Rapid diagnosis in pediatric infectious diseases: the past, the present and the future

Fast identification of Escherichia coli in urinary tract infections using a virulence gene based PCR approach in a novel thermal cycler

Uropathogenic Escherichia coli (UPEC) is the most common causal agent of urinary tract infections (UTIs) in humans. Currently, clinical detection methods take hours (dipsticks) to days (culturing methods), limiting rapid intervention. As an alternative, the use of molecular methods could improve speed and accuracy, but their applicability is complicated by high genomic variability within UPEC strains. Here, we describe a novel PCR-based method for the identification of E. coli in urine. Based on in silico screening of UPEC genomes, we selected three UPEC-specific genes predicted to be involved in pathogenesis (c3509, c3686 (yrbH) and chuA), and one E. coli-specific marker gene (uidA). We validated the method on 128 clinical (UTI) strains. Despite differential occurrences of these genes in uropathogenic E. coli, the method, when using multi-gene combinations, specifically detected the target organism across all samples. The lower detection limit, assessed with model UPEC strains, was approximately 10⁴ CFU/ml. Additionally, the use of this method in a novel ultrafast PCR thermal cycler (Nextgen PCR) allowed a detection time from urine sampling to identification of only 52 min. This is the first study that uses such defined sets of marker genes for the detection of E. coli in UTIs. In addition, we are the first to demonstrate the potential of the Nextgen thermal cycler. Our E. coli identification method has the potential to be a rapid, reliable and inexpensive alternative for traditional methods.

Paratyphoid fever: splicing the global analyses

The incidence of enteric fever caused by Salmonella enterica serovar Paratyphi A (S. Paratyphi A) is increasing in many parts of the world. Although there is no major outbreak of paratyphoid fever in recent years, S. Paratyphi A infection still remains a public health problem in many tropical countries. Therefore, surveillance studies play an important role in monitoring infections and the emergence of multidrug resistance, especially in endemic countries such as India, Nepal, Pakistan and China. In China, enteric fever was caused predominantly by S. Paratyphi A rather than by Salmonella enterica serovar Typhi (S. Typhi). Sometimes, S. Paratyphi A infection can evolve into a carrier state which increases the risk of transmission for travellers. Hence, paratyphoid fever is usually classified as a "travel-associated" disease. To date, diagnosis of paratyphoid fever based on the clinical presentation is not satisfactory as it resembles other febrile illnesses, and could not be distinguished from S. Typhi infection. With the availability of Whole Genome Sequencing technology, the genomes of S. Paratyphi A could be studied in-depth and more specific targets for detection will be revealed. Hence, detection of S. Paratyphi A with Polymerase Chain Reaction (PCR) method appears to be a more reliable approach compared to the Widal test. On the other hand, due to increasing incidence of S. Paratyphi A infections worldwide, the need to produce a paratyphoid vaccine is essential and urgent. Hence various vaccine projects that involve clinical trials have been carried out. Overall, this review provides the insights of S. Paratyphi A, including the bacteriology, epidemiology, management and antibiotic susceptibility, diagnoses and vaccine development.

Rapid and sensitive detection of major uropathogens in a single-pot multiplex PCR assay

Urinary tract infection (UTI) is among the most common bacterial infections and poses a significant healthcare burden. Escherichia coli is the most common cause of UTI accounting for up to 70 % and a variable contribution from Proteus mirabilis, Pseudomonas aeruginosa and Klebsiella pneumoniae. To establish a complete diagnostic system, we have developed a single-tube multiplex PCR assay (mPCR) for the detection of the above-mentioned four major uropathogens. The sensitivity of the assay was found to be as low as 10(2) cfu/ml of cells. The mPCR evaluated on 280 clinical isolates detected 100 % of E. coli, P. aeruginosa, P. mirabilis and 95 % of K. pneumonia. The assay was performed on 50 urine samples and found to be specific and sensitive for clinical diagnosis. In addition, the mPCR was also validated on spiked urine samples using 40 clinical isolates to demonstrate its application under different strain used in this assay. In total, mPCR reported here is a rapid and simple screening tool that can compete with conventional biochemical-based screening assays that may require 2-3 days for detection.

DNA-based diagnostic tests for Salmonella strains targeting hilA, agfA, spvC and sef genes

The goal of this study was to evaluate the suitability of the hilA, agfA, spvC and sef genes amplification by PCR as a method for detection of Salmonella strains. Twenty nine isolates of Salmonella spp. including 6 different serotypes were analyzed in this study. The bacteria were isolated between 2005 and 2007 and serotyped at the Clinical Hospital of Infectious Disease, Cluj-Napoca. Ten non-Salmonella strains were also tested by the same procedure. We used a direct PCR technique, DNA extraction had been skipped and the bacterial cell wall denaturated in the first step of the reaction. All Salmonella strains gave positive results by the PCR amplification of hilA gene. The utilization of the sef, and spvC genes or spvC and agfA genes in a multiplex PCR provides a valuable diagnostic tool for Salmonella enteritidis strains.

