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PubMed2026

Genomic characteristics and tracing analysis of an acute gastroenteritis outbreak associated with rotavirus C in a boarding high school.

BACKGROUND: Rotaviruses are major pathogens of childhood acute gastroenteritis, dominated by rotavirus A (RVA). Outbreaks caused by human rotavirus C (RVC) are rarely reported, and relevant genomic data remain scarce. This genomic investigation of an RVC outbreak improves our understanding of viral diversity and transmission dynamics. METHODS: We performed epidemiological surveys, nucleic acid testing and whole-genome sequencing (WGS) on specimens from a 2025 RVC-associated gastroenteritis outbreak at a Chinese boarding high school. Sequence alignment, phylogenetic and molecular tracing analyses were conducted to explore RVC evolution via point mutation, segment reassortment and genomic recombination. RESULTS: This typical point-source campus outbreak was linked to an indoor student gathering matching the incubation period of RVC. Thirteen RVC FX strains were recovered from 11 rectal swabs and two vomitus samples. Their viral protein (VP) 4 and VP7 sequences shared high homology with Russian reference strains, carrying distinct amino acid variations. No segment reassortment or recombination was detected in VP4/VP7 genes. CONCLUSIONS: Dense, closed campus settings facilitate RVC clustered transmission. Limitations included absent screening of asymptomatic canteen staff. Rapid nucleic acid testing enabled timely pathogen identification for outbreak control. Greater attention should be paid to the public health risk of RVC. These whole-genome sequencing data enrich resources for studying RVC evolution and vaccine development.

Acute gastroenteritis outbreak↗
PubMed2003

Molecular interactions between DNA and an aminated glass substrate.

With the development of DNA arrays, the immobilization of DNA strands onto solid substrates remains an essential research topic. DNA arrays have potential applications in DNA sequencing, mutation detection, and pathogen identification. DNA bound to solid substrates must still be accessible and retain the ability to hybridize with its complementary strands. One technology to produce these arrays involves linking DNA molecule probes to a silanized substrate in microspot patterns and exposing them to a solution of fluorescently labeled samples of DNA targets. The behavior of both the target and probe DNA and their interactions with each other at the substrate surface, particularly with respect to molecular interactions, are poorly understood at the present time. The objective of this work is to model simply the interface interactions between DNA and glass slides modified with an aminosilane (gamma-aminopropyltriethoxysilane, APTS). In aqueous solutions, DNA behaves as a polyacid over a wide range of pH. A glass substrate treated with APTS is positively or negatively charged, depending on the pH. A model of the surface charge of APTS-treated glass has been developed from results of wetting experiments performed at various pH. It has been demonstrated that the surface charge of APTS-treated glass is well described by a model of constant capacitance of the electrical double layer. A good correlation between experimental data on DNA retention at various pH's and the variation of the surface charge of the APTS-treated glass is obtained. This provides an indication of the role of ionic interactions in the adsorption of DNA molecules onto aminated glass slides.

Adsorption↗
PubMed1999

Vaccines and diagnostic methods for bovine mastitis: fact and fiction.

A number of problems are uniquely associated with vaccination of dairy cows for mastitis. One of these is that the number of mastitis pathogens is numerous and heterogeneous. Vaccine efforts have concentrated mainly on the major mastitis pathogens. While at least one S. aureus bacterin has been commercially available for a number of years, no large-scale, independent field trials have been published in refereed journals which support the efficacy of this vaccine. Experimental vaccines for S. aureus composed of pseudocapsule-enriched bacterins supplemented with alpha- and/or beta-toxoids appear promising, but none of these has been commercialized. With S. uberis, some protection against homologous strain challenges was reported recently with a live strain and a bacterin, but other data from the same laboratory showed this vaccine would not protect against heterologous challenge strains. At this time there is only one highly effective vaccine for mastitis, the core-antigen vaccine for coliform mastitis. All of the commercially available vaccines for this indication are bacterins of rough mutants of E. coli strain J5 or Salmonella spp. Preliminary success with an experimental vaccine based on the plasminogen activator of S. uberis is a very different approach for a mastitis vaccine. Little success has been reported with vaccination against other mastitis pathogens. For diagnostic methods, the high somatic cell count, as measured by direct count or indirect assays, remains the cornerstone of mastitis diagnosis. However, for subclinical mastitis, bacterial cell culture is a reliable diagnostic method. Pathogen identification may rely on older biochemical testing methods or newer commercial identification systems, depending on the laboratory budget. ELISA assays also have been used to assess herd infection status. Epidemiologic studies have used DNA fingerprinting and ribotyping, but none of these methods has yet produced an easily utilized commercial format. Within the next decade, additional efficacious vaccines for several of the most common agents for bovine mastitis are likely. A review written at that time then can be more fact than fiction.

