Identification Of Infection Sources Research Articles

Predicting the primary infection source of Escherichia coli bacteremia using virulence-associated genes

PurposeTo investigate the role of E. coli virulence-associated genes (VAGs) in predicting urinary tract infection (UTI) as the source of bacteremia in two distinct hospital populations, one with a large general catchment area and one dominated by referrals.MethodsE. coli bacteremias identified at Department of Clinical Microbiology (DCM), Hvidovre Hospital and DCM, Rigshospitalet in the Capital Region of Denmark from October to December 2018. Using whole genome sequencing (WGS), we identified 358 VAGs from 224 E. coli bacteremia. For predictive analysis, VAGs were paired with clinical source of UTI from local bacteremia databases.ResultsVAGs strongly predicting of UTI as primary infection source of bacteremia were primarily found within the pap gene family. papX (PPV 96%, sensitivity 54%) and papGII (PPV 93%, sensitivity 56%) were found highly predictive, but showed low sensitivities. The strength of VAG predictions of UTI as source varied significantly between the two hospital populations. VAGs had weaker predictions in the tertiary referral center (Rigshospitalet), a disparity likely stemming from differences in patient population and department specialization.ConclusionWGS data was used to predict the primary source of E. coli bacteremia and is an attempt on a new and different type of infection source identification. Genomic data showed potential to be utilized to predict the primary source of infection; however, discrepancy between the best performing profile of VAGs between acute care hospitals and tertiary hospitals makes it difficult to implement in clinical practice.

Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology.

Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.

Pyoperitoneum as a consequence of perinephric abscess spontaneous rupture. A case report

Intra-abdominal infections are a common cause of severe sepsis and have a significantly high morbidity and mortality rate. Patients continue to present to hospitals with unacceptable delays in diagnosis or management, resulting in sepsis and organ failure, which lower their survival chances. We reported a rare case of a 64-year-old Syrian woman with a spontaneous rupture of a perinephric abscess that resulted in intra-abdominal infection and ascites, which led to sepsis and multiple organ failure despite resuscitation and antibiotic treatment according to guidelines. Although the recommendations for patients with intra-abdominal infection and hemodynamic instability differ, there is an agreement that surgery should be considered early when other interventional approaches have failed. Rupture of the perinephric abscess rarely produces intra-abdominal infection and ascites; effective care requires early and appropriate infection source identification. To avoid delays, doctors need to use academic methods in developing diagnoses and management.

Epidemiology of Coronavirus Disease 2019 in Yamagata Prefecture, Japan, January-May 2020: the Importance of Retrospective Contact Tracing.

Public health interventions have played an important role in controlling coronavirus disease 2019 (COVID-19), which is a rapidly spreading infectious disease. To contribute to future COVID-19 countermeasures, we aimed to verify the results of the countermeasures employed by public health centers (PHCs) against the first wave of COVID-19 in Yamagata Prefecture, Japan (Yamagata). Between January and May 2020, 1,253 patients suspected of SARS-CoV-2 infection were invited for testing. Simultaneously, based on retrospective contact tracings, PHCs investigated the infection sources and transmission routes of laboratory-confirmed COVID-19 cases and tested 928 contacts. Consequently, 69 cases were confirmed between March 31 and May 4, 58 of whom were from among the contacts (84.1%; 95% confidence interval [CI] 75.5-92.7). The spread of infection was triggered in cases harboring epidemiological links outside Yamagata. Subsequently, the number of cases rapidly increased. However, PHCs identified epidemiological links in 61 (88.4%; 95% CI 80.8-96.0) of the 69 cases, and transmission chains up to the fifth generation. Finally, the spread of infection ended after approximately one month. Our results indicate that the identification of infection sources and active case finding from contacts based on retrospective contact tracing was likely to be an effective strategy in ending the first wave of COVID-19 in Yamagata.

Source identification of infectious diseases in networks via label ranking.