Diagnosing infections--current and anticipated technologies for point-of-care diagnostics and home-based testing

In recent years, we have witnessed many transitions in healthcare systems around the globe. For example, population expansion and ageing, and the human immunodeficiency virus (HIV)-AIDS epidemics, have exerted pressure to decentralize the practice of healthcare outside of traditional settings to bring care to those in need. Upstream of patient management, diagnosis is aimed at adequately orienting medical decisions, and considerable efforts have been made to make this process faster and more efficient. However, there are several diseases and medical conditions that may/will benefit from technologies and tests that can be performed closer to the patient, at the point of care or even in the home. In this review, and in light of the paradox that technology and assay developers and healthcare officials must take into consideration for advancing human health in developed and developing countries, we present an overview of rapid diagnosis of infectious diseases at the point of care and of technologies that may contribute to enhancement of the worldwide point-of-care testing market.

The increasing role of DNA molecular technologies in infection control-related medical bacteriology: what the infection prevention specialist needs to know

Molecular biology has the potential to revolutionise the way in which diagnostic tests are delivered in order to optimise care of infected patients, whether they are in hospital or in the community. Many routine hospital diagnostic laboratories are now beginning to adopt commercial molecular kits, which have dramatically expanded the availability of such tests into hospitals, which previously would not have used them. This has created a need among infection prevention specialists, microbiologists and infection control doctors as to what these tests mean, and how to formulate policy around them, so that there is added value for their use in the infection prevention scenario. This review wishes to explore their basis, their application in the infection prevention setting, their interpretation, as well as their advantages and disadvantages, in order to better inform infection prevention specialists.

New methods for selective isolation of bacterial DNA from human clinical specimens

Separation of bacterial DNA from human DNA in clinical samples may have an important impact on downstream applications, involving microbial diagnostic systems. We evaluated two commercially available reagents (MolYsis), Molzym GmbH & Co. KG, Bremen and Pureprove, SIRS-Lab GmbH, Jena, both Germany) for their potential to isolate and purify bacterial DNA from human DNA. We chose oral samples, which usually contain very high amounts of both human and bacterial cells. Three different DNA preparations each were made from eight caries and eight periodontal specimens using the two reagents above and a conventional DNA extraction strategy as reference. Based on target-specific real-time-quantitative PCR assays we compared the reduction of human DNA versus loss of bacterial DNA. Human DNA was monitored by targeting the beta-2-microglobulin gene, while bacteria were monitored by targeting 16S rDNA (total bacteria and Porphyromonas gingivalis) or the glycosyltransferase gene (Streptococcus mutans). We found that in most cases at least 90% of human DNA could successfully be removed, with complete removal in eight of 16 cases using MolYsis, and two (of 16) cases using Pureprove. Conversely, detection of bacterial DNA was possible in all cases with a recovery rate generally ranging from 35% to 50%. In conclusion, both strategies have the potential to reduce background interference from the host DNA which may be of remarkable value for nucleic-acid based microbial diagnostic systems.

Primers specific for the fimbrial major subunit gene stdA can be used to detect Salmonella enterica serovars

The feasibility of using two primers internal to the stdA gene (which encodes the fimbrial major subunit of the std fimbrial gene cluster in Salmonella enterica serovar Typhi) to detect Salmonella by PCR was explored. The 518-bp stdA specific sequence was conserved among 268 strains from 45 serovars of S. enterica. One Salmonella bongori CCUG 30042 strain and 34 non-Salmonella strains did not possess this sequence. A sensitivity test revealed that the stdA-specific primer set detected 3.4 x 10(-1) pg of genomic DNA and 3.0 x 10(5) CFU/ml with serial dilutions of Salmonella Typhimurium cells. In vitro testing for specificity using pig carcass sponge samples contaminated with Salmonella Typhimurium also was performed. An initial Salmonella Typhimurium inoculum of 4.4 x 10(1) CFU/ml in pig carcass exudates reached the stdA primer detection level after preenrichment in buffered peptone water at 37 degrees C for 18 h in the presence of indigenous non-Salmonella flora at 4.0 X 10(7) CFU/ml, but the detection level decreased to 4.4 x 10(0) CFU/ml after selective enrichment in Rappaport-Vassiliadis R10 broth for 18 h at 42 degrees C. The PCR method with primers specific for stdA is a quick and sensitive tool for detecting S. enterica, which is an important cause of foodborne disease.