Animals↗
PubMed2003

Unusual infectious complications of dermatologic procedures.

Because dermatologic procedures disrupt skin integrity, they alter the body's protective barrier and predispose individuals to cutaneous infection. Postoperative wound infections--even with common pathogens such as S. aureus--seldom complicate dermatologic procedures; however, unusual infections have been reported to complicate excisions, biopsies, skin grafts, chemical peels, dermabrasion, laser resurfacing, liposuction, blepharoplasty, and injections (eg, with anesthetic solutions or botulinum toxin). Numerous environmental and patient risk factors increase the rate of postoperative wound infections, but otherwise healthy individuals undergoing relatively simple procedures are sometimes affected. Obtaining a thorough patient, history (including history of prior HSV infection or any immunocompromising factors) is crucial. Patients should be warned of potential complications, particularly when they are undergoing cosmetic procedures. It is important to maintain a high index of suspicion for possible wound infection in all patients that extends several months postoperatively. Manifestations of unusual postoperative infections are highly variable, and they might be secondary to bacterial, fungal, viral, or parasitic pathogens. Bacterial lesions are often polymicrobial, and bacterial superinfection can exacerbate other wound complications such as HSV reactivation. Most wound infections remain localized, but occasionally systemic disease occurs. For example, cutaneous diphtheria or rapidly growing mycobacteria rarely disseminate, whereas TSS results in systemic disease caused by toxin release. Some unusual postsurgical infections are self-limited, but they can still be potentially life threatening or disfiguring. Antimicrobial prophylaxis might reduce the risk of wound infection in some cases. Clinicians can better care for patients by becoming familiar with the causes and clinical manifestations of unusual dermatologic postoperative wound infections (Table 1). Following the recognition of an infectious process, appropriate diagnostic procedures allow for pathogen identification and the prompt institution of indicated therapy.

Animals↗
PubMed2001

[Current concepts on the pathogenicity of phytopathogenic bacteria].

What are the molecular determinants that make a bacterium a plant pathogen? In the last 10-20 years, important progress has been made in answering this question. In the early 20th century soon after the discovery of infectious diseases, the first studies of pathogenicity were undertaken. These early studies relied mostly on biochemistry and led to the discovery of several major pathogenicity determinants, such as toxins and hydrolytic enzymes which govern the production of major disease symptoms. From these pioneering studies, a simplistic view of pathogenicity arose. It was thought that only a few functions were sufficient to transform a bacterium into a pathogen. This view rapidly changed when modern techniques of molecular genetics were applied to analyse pathogenicity. Modern analyses of pathogenicity determinants took advantage of the relatively simple organization of the haploid genome of pathogenic bacteria. By creating non-pathogenic mutants, a large number of genes governing bacterium-host interactions were identified. These genes are required either for host colonization or for the production of symptoms. Even though the role of motility and chemotaxis in these processes is still unclear, it is clear that a strong attachment of Agrobacterium to plant cells is a prerequisite for efficient plant transformation and disease. Other important pathogenicity factors identified with a molecular genetic approach include hydrolytic enzymes such as pectinases and cellulases which not only provide nutrients to the bacteria but also facilitate pathogen invasion into host tissues. The precise role of exopolysaccharide in pathogenicity is still under discussion, however it is has been established that it is crucial for the induction of wilt symptoms caused by Ralstonia solanacearum. Trafficking of effector proteins from the invading bacterium into the host cell emerged recently as a new central concept. In plant pathogenic bacteria, protein translocation takes place through the so-called 'type II secretion machinery' encoded by hrp genes in the bacterium. These genes are present in representatives of all the major groups of Gram negative plant pathogenic bacteria except Agrobacterium. Most of these genes have counterparts in pathogens of mammals (including those of human) and they also play a central role in pathogenicity. Additionally, recent evidence suggests that a 'type IV secretion machinery' injects bacterial proteins into host cells. This machinery, originally found to be involved in the transfer of t-DNA from Agrobacterium into plant cells, was recently shown to translocate pathogenicity proteins in pathogens of mammals such as Helicobacter pylori and Brucella. Discovery of the trafficking of proteins from the pathogen into host cells revolutionized our conception of pathogenicity. First, it rather unexpectedly established the conservation of basic pathogenicity strategies in plant and animal pathogens. Second, this discovery changes our ideas about the overall strategy (or mechanism) of pathogenicity, although we still think the end result is exploitation of host cell nutritive components. Rather than killing the host cell from outside, we envision a more subtle approach in which pathogens inject effector proteins into the host cell to effect a change in host cell biology advantageous to the pathogen. Identification of the effector proteins, of their function and of the corresponding molecular targets in the host is a new challenge which will contribute to the conception of new strategies to control diseases.

