic fields. In all insect groups, poor dispersers and/or specialists decreased with increasing arable land cover in the surrounding landscape. Increasing the area of long‐term fallows and perennial crops and enhancing within‐field plant diversity while maintaining landscape heterogeneity would promote insect species sensitive to agricultural disturbances and land use changes and their associated ecosystem services in boreal farmland.

Genomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam.

Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content. To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.

Molecular Diagnostics of Cryptococcus spp. and Immunomics of Cryptococcosis-Associated Immune Reconstitution Inflammatory Syndrome

Cryptococcal infection poses a significant global public health challenge, particularly in regions near the equator. In this review, we offer a succinct exploration of the Cryptococcus spp. genome and various molecular typing methods to assess the burden and genetic diversity of cryptococcal pathogens in the environment and clinical isolates. We delve into a detailed discussion on the molecular pathogenesis and diagnosis of immune reconstitution inflammatory syndrome (IRIS) associated with cryptococcosis, with a specific emphasis on cryptococcal meningitis IRIS (CM-IRIS). Our examination includes the recent literature on CM-IRIS, covering host cellulomics, proteomics, transcriptomics, and genomics.

Systematic Assessment of Deep Learning-Based Predictors of Fragmentation Intensity Profiles.

In recent years, several deep learning-based methods have been proposed for predicting peptide fragment intensities. This study aims to provide a comprehensive assessment of six such methods, namely Prosit, DeepMass:Prism, pDeep3, AlphaPeptDeep, Prosit Transformer, and the method proposed by Guan et al. To this end, we evaluated the accuracy of the predicted intensity profiles for close to 1.7 million precursors (including both tryptic and HLA peptides) corresponding to more than 18 million experimental spectra procured from 40 independent submissions to the PRIDE repository that were acquired for different species using a variety of instruments and different dissociation types/energies. Specifically, for each method, distributions of similarity (measured by Pearson's correlation and normalized angle) between the predicted and the corresponding experimental b and y fragment intensities were generated. These distributions were used to ascertain the prediction accuracy and rank the prediction methods for particular types of experimental conditions. The effect of variables like precursor charge, length, and collision energy on the prediction accuracy was also investigated. In addition to prediction accuracy, the methods were evaluated in terms of prediction speed. The systematic assessment of these six methods may help in choosing the right method for MS/MS spectra prediction for particular needs.

New Vaccine Therapy for Triple-Negative Breast Cancer

Abstract Purpose of the review The objective of this review is to provide an analysis of early-phase clinical trials investigating vaccine therapies for triple-negative breast cancer (TNBC). Specifically, the focus is on ongoing trials that are actively recruiting or in progress, while excluding vaccines that target neoantigens or those that have already completed trials. Recent findings Over the past decade, notable transformations have occurred in the strategy of breast cancer vaccine design. Traditional approaches to identifying tumor antigens, such as SEREX, have been replaced with modern techniques, such as RNA sequencing, HLA typing, and immunoinformatics. These new methods enable the identification and characterization of tumor antigens. Notably, current clinical investigations into tumor targets extend beyond mutated self-proteins or proteins that are overexpressed following neoplastic transformation. Clinical researchers are currently examining protein targets associated with cancer stem cells or non-malignant immune regulatory cell types within the tumor microenvironment. However, the application of up-to-date antigen delivery methods for certain types of breast cancer vaccine therapies still lags behind. Another significant transformation in comparison to previous breast cancer vaccine therapies is the emphasis on stimulating robust T-cell responses against breast cancer cells, independent of any B-cell response directed at the tumor. Summary In conclusion, we critically assessed the tumor antigens targeted by vaccine immunotherapies in these new clinical trials, the delivery methods used for these antigens, and conclude by discussing potential future directions for the development of new TNBC vaccine therapies.