Selective isolation of bacterial DNA from human clinical specimens

We evaluated two DNA preparation strategies (MolYsis, Molzym GmbH & Co. KG, Bremen, Germany) and Pureprove, SIRS-Lab GmbH, Jena, Germany) to selectively extract bacterial DNA from human clinical samples. By testing 16 oral samples we found that human DNA could be largely eliminated while detectable levels of bacterial DNA were obtained with all samples. Both approaches hold great potential for microbial diagnostic systems.

The role of perinatal pathological examination in subclinical infection in obstetrics

Infectious agents are associated with a wide range of obstetric complications and pathological processes affecting the placenta, membranes and fetus. In some cases there will be associated maternal symptoms and signs indicating an infectious aetiology, but in the majority such infection is subclinical, and specific diagnosis or confirmation is achieved following pathological examination of the delivered placenta and/or fetus. There are two major groups of microorganism-related mechanisms associated with significant perinatal morbidity and mortality. First, ascending genital-tract infection, almost always bacterial, which ranges from localized choriodecidual inflammation to frank chorioamnionitis with fetal sepsis; this is a major cause of mid-trimester miscarriage and severe preterm delivery, and more recent data suggest that it may also have potentially important effects via cytokine release mediating neonatal cerebral injury. Second, haematogenous spread of maternal systemic infection--bacterial, viral or parasitic--which may result in isolated placental effects or transmission to the fetus with associated developmental abnormalities and neonatal complications. In many cases distinctive histopathological findings are described, and in addition a wide range of techniques is now available for culture and microscopy to confirm these diagnoses; such techniques include highly specific immunohistochemical markers and sensitive molecular diagnostic techniques such as the polymerase chain reaction. It is likely that with increasingly widespread availability of these investigative approaches to obstetric pathology, a greater understanding of the role of infectious agents in obstetric complications will become apparent.

Novel ways of preventing antibiotic-resistant infections: what might the future hold?

Most antibiotic-resistant bacteria are opportunistic pathogens; they colonize the skin and mucosal surfaces and only cause infection when the opportunity arises. Thus, the processes that lead to an infection attributable to antibiotic-resistant bacteria can be broadly divided into those processes that lead to acquisition of antibiotic-resistant bacteria and those that lead to the development of an infection with that organism. We review the processes that lead to the development of infections attributable to antibiotic-resistant bacteria. We then discuss options that may become available to interrupt these processes and, thus, may reduce the rate of infections attributable to antibiotic-resistant bacteria in the future.

Molecular diagnosis of infectious diseases in dermatology

The molecular diagnosis of infectious disease has been growing considerably over the past decade. Nucleic acid amplification techniques, such as polymerase chain reaction, ligase chain reaction, transcription-mediated amplification, and nucleic acid sequence-based amplification, provide highly accurate diagnosis of numerous bacterial, viral, fungal, and parasitic infections involved in a variety of dermatologic diseases. In addition, signal amplification with hybrid capture, branched-DNA assays, and in situ hybridization have been used to detect numerous viral pathogens with high degrees of sensitivity and specificity. New technology that involves the use of DNA and protein microarrays has also enabled the detection of a variety of genes and gene mutations. With time, these diagnostic assays are decreasing in cost, gaining approval of the U.S. Food and Drug Administration, and becoming easier and more efficient to use. In the future, these assays will be able to deliver rapid and accurate diagnosis of infectious diseases within a single clinic visit.

LEARNING OBJECTIVE

At the completion of this learning activity, participants should be familiar with molecular diagnosis of infectious diseases in dermatology.

The evolution of neonatology

In 1960, the terms "neonatology" and "neonatologist" were introduced. Thereafter, an increasing number of pediatricians devoted themselves to full-time neonatology. In 1975, the first examination of the Sub-Board of Neonatal-Perinatal Medicine of the American Board of Pediatrics and the first meeting of the Perinatal Section of the American Academy of Pediatrics were held. One of the most important factors that improved the care of the neonate was the miniaturization of blood samples needed to determine blood gases, serum electrolytes, glucose, calcium, bilirubin, and other biochemical measurements. Another factor was the ability to provide nutrition intravenously, and the third was the maintenance of normal body temperature. The management of respiratory distress syndrome improved with i.v. glucose and correction of metabolic acidosis, followed by assisted ventilation, continuous positive airway pressure, antenatal corticosteroid administration, and the introduction of exogenous surfactant. Pharmacologic manipulation of the ductus arteriosus, support of blood pressure, echocardiography, and changes in the management of persistent pulmonary hypertension, including the use of nitric oxide and extracorporeal membrane oxygenation, all have influenced the cardiopulmonary management of the neonate. Regionalization of neonatal care; changes in parent-infant interaction; and technological changes such as phototherapy, oxygen saturation monitors, and brain imaging techniques are among the important advances reviewed in this report. Most remarkable, a 1-kg infant who was born in 1960 had a mortality risk of 95% but had a 95% probability of survival by 2000. However, errors in neonatology are acknowledged, and potential directions for the future are explored.