Outbreaks of infectious diseases would cause great losses to the human society. Source identification in networks has drawn considerable interest in order to understand and control the infectious disease propagation processes. Unsatisfactory accuracy and high time complexity are major obstacles to practical applications under various real-world situations for existing source identification algorithms. This study attempts to measure the possibility for nodes to become the infection source through label ranking. A unified Label Ranking framework for source identification with complete observation and snapshot is proposed. Firstly, a basic label ranking algorithm with complete observation of the network considering both infected and uninfected nodes is designed. Our inferred infection source node with the highest label ranking tends to have more infected nodes surrounding it, which makes it likely to be in the center of infection subgraph and far from the uninfected frontier. A two-stage algorithm for source identification via semi-supervised learning and label ranking is further proposed to address the source identification issue with snapshot. Extensive experiments are conducted on both synthetic and real-world network datasets. It turns out that the proposed label ranking algorithms are capable of identifying the propagation source under different situations fairly accurately with acceptable computational complexity without knowing the underlying model of infection propagation. The effectiveness and efficiency of the label ranking algorithms proposed in this study make them be of practical value for infection source identification.

A Revisit to the Infection Source Identification Problem under Classical Graph Centrality Measures

The high connectivity of the modern day world has lead to the easy diffusion of harmful information content like rumors, computer viruses, and contagions like diseases. This is detrimental to human societies in terms of compromised security, monetary loss and life threats. Therefore, to mitigate such damages, identifying and timely quarantining the sources of such diffusion processes is highly critical. Despite the difficulty and challenges of the problem, researchers have extensively studied source identification in complex networks over the past decade. Several approaches have been proposed, but limited attention has been given to the classical graph centrality measures. Moreover, researchers have generally advised against employing these measures for identifying infection sources. Motivated by the same, in this paper, we revisit these measures in context to source identification and raise the question: “Are classical graph centrality measures really not good enough?”, and perform an extensive experimental journey. We pick five such measures, viz., betweenness, closeness, degree, eigenvector and eccentricity, and conduct an in-depth analysis of their effectiveness in source detection. Our extensive results show that, contrary to the popular belief, a combination of eccentricity and closeness (EC+CC) generally performs better than several state-of-the-art source identification techniques, with higher accuracy and lower average hop error. We also analyze the impact of infection size on source identification and observe that EC+CC is generally highly scalable and stable as well. We also understand that as the infection size increases, the detection accuracy decreases, irrespective of the technique used. However, when we examine the effect of graph density, we observe that as the graph density increases, the detection accuracy increases as well, with EC+CC again outperforming state-of-the-art.

Structural equation model analysis of infectious disease-specific health literacy scale in China

Objective: To explore the relationship between different dimensions of infectious disease-specific health literacy scale in China. Methods: Structural equation model (SEM) was employed to assess the psychometric properties of the infectious disease-specific health literacy scale. Based on the database from a randomly selected sample of 4 499 adult residents in three provinces in China, from March to May 2015. AMOS 21.0 software was used to build the SEM for data analyses. Results: SEM analyses showed a good model fit of data, with the following satisfied parameters: goodness-of-fit index was 0.969, adjusted goodness-of-fit index was 0.962, root mean square residual was 0.038, root mean square error of approximation was 0.038, standardized root mean square residual was 0.032, Tacker-Lewis index/non-normed fit index was 0.926, comparative fit index was 0.934, normed fit index was 0.925, relative fit index was 0.915, incremental fit index was 0.934, parsimony goodness-of-fit index was 0.782, parsimony-adjusted normed fit index was 0.817, parsimony-adjusted comparative fit index was 0.825 and critical N was 702. The established SEM showed that the total influence path coefficient of "infectious disease-related knowledge and values" on the "infectious disease prevention" , "management or treatment of infectious diseases" and "identification of infection sources" were 0.771, 0.744 and 0.843, respectively. The total influence path coefficients of "identification of infection sources" , "infectious disease prevention" on "management or treatment of infectious diseases" were 0.164 and 0.535, respectively. The effect of "infectious disease-related knowledge and values" on "management or treatment of infectious diseases" appeared the greatest (55.4%), followed by "infectious disease prevention" (28.6%) and "identification of infection sources" (2.7%). Conclusion: This SEM could be optimistically used for planning and evaluation of health education and promotion programs on infectious diseases prevention.