Bacteria↗
PubMed2000

Febrile neutropenia in children.

Fever is frequent in neutropenic patients and often related to infection. Two major concepts, have contributed to the marked mortality decrease of those patients by the end of the 1960s: firstly, the duration and severity of neutropenia were the most important variables linked to infection and secondly, prompt administration of broad-spectrum antimicrobials empirically, was life-saving. At the same time it was universally admitted that a careful daily examination of all portals of entry for micro-organisms was mandatory and that laboratory and imaging investigations were needed at regular intervals, keeping constantly in mind the individual type and stage of immunosuppression. Through many studies, paediatricians contributed markedly in standardisation of management of febrile neutropenic patients. Neutropenic patients are not equally prone to infections, partly due to the underlying cancer, chemotherapy and co-morbidity factors. Neutropenic children are not only vulnerable to bacteria, fungi and viruses commonly encountered in adults, but also to common viruses and bacteria. Very few studies included a viral work-up. Epidemiological new trends are observed: Gram-positive bacteria and fungi are on the rise. Simplifying and shortening antibiotic regimens were made possible because new potent antibiotics were launched. Since the mid-1980s, many paediatric centres commonly discharge patients before complete bone marrow recovery, provided that patients meet certain low-risk criteria and do not exhibit any clinical or biological evidence of bacterial infection. However, a few prospective randomised studies have been conducted for assessing the safety of early antibiotics discontinuation and safe early discharge. The choice of oral agents up to now was complicated by the reluctance using fluoroquinolones in children. New challenges are numerous in terms of diagnostic tools, detection of epidemiological trends and emerging pathogens, identification and control of nosocomial threats including drug resistance, assessment of the real impact of prophylaxis, evaluation of new agents, the need for more accurate risk scoring systems, outpatient management and the necessity for an optimal use of resources.

Anti-Bacterial Agents↗
PubMed1996

Development of a multiplex PCR assay for the simultaneous detection and discrimination of HIV-1, HIV-2, HTLV-I and HTLV-II.

