Bridging the gap between molecular epidemiologists and evolutionists

Molecular epidemiology designates the various molecular methods that aim to identify the relevant units of analysis of pathogens involved in transmissible diseases: species, subspecies, strains, clones and genes of interest. It is frequently based on an empirical approach. I advocate that evolutionary concepts enrich this discipline considerably and should be considered as an integral part. In turn, the experience and questioning of field experts are crucial to evolutionists who use transmissible diseases as models. A molecular epidemiology aim gives evolutionary studies a practical goal, putting a stop to approaches that are overly speculative.

Pathogen-driven selection and worldwide HLA class I diversity

The human leukocyte antigen (HLA; known as MHC in other vertebrates) plays a central role in the recognition and presentation of antigens to the immune system and represents the most polymorphic gene cluster in the human genome [1]. Pathogen-driven balancing selection (PDBS) has been previously hypothesized to explain the remarkable polymorphism in the HLA complex, but there is, as yet, no direct support for this hypothesis [2 and 3]. A straightforward prediction coming out of the PDBS hypothesis is that populations from areas with high pathogen diversity should have increased HLA diversity in relation to their average genomic diversity. We tested this prediction by using HLA class I genetic diversity from 61 human populations. Our results show that human colonization history explains a substantial proportion of HLA genetic diversity worldwide. However, between-population variation at the HLA class I genes is also positively correlated with local pathogen richness (notably for the HLA B gene), thus providing support for the PDBS hypothesis. The proportion of variations explained by pathogen richness is higher for the HLA B gene than for the HLA A and HLA C genes. This is in good agreement with both previous immunological and genetic data suggesting that HLA B could be under a higher selective pressure from pathogens.

Threshold effects for two pathogens spreading on a network

Diseases spread through host populations over the networks of contacts between individuals and a number of results about this process have been derived in recent years by exploiting connections between epidemic processes and bond percolation on networks. Here we investigate the case of two pathogens in a single population, which has been the subject of recent interest among epidemiologists. We demonstrate that two pathogens competing for the same hosts can both spread through a population only for intermediate values of the bond occupation probability that lie above the classic epidemic threshold and below a second higher value, which we call the coexistence threshold, corresponding to a distinct topological phase transition in networked systems.

Epidemiology and management of infectious diseases in international adoptees

International adoptees represent a group of children with unique health care needs. Data from published studies, along with the recent experience of the Yale International Adoption Clinic, suggest that the risk of serious infections in adoptees is low, although infections associated with institutionalization still occur commonly. Interpretation of these data must be undertaken with caution, however, since many, if not most, international adoptees are not evaluated in specialty clinics. Thus, prospective studies designed to minimize selection and referral bias are needed in order to accurately define the risk of infectious and noninfectious diseases in all international adoptees.

Phylogenetic analysis as a tool in molecular epidemiology of infectious diseases

Phylogenetics is a powerful tool for microbial epidemiology, but it is a tool that is often misused and misinterpreted by the field. Microbial epidemiologists are cautioned that in order to draw any inferences about the order of descent from a common ancestor it is necessary to correctly root a phylogenetic tree. Epidemiological samples of microbial populations typically include both ancestors and their descendants. In order to illustrate the relationships of those isolates, the phylogenetic method used must be able to detect zero-length branches. Unweighted Pair-Group Method (UPGMA) is the phylogenetic method that is most widely used in microbial epidemiology. Because UPGMA cannot detect zero length branches, and because it places the root of the tree based on a usually-false assumption, UPGMA is the worst possible choice among the several phylogenetic methods available. Because microbial epidemiology deals with relationships among strains within a species, rather than with relationships among species, recombination within those species can render phylogenetic trees meaningless and positively misleading. When there is evidence of significant recombination within the species of interest phylogenetic trees should not be used at all. Instead, alternative tools such as eBURST should be used to understand relationships among isolates.

Antibiotic prescribing pattern in a medical intensive care unit in Qatar

OBJECTIVES

The primary objectives were to evaluate the current usage of anti-microbial agents in the Medical Intensive Care Unit (MICU) of Hamad Medical Corporation (HMC) in Doha, State of Qatar and to correlate this with: a) the infectious disease pattern, b) the isolated microorganisms and their sensitivity pattern, and, importantly, c) the patient's clinical outcome. A secondary objective was to evaluate the influence of the use of steroid therapy on the development of fungal infections.