Burkholderia mallei: The dynamics of networks and disease transmission.

Glanders is a highly infectious zoonotic disease caused by Burkholderia mallei. The transmission of B.mallei occurs mainly by direct contact, and horses are the natural reservoir. Therefore, the identification of infection sources within horse populations and animal movements is critical to enhance disease control. Here, we analysed the dynamics of horse movements from 2014 to 2016 using network analysis in order to understand the flow of animals in two hierarchical levels, municipalities and farms. The municipality-level network was used to investigate both community clustering and the balance between the municipality's trades and the farm-level network associations between B.mallei outbreaks and the network centrality measurements, analysed by spatio-temporal generalized additive model (GAM). Causal paths were established for the dispersion of B.mallei outbreaks through the network. Our approach captured and established a direct relationship between movement of infected equines and predicted B.mallei outbreaks. The GAM model revealed that the parameters in degree and closeness centrality out were positively associated with B.mallei. In addition, we also detected 10 communities with high commerce among municipalities. The role of each municipality within the network was detailed, and significant changes in the structures of the network were detected over the course of 3years. The results suggested the necessity to focus on structural changes of the networks over time to better control glanders disease. The identification of farms with a putative risk of B.mallei infection using the horse movement network provided a direct opportunity for disease control through active surveillance, thus minimizing economic losses and risks for human cases of B.mallei.

EFFECTIVENESS OF MOLECULAR-GENETIC DIAGNOSTICS DURING PERTUSSIS INFECTION FOCI EXAMINATION

Purpose: whooping cough diagnostics by molecular-genetic methods.Materials and methods. Under observation there were 4930 people during the period from 2012 to 2015. All samples were received in 8 schools of Moscow and the Moscow region: in 3 schools had been found children with whooping cough, in other 5 schools – only children with prolonged cough. Whooping cough diagnosis had been given earlier by bacteriological and serological methods. 430 clinical samples were studied by 2 methods: PCR with fluorescent hybridized detection of amplified products and isothermal amplification.Results. In three of eight schools whooping cough cases at 7 children at the age of 7, 9, 11 and 15 years were revealed earlier. The diagnosis of whooping cough at them was confirmed by means of bacteriological and serological methods. 33 positive DNA samples (7.7%) are revealed. DNA-positive samples are allocated from 18 pupils and 15 employees of schools. In two schools where earlier infection sources were established, 15 DNA-positive samples from which in three cases clinical manifestations were observed are revealed. In those schools where it wasn’t earlier established a source of an infection and examinations conducted it is long the coughing children, 18 DNA-positive samples are revealed, and in two cases clinical manifestations in the form of cough were observed.Conclusion. Performed research confirmed high efectiveness of molecular-genetic methods during pertussis infection foci examination in schools for infection source identification also amongst long coughing children.

Accurate Identification of Infection Source in Burn Trauma Patients With Central Line Infection to Determine Appropriate Treatment Option As Well As Proper Public Reporting.

With the advent of the Patient Safety Movement in the late 1990s and the CMS (Centers for Medicare & Medicaid Services) nonreimbursement program for never events, there has been much focus on the prevention and accurate identification of health care-associated infections such as central line-associated bloodstream infections (CLABSIs). There has certainly been a national effort to decrease the occurrence of these infections. With the implementation of patient safety initiatives such as the central line prevention bundle, there has been a considerable reduction in the number of CLABSIs except for patients with burn trauma. Because of the compromised nature of these patients, the number of CLABSIs has not decreased similarly to other types of patients. In addition, these patients may have a secondary infection that was not accurately or timely identified. With CLABSIs, proper identification of primary and secondary infections is very important, particularly when identifying treatment options and ensuring accurate public reporting of health care-associated infection information.