A comparison between physics-based Li-ion battery models

Physics-based electrochemical battery models, such as the Doyle-Fuller-Newman (DFN) model, are valuable tools for simulating Li-ion battery behavior and understanding internal battery processes. However, the complexity and computational demands of such models limit their applicability for battery management systems and long-term aging simulations. Reduced-order models (ROMs), such as the Extended Single Particle Model (ESPM), Single Particle Model (SPM) and Polynomial and Padé approximations, here all referred to as simplifications, lead to faster computational speeds. Choosing the appropriate simplification method for a specific cell type and operating condition is a challenge. This study investigates the simulation accuracy and calculation speed of various simplifications for high-energy (HE) and high-power (HP) batteries at different current loading conditions and compares those to the full-order DFN model. The results indicate that among the ROMs, the ESPM consistently offers the best combination of high computational speed and relatively good accuracy in most conditions in comparison to the full-order DFN model. Among the approximations, higher-order polynomial approximation, third and fourth-order Padé approximation perform the best in terms of accuracy. The higher-order polynomial approximation shows an advantage in terms of computing speed, while the fourth-order Padé approximation achieves the highest overall accuracy among the different approximations.

Deformation mechanism and minimum energy path in Silicon–graphite composites with lattice defects

Edge-on atomic layers in layered solids undergo buckling, which creates a structure referred to as a “ripplocation.” A collective set of multiple ripplocations is referred to as a “ripplocation boundary.” In this study, in order to investigate the impact of lattice defects on ripplocation, we investigate the buckling deformation of graphene with lattice defects under confinement. To this end, we conducted confined uniaxial compression simulations by placing graphene sheets with various lattice defects between silicon atomic layers. Different types of lattice defects affect the mechanical properties of graphene, the results show that Young's modulus of graphene with the (1,0)_5 dislocation pair was the maximum at 494.6 GPa, whereas the Young's modulus of the (1,2)_10 dislocation pair was the minimum at 309.5 GPa. In addition, we employed a differential geometry method to study the out-of-plane deformation of a single-layer graphene system. Further, we used the nudged elastic band method for various types of lattice defects in graphene to uncover the minimum transition pathways, activation energy required to move from the (1, 0) dislocation pair to the (1, 1) pair is 44.916 eV. In particular, the results indicate that graphene with lattice defects exhibit kink deformation after buckling compared to that of perfect graphene. Our study not only explores the deformation of ripplocations and kink boundaries in layered solids but also provides a more comprehensive description influencing lattice defects on the nucleation mechanism and mechanical changes of ripplocations in graphene.

Numerical methods for highly oscillatory Volterra integral equations with general oscillators

In this paper, collocation methods for linear Volterra integral equations with highly oscillatory trigonometric kernels are considered. Different from the cases with linear oscillator, we need a further action to obtain a practical scheme for general oscillators. To deal with it, the moment free Filon type method is employed in the exact collocation equation resulting to a fully discretized one. In order to conduct the convergence analysis, we firstly study the highly oscillatory integrals occurring in the error equations. Both the theoretical and numerical results show that our method not only converges with respect to step length but also has an asymptotic order which could be two. The asymptotic order indicates that the numerical results will become more accurate as the increase of frequency.

Application of nanoparticles in breast cancer treatment: a systematic review.

It is estimated that cancer is the second leading cause of death worldwide. The primary or secondary cause of cancer-related mortality for women is breast cancer. The main treatment method for different types of cancer is chemotherapy with drugs. Because of less water solubility of chemotherapy drugs or their inability to pass through membranes, their body absorbs them inadequately, which lowers the treatment's effectiveness. Drug specificity and pharmacokinetics can be changed by nanotechnology using nanoparticles. Instead, targeted drug delivery allows medications to be delivered to the targeted sites. In this review, we focused on nanoparticles as carriers in targeted drug delivery, their characteristics, structure, and the previous studies related to breast cancer. It was shown that nanoparticles could reduce the negative effects of chemotherapy drugs while increasing their effectiveness. Lipid-based nanocarriers demonstrated notable results in this instance, and some products that are undergoing various stages of clinical trials are among the examples. Nanoparticles based on metal or polymers demonstrated a comparable level of efficacy. With the number of cancer cases rising globally, many researchers are now looking into novel treatment approaches, particularly the use of nanotechnology and nanoparticles in the treatment of cancer. In order to help clinicians, this article aimed to gather more information about various areas of nanoparticle application in breast cancer therapy, such as modifying their synthesis and physicochemical characterization. It also sought to gain a deeper understanding of the mechanisms underlying the interactions between nanoparticles and biologically normal or infected tissues.