BACKGROUND: Multiplex polymerase chain reaction (PCR) has been established as a general technique for the simultaneous amplification of different target sequences. Uses of multiplex include pathogens identification, linkage analysis and genetic disease diagnosis. The high sensitivity of PCR may produce false-positive results due to contamination with previously amplified material. OBJECTIVES: To develop a multiplex PCR technique that can simultaneously detect and discriminate human immunodeficiency virus types 1 and 2 (HIV-1/2) and human T-lymphotropic virus types 1 and 2 (HTLV-I/II) proviral sequences. Such a method should incorporate a system that prevents the occurrence of false-positive results. STUDY DESIGN: Combinations of four primer pairs, one for each retrovirus, were assayed in order to determine the combination of oligonucleotides as well as the PCR conditions that yield the most specific and sensitive coamplification of proviral sequences. To prevent contamination with DNA from previous PCR amplifications, the uracil N-glycosylase (UNG) system was incorporated into the coamplification format. RESULTS: A combination of primer pairs from the gag region of HIV-1, env of HIV-2, pol of HTLV-I and tax of HTLV-II yielded specific and sensitive coamplification of proviral sequences. The UNG system was incorporated and shown to be efficient in the degradation of contaminating DNA. In the evaluation of a serologically well established panel of singly and dually infected individuals, the assay detected 20/22 HIV-1, 8/10 HIV-2, 8/8 HTLV-I and 8/8 HTLV-II infections.

Cell Line↗
PubMed2000

Using genetics to probe host-virus interactions; the mouse mammary tumor virus model.

It is clear that there is genetic variation among different individuals in their susceptibility to infection by viruses and other pathogens. Identification of the genes involved in conferring resistance or susceptibility to viral infection will allow us to understand both mechanisms of infection and pathogenesis and to develop reagents for treating or preventing them. Because of the large number of genetically well-characterized inbred mouse strains and the ability to generate targeted germ line mutations, this species is particularly well-suited for such analysis. This review focuses on how the use of genetics to study the retrovirus mouse mammary tumor virus allowed the dissection of both the viral infection pathway and the response of the host to this infection.

Animals↗
PubMed1998

Vaccination against enteric pathogens: from science to vaccine trials.

Recent advances in scientific research and clinical trials have shown promise for vaccine development against enteric pathogens. Identification of new virulence factors, such as the two distinct shigella enterotoxins, has allowed the development of new immunogen or new attenuated strains. Improved knowledge facilitated the development of safer attenuated live microorganism and construction of multivalent vaccines. Finally, an important advantage is the use of nonreplicating plasmid DNA vectors to express protective antigens in the host.

Bacterial Vaccines↗
PubMed2001

Tick-borne infectious diseases of dogs.

Tick-transmitted infections are an emerging problem in dogs. In addition to causing serious disease in traditional tropical and semi-tropical regions, they are now increasingly recognized as a cause of disease in dogs in temperate climates and urban environments. Furthermore, subclinically infected companion animals could provide a reservoir for human tick-transmitted infectious agents, such as Ehrlichia chaffeensis, Ehrlichia ewingll, the Ehrlichia phagocytophila group and Rickettsia conorii. Here, we discuss the emergence of new canine tick-transmitted diseases, which results from several factors, including the expansion of the tick range into urban and semi-urban areas worldwide, the movement of infected dogs into previously non-endemic areas, and the advent of novel molecular techniques for diagnosis and pathogen identification.

Animals↗
PubMed2002

Co-existent cutaneous cryptococcosis of the forearm and cutaneous alternariosis of the leg in patient with metastatic thymoma.

BACKGROUND: Cryptococcosis and alternariosis are rare opportunistic infections often observed in immunocompromised patients. Because Cryptococcus and Alternaria are ubiquitous fungi found in soil, the presence of fungi in the dermis has to be observed on histological examination to confirm a real cutaneous, invasive, infection. PATIENT: We report the first case of concomitant cutaneous cryptococcosis and cutaneous alternariosis, in an immunocompromised patient treated for a metastatic thymoma. CONCLUSION: This observation underlines the fact that the possible co-existence of several rare infections in immunocompromised patients should take into consideration pathogen identification in order to adapt the therapy to individual patient requirements.

Aged↗
PubMed1994

[Sputum examination in the diagnosis of Pneumocystis carinii pneumonia in HIV-infected patients].

