New and emerging infectious diseases

PHILM2Web: A high-throughput database of macromolecular host–pathogen interactions on the Web

During infection, the pathogen’s entry into the host organism, breaching the host immune defense, spread and multiplication are frequently mediated by multiple interactions between the host and pathogen proteins. Systematic studying of host–pathogen interactions (HPIs) is a challenging task for both experimental and computational approaches and is critically dependent on the previously obtained knowledge about these interactions found in the biomedical literature. While several HPI databases exist that manually filter HPI protein–protein interactions from the generic databases and curated experimental interactomic studies, no comprehensive database on HPIs obtained from the biomedical literature is currently available. Here, we introduce a high-throughput literature-mining platform for extracting HPI data that includes the most comprehensive to date collection of HPIs obtained from the PubMed abstracts. Our HPI data portal, PHILM2Web (Pathogen–Host Interactions by Literature Mining on the Web), integrates an automatically generated database of interactions extracted by PHILM, our high-precision HPI literature-mining algorithm. Currently, the database contains 23 581 generic HPIs between 157 host and 403 pathogen organisms from 11 609 abstracts. The interactions were obtained from processing 608 972 PubMed abstracts, each containing mentions of at least one host and one pathogen organisms. In response to the coronavirus disease 2019 (COVID-19) pandemic, we also utilized PHILM to process 25 796 PubMed abstracts obtained by the same query as the COVID-19 Open Research Dataset. This COVID-19 processing batch resulted in 257 HPIs between 19 host and 31 pathogen organisms from 167 abstracts. The access to the entire HPI dataset is available via a searchable PHILM2Web interface; scientists can also download the entire database in bulk for offline processing.

Database URL: http://philm2web.live

Oral lichen planus: a microbiologist point of view

Oral lichen planus (OLP) is a chronic disease of uncertain etiology, although it is generally considered as an immune-mediated disease that affects the mucous membranes and even the skin and nails. Over the years, this disease was attributed to a variety of causes, including different types of microorganisms. This review analyzes the present state of the art of the disease, from a microbiological point of view, while considering whether or not the possibility of a microbial origin for the disease can be supported. From the evidence presented here, OLP should be considered an immunological disease, as it was initially proposed, as opposed to an illness of microbiological origin. The different microorganisms so far described as putative disease-causing agents do not fulfill Koch’s postulates; they are, actually, not the cause, but a result of the disease that provides the right circumstances for microbial colonization. This means that, at this stage, and unless new data becomes available, no microorganism can be envisaged as the causative agent of lichen planus.

Subcutaneous Mycoses in Travelers

Purpose of Review

The increase in international travel in recent decades has contributed to the risk of acquiring diseases considered endemic to a region or country and the change in the epidemiology of these diseases. Endemic mycoses that may be acquired by travelers in the short or long term are endemic subcutaneous mycoses such as sporotrichosis and lobomycosis, while endemic systemic mycoses are a group of serious diseases including histoplasmosis and coccidioidomycosis. Herein, we review the current knowledge and highlight the most important aspects of these fungal infections in travelers.

Recent Findings

The most relevant advances in the study of these mycoses involve the epidemiological distribution; human mycoses can be fatal and there are few antifungal drugs available, increasing drug resistance, and a risk of emerging fungal diseases associated with climate change, as well as the increasing virulence, and the diagnostic strategies that may be limited in many countries.

Summary

Although endemic mycoses are relatively rare, they should be considered as potentially travel-related illnesses. A recent or late trip to an endemic country may guide the clinical suspicion, an early diagnosis, and the institution of effective therapy.

Prevalence of and risk factors for methicillin-resistant Staphylococcus aureus skin and soft tissue infection in a Canadian emergency department

Objective:

We sought to estimate the period prevalence of methicillin-resistant Staphylococcus aureus (MRSA) skin and soft tissue infection (SSTI) and evaluate risk factors for MRSA SSTI in an emergency department (ED) population.

Methods:

We carried out a cohort study with a nested case–control design. Patients presenting to our ED with a wound culture and a discharge diagnosis of SSTI between January 2003 and September 2004 were dichotomized as MRSA positive or negative. Fifty patients with MRSA SSTI matched by calendar time to 100 controls with MRSA-negative SSTI had risk factors assessed using multivariate conditional logistic regression.

Results:

Period prevalence of MRSA SSTI was 54.8% (95% confidence interval [CI] 50.2%–59.4%). The monthly period prevalence increased from 21% in January 2003 to 68% in September 2004 (p < 0.01). Risk factors for MRSA SSTI were injection drug use (IDU) (odds ratio [OR] 4.6, 95% CI 1.4–16.1), previous MRSA infection and colonization (OR 6.4, 95% CI 2.1–19.8), antibiotics in 8 weeks preceding index visit (OR 2.6, 95% CI 1.2–8.1), diabetes mellitus (OR 4.1, 95% CI 1.4–12.1), abscess (OR 5.6, 95% CI 1.8–17.1) and admission to hospital in previous 12 months (OR 2.6, 95% CI 1.1–11.2).

Conclusion:

The period prevalence of MRSA SSTI between January 2003 and September 2004 was 54.8% at our institution. There was a marked increase in the monthly period prevalence from the beginning to the end of the study. Risk factors are IDU, previous MRSA infection and colonization, prescriptions for antibiotics in previous 8 weeks and admission to hospital in the preceding 12 months. On the basis of local prevalence and risk factor patterns, emergency physicians should consider MRSA as a causative agent for SSTI.

Antimicrobial prevention and therapy for travelers' infection

International journeys are increasing and more than 70 million people from industrialized countries cross the borders of tropical countries every year. More than 50% of them will suffer from some form of infectious illness, ranging from mild travelers' diarrhea to severe dengue fever to fatal malaria, with a wide spectrum of microbiological entities. Travel-related respiratory infections, including TB, and sexually transmitted infections are also increasingly reported. Awareness of travel-related risk is not always adequate among international travelers. Specific training on travel medicine-related issues, as well as better diagnostic facilities for imported diseases, is crucial for physicians and nurses in industrialized countries.