Changes in patient recruitment parameters and their derivatives under the influence of external factors – population size and density of residence in a certain area

Background. The lack of targeted patient recruitment for clinical trials reaches 90%, which leads to failures of a trial as a whole and insufficient access to the necessary treatment or diagnostic method for patients. To find out the reasons for recruitment failures, many factors are considered, the action of which is difficult to assess due to high variability. In general, various factors are named that reduce patient recruitment, while factors that improve it are much less known.Objective: to investigate changes in the parameters and indicators of patient recruitment for clinical trials depending on the influence of external factors.Material and methods. A retrospective analysis of four international multicenter clinical trials of phases II–III was performed by 16 patient recruitment parameters and their 6 derivatives (indicators) – both widely used in the literature and newly proposed. A total of 622 patients from 70 clinical centers located in 59 cities of Russia, Ukraine, and Belarus were included in the study. The methods of descriptive statistics and typing were used. To study the influence of factors, internal and external factors were selected, external factors including population size, area and density of residence were analysed, and changes in parameters and indicators depending on the influence of each factor were examined. The area and population density were studied in inseparable connection with each other.Results. A simple classification of factors was proposed – external and internal to the clinical center where patients were recruited. The factors classified as external were analyzed depending on the change in the proposed parameters of patient recruitment for clinical trials and their relationships – indicators (derivatives). The final rate of patient recruitment and the final number of patients recruited in the population group of 1–2 million people had statistically significant (p&lt;0.05) higher values (0.57±0.20 and 15.08±5.06, respectively) than in group with up to 1 million people – 0.14±0.05 and 3.75±1.24.Conclusion. For the first time, an extended panel of parameters and indicators that allow evaluating the influence of various factors on patient recruitment for clinical trials was proposed. The value of the proportion of parameters and indicators that had statistical differences among themselves in the group influenced by the population size factor was more than twice as large as the proportion of similar parameters and indicators in the group influenced by area and population density: 47% and 23%, respectively, which may indicate more strong influence of the first factor.

The Way to Construct Innovative Methods for Solving Initial-Value Problem of the Volterra Integro-Differential Equation

Mathematical models for many problems in the natural sciences are often simplified to solving initial-value problems (IVPs) for the Volterra integro-differential equations (VIDE). Numerical methods of a multistep type are typically used to solve these problems. It is known that in some cases, the multi-step method (MSM) is applied to solving the IVPs of both ordinary differential equations (ODEs) and VIDE encountered in solving some problems in mathematical biology. Here, to solve such problems by combining different methods, some modifications of established methods were developed, and it was demonstrated that these methods outperform the existing ones. As is known, one of the main issues in solving the aforementioned problems is determining the reliability of calculating values using the known mathematicalstatistical models (MSMs). In this regard, some experts utilize the predictor-corrector method. Having highlighted the disadvantages of this method, the proposal is to develop an innovative approach and assess the errors that may arise when applying this method to solve various problems. Here, the IVPs for the VIDE of the first order are primarily investigated. To illustrate the benefits of the innovative methods proposed here, we discuss the use of simple numerical methods to solve some common examples.