To assess the sensitivity and negative predictive value of sputum examination for Pneumocystis carinii in HIV-positive patients, follow-ups were performed in HIV-infected patients who had been investigated for the presence of Pneumocystis carinii (376 examinations of sputum and 71 bronchoalveolar lavages). Pneumocystis carinii pneumonia was diagnosed 65 times in 64 patients (57 male and 7 female, median age 35 [23-67]years). In 52% of the cases (n = 34) the pathogen was identified in the sputum, in 48% (n = 31) by means of the bronchoalveolar lavage. Of 342 negative findings in sputum examination, five were definitely false negative since the subsequent lavage yielded pneumocysts. In nine further cases Pneumocystis carinii pneumonia could not be excluded because of the course of the disease. In patients from whom sputum samples were available the sensitivity of pathogen identification was at least 70.8% and the negative predictive value at least 95.9%. Since preceding prophylaxis did not render identification in the sputum more difficult, examination of spontaneous or provoked sputum is indicated as a first hand measure in all patients infected with HIV in whom Pneumocystis carinii pneumonia is suspected.

AIDS-Related Opportunistic Infections↗
PubMed2002

Maxillary sinus puncture and culture in the diagnosis of acute rhinosinusitis: the case for pursuing alternative culture methods.

OBJECTIVE: Traditional assessments of the microbial flora associated with acute bacterial rhinosinusitis have relied on maxillary sinus punctures (taps) and culture. These taps are now considered the gold standard for obtaining cultures and are used as the method of identifying bacterial pathogens in antimicrobial trials. Maxillary sinus taps are limited by discomfort to the patients and technical concerns. Because of these factors, the standard of performing taps has limited antibiotic trials and microbial surveillance. Alternatives to maxillary sinus taps have been explored. STUDY DESIGN: We conducted a retrospective, systematic review of the literature from 1950 to 2000 of articles comparing culture techniques in the nose and paranasal sinuses for acute bacterial rhinosinusitis. RESULTS: Nasal cultures have poor correlation to maxillary sinus cultures, whereas there is 60% to 85% concordance between endoscopically guided middle meatal cultures and maxillary sinus cultures. These studies, however, are all limited by small sample sizes and therefore are inadequate to make any concrete recommendations regarding the relative role of endoscopically guided middle meatal cultures as a formal method of pathogen identification in acute bacterial rhinosinusitis. CONCLUSION: A formal prospective study with sufficient sample size to assess the concordance between the microbial flora of the maxillary sinus punctures and middle meatal cultures in acute rhinosinusitis is recommended.

Acute Disease↗
PubMed2026

Artificial intelligence in molecular diagnostics for pandemic preparedness.

INTRODUCTION: Molecular diagnostics focusing on the detection and analysis of nucleic acids are indispensable tools for early pathogen identification, transmission monitoring, and genomic surveillance during pandemics. Recent technological advances have broadened the diagnostic landscape, incorporating PCR-based methods, isothermal amplification, high-CRISPR-based amplification detection, and sequencing. Despite their diagnostic potential, widespread implementation remains limited by high validation costs, time and logistical constraints, the need for specialized professional knowledge, and a lack of adaptability in resource-limited settings. Artificial intelligence (AI) is increasingly recognized as a promising but challenging approach, offering tools that streamline assay development, automate data interpretation, and optimize real-time diagnostic performance. AREAS COVERED: This review introduces recently published AI tools with potential to enhance the in-silico design validation process of oligonucleotides for molecular assays. These cover tools for initial assay design and optimization to validation and continuous assay updates. The limitations, including concerns regarding data accuracy, the lack of transparency in data processing ('black box' models), and unresolved licensing and regulatory issues, are highlighted for each tool and as expert opinion. EXPERT OPINION: Collectively, these challenges currently confine most AI-based approaches to research settings and prevent their routine implementation in clinical molecular diagnostics. Their widespread adoption depends on addressing remaining technical, regulatory, and practical challenges.

Humans↗
PubMed1989

Nonperforative appendicitis: a continuing surgical dilemma.