METHODS

A prospective study covering a 2-month period from February through April 2004, including all patients admitted to the MICU for a minimum of 48 hours, and receiving a systemic antibiotic.

RESULTS

From the 71 eligible patients admitted, 54 (76%) were treated for presumed or proven infections and received antibiotics, corresponding with 280 (89%) of the 313 patient days. Respiratory infections accounted for 57%. A total of 159 antibiotics (134 intravenously and 25 orally) were administered to the 54 patients during their stay in the MICU, corresponding with an average of almost 3 antibiotics per patient. Ceftriaxone was prescribed in 31 patients (57%) as initial therapy. Throughout the study period, a total of 385 microbiology samples for culturing were taken, corresponding with almost one sample per patient per day. Fifty-two percent of patients had a microbiologically proven infection (MPI): 18% with community-acquired pneumonia (CAP), 18% ventilated-acquired pneumonia (VAP), and 11% with hospital-acquired pneumonia (HAP). In the group of bacterial MPI, sensitivity pattern resulted in change in empirical antibiotic therapy in 12 of 23 patients (52%). In the group of patients with non-MPI, antibiotherapy was changed in 5 of the 26 patients (19%). Yeast infections developed in 13 of 30 (43%) patients receiving steroids (with 3 out of 9 patients (33%) receiving steroids for severe sepsis, and septic shock) compared to 5 of 24 (21%) patients receiving no steroids.

CONCLUSION

This study highlights the urgent need for updated empiric and treatment guidelines as well as the monitoring of the antibiotic usage.

A national study on the residential impact of biological aerosols from the land application of biosolids

AIMS

The purpose of this study was to evaluate the community risk of infection from bioaerosols to residents living near biosolids land application sites.

METHODS AND RESULTS

Approximately 350 aerosol samples from 10 sites located throughout the USA were collected via the use of six SKC Biosamplers. Downwind aerosol samples from biosolids loading, unloading, land application and background operations were collected from all sites. All samples were analysed for the presence of HPC bacteria, total coliform bacteria, Escherichia coli, Clostridium perfringens, coliphage, enteroviruses, hepatitis A virus and norovirus. Total coliforms, E. coli, C. perfringens and coliphage were not detected with great frequency from any sites, however, biosolids loading operations resulted in the largest concentrations of these aerosolized microbial indicators. Microbial risk analyses were conducted on loading and land application operations and their subsequent residential exposures determined.

CONCLUSIONS

The greatest annual risks of infection occurred during loading operations, and resulted in a 4 x 10(-4) chance of infection from inhalation of coxsackievirus A21. Land application of biosolids resulted in risks that were <2 x 10(-4) from inhalation of coxsackievirus A21. Overall bioaerosol exposure from biosolids operations poses little community risk based on this study.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study evaluated the overall incidence of aerosolized micro-organisms from the land application of biosolids and subsequently determined that microbial risks of infection were low for residents close to biosolids application sites.

Symptoms in the host: infection and treatment model

AIMS AND OBJECTIVES

The aim is to devise a decision-making model to help nurses and allied professionals treat the symptoms of infectious diseases in a logical way that maximizes the benefits of symptoms and minimizes any harm that they might do.

BACKGROUND

This paper considers the symptoms of infectious diseases from an evolutionary perspective, applying theories from ecology and evolution to nursing. Building upon evolutionary theories that suggest symptoms occur as the result of host defences, pathogen manipulations or as pure side-effects, it is suggested that those symptoms that have evolved as host defences should not always be treated because of their beneficial effects. However, clinical decision-making is more complex because of the rapid changes in environment and behaviour, which may impact upon the usefulness of symptoms to the host.

CONCLUSIONS

Although some symptoms can be identified as being beneficial adaptations, this alone is not sufficient indication to decide which symptoms should or should not be treated. Other considerations include any negative outcomes and behavioural and environmental changes that may affect the significance of any adaptation.

RELEVANCE TO CLINICAL PRACTICE

Nurses should aim to maximize the host defences of the patients they are caring for in order to speed recovery and to reduce transmission and the need for antibiotics. This model helps nurses to identify factors that should be considered when these decisions are made and suggests some principles that might be followed in other situations.