Biomechanical evaluation of the modified lasso technique

BackgroundThe Terrible Triad of the elbow is a constellation of elbow dislocation, radial head fracture and coronoid process fracture. A common type of coronoid fracture documented with this triad is type II Regan-Morrey coronoid fractures. The preferred fixation method for this fracture type is the lasso technique, medial-lateral tunnel orientation being the traditional approach. Considering elbow anatomy, we saw an opportunity to potentially improve fixation by altering the suture lasso tunnel orientation to a proximal-distal orientation. HypothesisTwo tunnels in the proximal-distal direction would result in greater biomechanical stability as compared to the traditional lasso technique. Material and methodsA type 2 Regan-Morrey fracture was created in 12 fresh frozen cadaveric elbows at 50% of the coronoid height using an oscillating saw. The humero-ulnar joint was placed in 0 degrees flexion then loaded at a rate of 10mm/min to failure. ResultsThe control technique (medio-lateral tunnels) showed failure load of 150±81N that was not significantly different (p=0.825) than the 134±116N measured for the modified technique (distal-proximal tunnels). The portion of the load-displacement curve used to calculate stiffness was linear (R^2=0.94±0.04) with determination coefficients that did not differ between the two groups (p=0.351). For stiffness, we measured 17±13N/mm and 14±12N/mm respectively for control and modified techniques that did not result in a significant difference (p=0.674). ConclusionIn this attempt to improve the shortcomings of the lasso technique, we found that changing from medio-lateral to proximal-distal drilling directions did not result in an appreciable biomechanical benefit. Level of evidenceBasic science study; Biomechanics.

Mycotoxin contamination in organic and conventional cereal grain and products: A systematic literature review and meta-analysis.

There is still considerable controversy about the relative risk of mycotoxin exposure associated with the consumption of organic and conventional cereals. Using validated protocols, we carried out a systematic literature review and meta-analyses of data on the incidence and concentrations of mycotoxins produced by Fusarium, Claviceps, Penicillium, and Aspergillus species in organic and conventional cereal grains/products. The standard weighted meta-analysis of concentration data detected a significant effect of production system (organic vs. conventional) only for the Fusarium mycotoxins deoxynivalenol, with concentrations ∼50% higher in conventional than organic cereal grains/products (p<0.0001). Weighted meta-analyses of incidence data and unweighted meta-analyses of concentration data also detected small, but significant effects of production system on the incidence and/or concentrations of T-2/HT-2 toxins, zearalenone, enniatin, beauvericin, ochratoxin A (OTA), and aflatoxins. Multilevel meta-analyses identified climatic conditions, cereal species, study type, and analytical methods used as important confounding factors for the effects of production system. Overall, results from this study suggest that (i) Fusarium mycotoxin contamination decreased between the 1990s and 2020, (ii) contamination levels are similar in organic and conventional cereals used for human consumption, and (iii) maintaining OTA concentrations below the maximum contamination levels (3.0μg/kg) set by the EU remains a major challenge.

Molecular epidemiology and molecular typing methods of Acinetobacter baumannii: An updated review.

The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant Acientobacter baumannii (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by Acientobacter baumannii (A. baumannii) and acquired resistance to antimicrobials. Nowadays, there is gradual shift from traditional typing methods to modern molecular methods to study molecular epidemiology and infection control. Molecular typing of A. baumannii strains has been revolutionized significantly in the last 2 decades. A few sequencing-based techniques have been proven as a breakthrough and opened new prospects, which have not been achieved by the traditional methods. In this review, discussed different pre-existing and recently used typing methods to explore the molecular epidemiology of A. baumannii pertaining in context with human infections.

PENGUATAN KAPASITAS TOKOH AGAMA DALAM UPAYA PENANGGULANGAN STUNTING WILAYAH KABUPATEN KUPANG ALOR

The problem of stunting has the potential to disrupt the quality of human resources and is related to health levels and even child mortality. In this case, religious leaders are parties who play a direct role, especially in preventing stunting through shaping family consumption patterns in religious service areas. Family mothers who cultivate and implement nutritious food consumption patterns can prevent family members, including children under five, from nutritional problems, including stunting. The activity was carried out in Alor Regency on 21-23 October 2023 with the aim of strengthening Christian, Catholic, Hindu and Islamic religious leaders in carrying out service duties to families, especially family mothers, in order to increase knowledge about consuming diverse, nutritious, balanced and safe food. and be able to take preventive action at the stage of preparing nutritious food for family consumption. Implementation uses the "Education and/or counseling" method. Where, all religious leaders are given teaching or material with the aim that they can determine the source of the problem and form services related to overcoming and preventing nutritional problems including stunting through choosing healthy, varied and safe types of food. The evaluation process was carried out before and after the activity to measure the abilities and changes in attitudes of 60 religious leaders regarding the counseling material. The pre-test results found that the majority (69.7%) of religious leaders already knew about stunting but did not understand consumption patterns including the type, quantity and correct method of food processing and the impact on the incidence of stunting. However, after confirmation from the results of the counseling, it was discovered that 100% of religious leaders could understand the correct consumption patterns. This starts from indicators of the ability to choose the type of food, compiling a simple but nutritious menu using a processing method that is friendly to the availability of sufficient and appropriate nutritional content as needed and can ensure that the amount of food consumed is according to the needs per day per age per gender of family members.