A NOVEL APPROACH TO GENOTYPING OF HOSPITAL ISOLATES OF CLOSTRIDIUM DIFFICILE

Development of a novel approach in genotyping of Clostridium difficile and its testing on the example of 140 hospital isolates. The approach is based on an idea of double digest and selective label (DDSL), used previously during genotyping of other bacterial pathogens. Selection of optimal enzymes for restriction of MluI and Mph1103I was carried out, condition of DDSL reaction execution were optimized. Genotyping of C. difficile hospital isolates was carried out, index of strain discrimination was calculated, conclusions regarding possibilities of the method in elucidation of spread pathways and identification of infection sources were made. The developed method of genotyping has a number of advantages over the existing method and can be used to'address issues in epidemiology of infections caused by C. difficile.

Critical Success Factors to Control Nosocomial Infection by “Wireless Sensor Network” in Intensive Care Unit

New information technologies (IT) can be effective in the prevention, identification, and reduction of transmission of nosocomial infection and consequently decreasing time and additional costs in the hospital. Among these technologies, wireless sensor network (WSN) is able to simultaneously cover the activities of data management, infection source identification and tracking, warning, and preventing infection transmission. For acceptance and successful implementation of WSN-based project in the hospital, identifying and paying attention to the indexes and critical success factors by IT managers and officials of care organization and the hospital is required that acceptance and implementation of the technology does not face failure and paying high costs. Hence, the aim of this study was to identify critical success factors of accepting infection diagnosis by wireless sensor network in the hospital that helps healthcare managers and staff to adopt and facilitate the WSN technology acceptance process at health care centers. This study was narrative review, which search was conducted with the help of libraries, books, conference proceedings, through databases of Science Direct, PubMed, Proquest, Springer, and SID (Scientific Information Database). We employed the following keywords and their combinations; Wireless Sensor Networks, Critical Success Factors, Nosocomial, and Hospital. The preliminary search resulted in 150 articles, which were published between 2003 and 2015. After a careful analysis of the content of each paper, a total of 43 sources was selected based on their relevancy.

The use of genetic markers in the molecular epidemiology of histoplasmosis: a systematic review.

Histoplasmosis is a systemic mycosis caused by Histoplasma capsulatum, a dimorphic fungal pathogen that can infect both humans and animals. This disease has worldwide distribution and affects mainly immunocompromised individuals. In the environment, H. capsulatum grows as mold but undergoes a morphologic transition to the yeast morphotype under special conditions. Molecular techniques are important tools to conduct epidemiologic investigations for fungal detection, identification of infection sources, and determination of different fungal genotypes associated to a particular disease symptom. In this study, we performed a systematic review in the PubMed database to improve the understanding about the molecular epidemiology of histoplasmosis. This search was restricted to English and Spanish articles. We included a combination of specific keywords: molecular typing [OR] genetic diversity [OR] polymorphism [AND] H. capsulatum; molecular epidemiology [AND] histoplasmosis; and molecular epidemiology [AND] Histoplasma. In addition, we used the specific terms: histoplasmosis [AND] outbreaks. Non-English or non-Spanish articles, dead links, and duplicate results were excluded from the review. The results reached show that the main methods used for molecular typing of H. capsulatum were: restriction fragment length polymorphism, random amplified polymorphic DNA, microsatellites polymorphism, sequencing of internal transcribed spacers region, and multilocus sequence typing. Different genetic profiles were identified among H. capsulatum isolates, which can be grouped according to their source, geographical origin, and clinical manifestations.

The role of leptospirosis reference laboratories.