Infectious complications in patients with hematological malignancies consulted by the Infectious Diseases team: a retrospective cohort study (1997–2001)

In order to identify the characteristics of patients with hematological malignancies (HM) in the presence/suspicion of any accompanying infectious disease, and to find the predictors of mortality in this group, hospital charts of patients with HM consulted by the Infectious Diseases (ID) team for signs/symptoms of any infection between January 1, 1997 and December 31, 2001 were retrospectively reviewed. A total of 1,132 consultations were done for 641 patients: 59.4% of the patients were male and the mean (+/-standard deviation) age of the study participants was 47.9+/-1.4 years. The most common underlying diseases were non-Hodgkin's lymphoma (30.9%), acute myelogenous leukemia (26.2%), and multiple myeloma (10.9%). Clinically and microbiologically documented infections and fever of unknown origin were observed in 43.3%, 38.1%, and 18.5% of the participants, respectively. Bloodstream infections were detected in 134 episodes (20.9%): 56.5% were caused by gram-negative microorganisms. In logistic regression analysis, the presence of pneumonia (OR 7.56, 95% CI 4.84-12.486), invasive fungal infection (OR 4.12, 95% CI 1.78-9.55), relapse or recent diagnosis of the underlying disease (OR 2.82, 95% CI 1.53-5.21) and neutropenia (OR 2.70, 95% CI 1.70-4.31) were identified as statistically significant predictors of mortality.

Threat of infection: microbes of high pathogenic potential--strategies for detection, control and eradication

Infectious diseases due to microbes of high pathogenic potential remain a constant and variable threat for human and animal health. The emergence of new diseases or the re-emergence of diseases that were previously under control complicates the situation to date. Infectious disease research, which has undergone a dramatic progress in understanding disease mechanisms such as host-pathogen interactions, is now focusing increasingly on new strategies for prevention and therapy. Significant progress has been achieved in the development of delivery systems for protective heterologous protein antigens and in veterinary vaccinology. A landmark of infectious diseases research is the chemical synthesis of genomes, a major new field of research referred to as "synthetic biology", that to date has resulted in the chemical synthesis of the poliovirus and of phage phiX174 genomes and their expression as infectious viruses. On the molecular level the evolution of pathogens and mechanisms of genome flexibility, which account for several pathogenic properties of infectious agents, have received increased attention. Bacterial toxins are an additional threat to human health and their interference with host cells and cellular functions is receiving more attention.

New microbiology tools for public health and their implications

The realm of diagnostic assays for detection of acute infections is rapidly changing from antibody detection to pathogen detection, from clinical laboratory based to point-of-care based, from single analyte detection to multiple analyte detection, and is more focused on detection using less invasive approaches for collecting biological samples. New assays are typically more sensitive than are conventional assays and have the capability of providing more information that characterizes the pathogen or the host response to the pathogen. From a public health perspective, the advent of molecular epidemiology, which allows tracking of pathogens based on unique genetic sequences or antigenic properties, has revolutionized how epidemiologists investigate and evaluate epidemics and assess endemic diseases. In addition, the use of point-of-care (POC) devices can impact the detection and surveillance of infections and will enhance our ability to accurately identify the causes of illnesses.

Avoiding laboratory pitfalls in infectious diseases

In today's medical care environment, clinicians are challenged to order clinically relevant, cost effective laboratory tests and antibiotic therapy. Together, physicians and laboratories must have guidelines and strategies that can provide quality patient care, while minimising costs and preventing further emergence of antimicrobial drug resistance. Five clinical vignettes that demonstrate these principles are presented.

A model for pathogen population structure with cross-protection depending on the extent of overlap in antigenic variant repertoires

The persistence of discrete antigenic types among pathogens with multiple immunogenic loci can be explained by the action of immune-mediated competition. It has previously been shown that pathogen populations will self-organize into non-overlapping subsets of antigenic variants if cross-protection between pathogen types sharing any variants is high. Here, we examine the critical question of whether such strain structure will emerge if the degree of immune-mediated competition is dependent on the number of variants shared between pathogen types, rather than in an all-or-nothing manner. Our analysis uncovers a progression from no strain structure through to discrete stable strain structure through intermediate partially structured states. This suggests that the number of loci or epitope regions required to detect linkage disequilibrium (as a manifestation of stable discrete strain structure) in pathogen populations correlates inversely with the strength of immune selection.