New Species-Specific Real-Time PCR Assays for Colletotrichum Species Causing Bitter Rot of Apple

Bitter rot of apple is an economically important worldwide disease caused by different Colletotrichum species, depending on many factors such as climate, geography, other hosts, and crop management practices. Culture, morphology, and single-locus sequencing-based methods for identifying the Colletotrichum species are severely limited in effectiveness, while the multilocus sequence typing methods available for delineating species are costly, time-intensive, and require high expertise. We developed species-specific hydrolysis probe real-time PCR assays for the following nine Colletotrichum species causing bitter rot in the Mid-Atlantic U.S.A.: C. fructicola, C. chrysophilum, C. noveboracense, C. gloeosporioides s.s., C. henanense, C. siamense and C. theobromicola from the C. gloeosporioides species complex, and C. fioriniae and C. nymphaeae from the C. acutatum species complex. After searching 14 gene regions, we designed primers and probes in 5 of them for the nine target species. Four primer–probe set pairs were able to be duplexed. Sensitivity tests showed as little as 0.5 pg DNA were detectable. These real-time PCR assays will provide rapid and reliable identification of these key Colletotrichum species and will be critically important for studies aiming to elucidate their biology, epidemiology, and management on apples as the number one produced and consumed tree fruit in the U.S.A.

Benefits of applying hourly resolution in the assessment of the climate aptitude to manage tourist activities in arid regions.

The availability of reliable information on local climatic-tourism conditions is a growing need due to the influence it exerts on the quality of the organizational strategy of tourist destination's, and travel experience. Evaluations of the tourism potential of the climate have been carried out on a daily or monthly resolution, thus limiting the collection of detailed information that makes it possible to fine-tune tourism management and operational decision-making on an intraday scale. This research is the first case study to analyse the climatic suitability for nature tourism, using the weather types method at hourly resolution. The study applies to arid tourist destinations in Isfahan province (Iran). The detailed resolution has made it possible to identify the time slots favourable to the development of nature tourism in those periods of the year recognized as critical in the daily resolution analyses. In the same way, the hourly resolution has also identified critical bands in those periods indicated as favourable in the evaluations to daily resolution. The hourly resolution provides detailed information that can allow tourists and also tourism managers to establish intraday adaptation strategies that make it possible to develop the activity even in places with extreme climates.

From Investigating a Case of Cellulitis to Exploring Nosocomial Infection Control of ST1 Legionella pneumophila Using Genomic Approaches

Legionella pneumophila can cause a large panel of symptoms besides the classic pneumonia presentation. Here we present a case of fatal nosocomial cellulitis in an immunocompromised patient followed, a year later, by a second case of Legionnaires’ disease in the same ward. While the first case was easily assumed as nosocomial based on the date of symptom onset, the second case required clear typing results to be assigned either as nosocomial and related to the same environmental source as the first case, or community acquired. To untangle this specific question, we applied core-genome multilocus typing (MLST), whole-genome single nucleotide polymorphism and whole-genome MLST methods to a collection of 36 Belgian and 41 international sequence-type 1 (ST1) isolates using both thresholds recommended in the literature and tailored threshold based on local epidemiological data. Based on the thresholds applied to cluster isolates together, the three methods gave different results and no firm conclusion about the nosocomial setting of the second case could been drawn. Our data highlight that despite promising results in the study of outbreaks and for large-scale epidemiological investigations, next-generation sequencing typing methods applied to ST1 outbreak investigation still need standardization regarding both wet-lab protocols and bioinformatics. A deeper evaluation of the L. pneumophila evolutionary clock is also required to increase our understanding of genomic differences between isolates sampled during a clinical infection and in the environment.