The general goal of reference centres is to support the community, from diagnostic laboratories to research institutions, in the execution of their work by providing reference strains and reagents and giving instructions and recommendations to individual colleagues and national and international organisations on a wide variety of issues. There are different levels of reference centres, from local to international, with an increasing package of tasks and responsibilities. Local reference centres might limit activities to diagnostic confirmation by applying standard testing, while international reference centres cover a wider range of activities from design, validation and harmonisation of diagnostic and reference technologies to international monitoring associated with recommendations on the global burden and distribution of leptospirosis and its prevention and control to national and international health decision makers. This chapter focusses on four major pillars constituting reference tasks in addition to the obvious provision of reference substances, i.e. Research and training, Diagnosis, Identification of Leptospira and Surveillance. Due to financial and organisational constraints, reference centres are restricted in their capacity for basic research and consequently focus on applied research into various aspects of leptospirosis. They offer training, either individually or groupwise, that might vary from standard technologies to novel sophisticated methodologies, depending on the need and requests of the trainee. Most reference centres are involved in the confirmation of preliminary diagnosis obtained at peripheral levels, such as local hospitals and health centres, while other major activities involve the design and validation of diagnostics, their international harmonisation and quality assurance. Identification of causative Leptospira strains (or serovars) is key to the identification of infection sources and is critical for surveillance. Hence, reference centres also focus on the development, application and provision of methods that are required for unambiguous characterisation of new and recognised Leptospira strains and the maintenance of the integrity of strain collections. In line with their central role, reference centres are frequently associated with local, national and/or international surveillance activities linked to an advisory role and the production of guidelines. Such surveillance activities usually comprise collation of morbidity and mortality data, signalling of outbreaks and the investigation of infection sources and risks.

Computed tomography for the identification of a potential infectious source in critically ill surgical patients

IntroductionComputed tomography (CT) seems already to have an important role to identify an infectious source in the management of patients with sepsis. However, our daily clinical behavior in ordering CT imaging was never scrutinized. MethodsWe conducted a retrospective single-center analysis of CT and its therapeutic consequences in an operative intensive care unit in a tertiary care hospital in Germany. All CTs of the abdomen and/or thorax between 1st January and 31st December 2012 were included. One hundred forty-four CT studies were enrolled: 60.4% visceral, 6.9% vascular, 17.4% thoracic, and 14.6% trauma surgical cases and in 0.7% other disciplines. ResultsIn 76 CT studies (52.8%), a source of infection was found and was associated with a change in treatment in 65 (85.5%) cases. In contrast, in patients without identification of an infectious source in the CT imaging, treatment was changed after CT imaging in 11 (16.2%) cases. Computed tomography provided positive findings predominantly in the organ or the region of the surgical field. ConclusionsComputed tomographic imaging detected an infectious source in more than 50% of cases. Our data suggest that CT should be recommended to identify a source of infection in critically ill patients. Furthermore, prospective studies are needed to investigate the potential impact of CT imaging on outcome and to define criteria when to perform a CT imaging study.

Genotyping of Mycobacterium avium subsp. avium isolates from naturally infected lofts of domestic pigeons by IS901 RFLP

ObjectivesAvian tuberculosis is one of the most important infections affecting most species of birds. Several mycobacterial species have been identified causing avian tuberculosis, but the organisms confirmed most frequently are Mycobacterium avium and Mycobacterium genavense. All species of birds can be infected with M. avium. M. avium cannot only infect all species of birds, but can also infect some domesticated mammals to cause the disease, usually with localized lesions. Disseminated tuberculosis caused by M. avium has also been reported in rabbits and swine. In immune-competent humans, M. avium complex)MAC(isolates produce localized soft tissue infections, including chronic pulmonary infections in the elderly and cervical lymphadenitis in children, but rarely any disseminated disease. In HIV infected and AIDS patients, or in other immuno-compromised persons, MAC isolates frequently cause severe systemic infections.The most crucial aspect of control and eradication of the disease is identification of infection sources and transmission routes. The use of serotyping for epidemiological studies of virulent M. avium subsp. avium isolates in birds is limited by the prevalence of only three serotypes and untypable auto-agglutinating isolates. Molecular techniques, such as restriction fragment length polymorphism and pulse field gel electrophoresis, have been shown to be much more discriminatory and therefore suitable for use in the epidemiological study of M. avium complex infections. Materials and methodsEighty suspected pigeons with avian tuberculosis based on their clinical signs were subjected to the study. Forty M. avium subsp. avium isolates out of a total of 51 identified isolates were subjected to the test. Results and discussionClinical signs, necropsy findings, ZN staining and molecular identification confirmed that the pigeons were infected with M. avium subsp. avium. IS901-RFLP using PvuII was successfully conducted on 40 isolates and produced 7 patterns. The majority of isolates (60%) were RFLP type PI.1 and in comparison this type was the most similar type to the standard strain; however, all the patterns obtained in this study were different from the standard strain (M. avium subsp. avium D4 strain, ATCC number 35713). This is probably due to these isolates belonging to this region. In addition, no common pattern between this study and the only other similar study in Iran was found, and it indicates that the sources of their infection are not same. In conclusionIt is suggested that more DNA fingerprinting tests for non-tuberculous Mycobacteria, particularly M. avium complex isolated from infected birds and humans, be conducted to find the source of their infections.