Acute appendicitis continues as a medical challenge with newer approaches failing to improve diagnostic accuracy. The role of antibiotics in acute nonperforative appendicitis (NPA) remains unclear. In 175 patients studied at two hospitals, preoperative guidelines were used to exclude perforative appendicitis. Nevertheless, 14% of patients were found to have this condition. Surgeon's reports significantly underestimated the diagnosis when compared with the pathologists' reports. Antibiotic prophylaxis in 122 patients with NPA was studied prospectively comparing ceftizoxime (CTZ), cefamandole (CFM), and placebo (PLA). Ceftizoxime decreased the infection rate compared with PLA (0 vs. 8; P less than .01). Use of antibiotics (CTZ or CFM) resulted in decreased infections when compared with PLA (3 vs. 8; P less than .01) and fewer days of hospitalization (3.8 vs. 5.4 d, P less than .005). Analysis of infection risk factors showed no correlations except for failure to administer antibiotics and the finding of a gangrenous appendix. Operative culture results had no predictive value for either infection or pathogen identification. It is recommended that all patients undergoing surgery for NPA be given 1 d of antibiotic prophylaxis.

Acute Disease↗
PubMed1994

Aspoxicillin versus piperacillin in severe abdominal infections--a comparative phase III study.

We compared aspoxicillin, a new broad-spectrum penicillin derivative, with piperacillin in severe abdominal infection. Aspoxicillin 4 g administered tds (n = 52) or piperacillin 4 g qds (n = 53) usually as monotherapy were randomly given to patients suffering from perforated appendicitis, acute cholecystitis, ulcer or colon perforation, or intra-abdominal abscess. Blood, tissue and exudate cultures were obtained when applicable for pathogen identification and susceptibility testing. The efficacy rates were similar in the two study groups. Of the 50 evaluable aspoxicillin patients 45 (90%) were considered as treatment responders compared with 48 patients out of 53 (91%) in the piperacillin group (NS). The 95% confidence interval for the efficacy difference was -12% to +11% thus showing no difference between the two drugs. Both drugs were generally well tolerated and no serious drug-related adverse events were noted. However, five patients died because of their illness and one patient had a fatal myocardial infarction. In conclusion, aspoxicillin 4 g tds was shown to be equal to piperacillin 4 g qds in severe abdominal infections.

Abdominal Abscess↗
PubMed2006

Rapid DNA mapping by fluorescent single molecule detection.

DNA mapping is an important analytical tool in genomic sequencing, medical diagnostics and pathogen identification. Here we report an optical DNA mapping strategy based on direct imaging of individual DNA molecules and localization of multiple sequence motifs on the molecules. Individual genomic DNA molecules were labeled with fluorescent dyes at specific sequence motifs by the action of nicking endonuclease followed by the incorporation of dye terminators with DNA polymerase. The labeled DNA molecules were then stretched into linear form on a modified glass surface and imaged using total internal reflection fluorescence (TIRF) microscopy. By determining the positions of the fluorescent labels with respect to the DNA backbone, the distribution of the sequence motif recognized by the nicking endonuclease can be established with good accuracy, in a manner similar to reading a barcode. With this approach, we constructed a specific sequence motif map of lambda-DNA. We further demonstrated the capability of this approach to rapidly type a human adenovirus and several strains of human rhinovirus.

Adenoviruses, Human↗
PubMed2003

RNase T1 mediated base-specific cleavage and MALDI-TOF MS for high-throughput comparative sequence analysis.

Here we devise a new method for high-throughput comparative sequence analysis. The developed protocol comprises a homogeneous in vitro transcription/RNase cleavage system with the accuracy and data acquisition speed of matrix-assisted laser desorption/ionization coupled with time-of-flight mass spectrometry (MALDI-TOF MS). In summary, the target region is PCR amplified using primers tagged with promoter sequences of T7 or SP6 RNA polymerase. Using RNase T1, the in vitro transcripts are base-specifically cleaved at every G-position. This reaction results in a characteristic pattern of fragment masses that is indicative of the original target sequence. To enable high-throughput analysis, samples are processed with automated liquid handling devices and nanoliter amounts are dispensed onto SpectroCHIP arrays for reliable and homogeneous MALDI preparation. This system enables rapid automated comparative sequence analysis for PCR products up to 1 kb in length. We demonstrate the feasibility of the devised method for analysis of single nucleotide polymorphisms (SNPs) and pathogen identification.

Apolipoproteins B↗