The binding of MBL to common bacteria in infectious diseases of children

OBJECTIVE

To purify Mannan-binding lectin (MBL) from human serum and detect its binding ability to several kinds of bacteria common in infectious diseases of children.

METHODS

MBL was purified from human serum by affinity chromatography on mannan-Sepharose 4B column. Its binding ability to eight species, 97 strains of bacteria was detected by enzyme-linked lectin assay (ELLA).

RESULTS

MBL has different binding ability to bacteria and shows strong binding ability to Klebsiella ornithinolytica and Escherichia coli, but shows relatively lower binding ability to Staphylococcus haemolyticus, Enterobacter cloacae and Staphylococcus epidermidis. To different isolates of Klebsiella pneumoniae, Haemophilus influenzae and Staphylococcus aureus, MBL shows quite different binding ability.

CONCLUSIONS

MBL has different binding ability to different bacteria, and has relatively stronger binding ability to Gram-negative bacteria. Its binding ability to different isolates of certain kinds of bacteria is quite different.

Role of infectious diseases in human carcinogenesis

The burden of human infectious diseases remains a public health problem worldwide. At least 2 billion people are affected by viral infections, and a similar number by bacteria or helminths. The long-term effects of these maladies have raised particular concern since some infectious agents have been associated with chronic human diseases, especially cancer. It is estimated that 13-20% of the world cancer cases are associated with some virus, bacteria, or helminth, e.g., human papillomavirus, Helicobacter pylori, and Schistosoma haematobium that cause cervical, stomach, and urinary bladder cancer, respectively. Certain associations between infection and malignancy are strong and irrefutable; others are still speculative. This article reviews the infectious agents that have been associated with cancer and current knowledge about the mechanisms underlying these associations.

[Resistance to a causative agent of infection and immune response]

An analytical literature review dealing with the problems of resistance to causative agents of infections. The review includes the data of experimental research, as well as the author's own immunological studies in children at the clinic of acute infections. Mechanisms of resistance at different phases of the infectious process, the multivalued role of Th1- and Th2-dependent responses in different infections, the role of vaccinal immunity in the resistance of children to the causative agents of vaccine-preventable infections (diphtheria and parotitis) are analyzed.

Compilation of a MALDI-TOF mass spectral database for the rapid screening and characterisation of bacteria implicated in human infectious diseases

A database of MALDI-TOF mass spectrometry (MS) profiles has been developed with the aim of establishing a high throughput system for the characterisation of microbes. Several parameters likely to affect the reproducibility of the mass spectrum of a taxon were exhaustively studied. These included such criteria as sample preparation, growth phase, culture conditions, sample storage, mass range of ions, reproducibility between instruments and the methodology prior to database entry. Replicates of 12 spectra per sample were analysed using a 96-well target plate containing central wells for peptide standards to correct against mass drift during analysis. The quality of the data was assessed statistically prior to database addition using root mean squared values of <3.0 as the criterion for rejection. Cluster analysis using a nearest neighbour algorithm also enabled subsets of data to be compared. This was achieved using the bespoke MicrobeLynx trade mark software. Columbia blood agar was used to standardise all procedures for the database, since it permitted the culture of most human pathogens and also produced spectra with a broad range of mass ions. In some instances, alternative media such as CLED were used in specific studies with greater success. Following standardisation of the procedure, a database was developed comprising ca. 3500 spectra with multiple strain entries for most species. The results to date show unequivocally that as the number of strains per species increased, so too did the success of species matching. The technique demonstrated unique mass spectral profiles for each genus/species, with the variation in mass ions among strains/species being dependent on the intra-specific diversity. The success of identification against the database for wild-type strains ranged between 33 and 100%; the lower percentage results being generally associated with poor representation of some species within the database. These findings provide a new dimension for the rapid and high throughput characterisation of human pathogens with potentially broad applications across the field of microbiology.

Update on antimicrobial resistance

WHO experts believe that antimicrobial resistance is potentially containable, but the window of opportunity to control and eventually eliminate the most dangerous infectious diseases is closing. If we miss our opportunity, it may become very difficult and expensive--and in some cases impossible--to treat infectious diseases. WHO's global strategy to contain antimicrobial resistance requires a massive effort and an alliance among countries, governments, international organizations, drug manufacturers, and private and public health care sectors. If infectious diseases are fought wisely and widely by the international community, drug resistance can be controlled and lives saved.