Molecular monitoring and determination of N. gonorrhoeae sensitivity to antimicrobial drugs as tools to control the propagation of gonococcal infection in the Arkhangelsk Region

As a result of studying the sensitivity indices concerning antimicrobial drugs (AMD) for 203 strains of N. gonorrhoeae obtained from patients suffering from the gonococcal infection in the Arkhangelsk region, it was established that the trends of N. gonorrhoeae strains propagation, which are resistant to AMD, match the trends in Russia in general. Ceftriaxone is the drug of choice to treat the gonococcal infection in the territory of the region. It was observed that N. gonorrhoeae strains started developing resistance to the AMD in the territory of the region. The authors conducted a study of 51 N. Gonorrhoeae strains obtained from patients suffering from the gonococcal infection in 2011 using molecular epidemiology methods (sequence and phylogenetic analysis). Heterogeneity in the sample of the N. gonorrhoeae strains circulating in the territory of the Arkhangelsk region as well as high rate of their genetic variability were revealed. It was noted that N. gonorrhoeae strains, which are unique for this geographic region (dominating sequence types No. 343, 5042, 1523, 1152, 387, 6238, 5825 and 6234 as well as single sequence types), are registered in the territory of the Arkhangelsk region. The authors demonstrated the possibility to use molecular methods (PCR and sequence analysis) for individual identification of infection sources and sexual partners of patients suffering from the gonococcal infection and for the purposes of epidemiological monitoring. The authors established associations between the fact that the N. gonorrhoeae strains obtained from patients suffering from the gonococcal infection in the Arkhangelsk region belong to sequence types No. 343, 285, 2625 and 6237, and their multi-resistance, which demands a thorough examination to determine the treatment tactics for such patients. Taking into consideration the results of these studies, the authors prepared recommendations on how to control the propagation of the gonococcal infection in the territory of the Arkhangelsk region.

Molecular comparison of Neospora caninum oocyst isolates from naturally infected dogs with cell culture-derived tachyzoites of the same isolates using nested polymerase chain reaction to amplify microsatellite markers

Neospora caninum infection is an important cause of bovine abortion. The infection can be transmitted transplacentally or by ingestion of oocysts shed by definitive hosts. There are few reports of dogs naturally shedding N. caninum oocysts and only some oocyst isolates were transferred into cell culture. The aim of the present study was to analyse N. caninum oocysts from the faeces of naturally infected dogs using a microsatellite-based typing technique and to compare them with cell culture-derived tachyzoites of the same isolates. To this end, N. caninum oocysts from six naturally infected dogs were inoculated into γ-interferon knockout mice. After these mice had developed disease, tissue samples or peritoneal washings from necropsied mice were transferred into cell culture. Nested-PCR techniques were developed for the sensitive and specific amplification of N. caninum microsatellite-containing regions (MS1B, MS2, MS3, MS4, MS5 and MS10). DNA was extracted from oocysts and cell culture tachyzoites of each isolate, followed by amplification and sequence analysis of microsatellite-containing regions. Each parasite isolate examined yielded a unique microsatellite genotype, while no differences were revealed when data for N. caninum oocysts were compared with cultured tachyzoites of the same isolate. Our technique may allow the typing of clinical samples and different strains of N. caninum at the molecular level. This method may prove useful for the identification of infection sources in molecular epidemiological studies.