Fungal infection in the very low birthweight infant

PURPOSE OF REVIEW

Fungal infections are prevalent in very low birthweight (<1500 g) infants and are associated with significant morbidity and mortality. A better understanding of the adherence factors, molecular diagnostics and risk factors for invasive fungal infection are important in treatment and prevention.

RECENT FINDINGS

Animal studies have demonstrated that Candida readily adheres to apical microvilli and the junctions between enterocytes. Although antibiotics facilitate colonization, dissemination occurs with immunosuppression. The INT1 gene is associated with enhanced colonization and dissemination in these animal models. Dissemination is probably caused by yeast cell adherence and invasion, whereas tissue injury may be related to filamentous formation. Polymerase chain reaction techniques have demonstrated promise in neonatal patients and may not only detect bloodstream infection, but fungal infection at other sites. At the time of fungal sepsis, less than 28 weeks' gestation, thrombocytopenia, and previous exposure to broad-spectrum antibiotics continue to be risk factors for infection. Empiric therapy is still being defined and investigated. Fluconazole prophylaxis should be strongly considered in the most immature infants.

SUMMARY

Preventative strategies against fungal colonization and infection are critical in high-risk very low birthweight infants. Also promising is the ability of molecular diagnostics to detect infection earlier, allowing for prompt treatment, including central venous catheter removal. Identifying the highest risk very low birthweight infants for prophylaxis and empiric therapy may lead to better outcomes. Multicenter clinical trials of fluconazole prophylaxis to confirm its safety and efficacy, and of empiric treatment to test safety and outcomes are urgently needed.

Clinical microbiology of bacterial and fungal sepsis in very-low-birth-weight infants

Twenty percent of very-low-birth-weight (<1500 g) preterm infants experience a serious systemic infection, and despite advances in neonatal intensive care and antimicrobials, mortality is as much as threefold higher for these infants who develop sepsis than their counterparts without sepsis during their hospitalization. Outcomes may be improved by preventative strategies, earlier and accurate diagnosis, and adjunct therapies to combat infection and protect the vulnerable preterm infant during an infection. Earlier diagnosis on the basis of factors such as abnormal heart rate characteristics may offer the ability to initiate treatment prior to the onset of clinical symptoms. Molecular and adjunctive diagnostics may also aid in diagnosing invasive infection when clinical symptoms indicate infection but no organisms are isolated in culture. Due to the high morbidity and mortality, preventative and adjunctive therapies are needed. Prophylaxis has been effective in preventing early-onset group B streptococcal sepsis and late-onset Candida sepsis. Future research in prophylaxis using active and passive immunization strategies offers prevention without the risk of resistance to antimicrobials. Identification of the differences in neonatal intensive care units with low and high infection rates and implementation of infection control measures remain paramount in each neonatal intensive care unit caring for preterm infants.

Simple and rapid detection of Salmonella strains by direct PCR amplification of the hilA gene

The suitability of a PCR procedure using a pair of primers targeting the hilA gene was evaluated as a means of detecting Salmonella species. A total of 33 Salmonella strains from 27 serovars and 15 non-Salmonella strains from eight different genera were included. PCR with all the Salmonella strains produced a 784 bp DNA fragment that was absent from all the non-Salmonella strains tested. The detection limit of the PCR was 100 pg with genomic DNA and 3 x 10(4) c.f.u. ml(-1) with serial dilutions of bacterial culture. An enrichment-PCR method was further developed to test the sensitivity of the hilA primers for the detection of Salmonella in faecal samples spiked with different concentrations of Salmonella choleraesuis subsp. choleraesuis serovar Typhimurium. The method described allowed the detection of Salmonella Typhimurium in faecal samples at a concentration of 3 x 10(2) c.f.u. ml(-1). In conclusion, the hilA primers are specific for Salmonella species and the PCR method presented may be suitable for the detection of Salmonella in faeces.

Adenovirus: an increasingly important pathogen in paediatric bone marrow transplant patients

Adenovirus is increasingly being recognised as a significant pathogen in children following bone marrow transplantation. The virus is endemic in the general paediatric population, and frequently causes severe disease in immunocompromised patients, especially children. Immune responses to adenovirus infection are not fully understood but T-cell responses appear to be important for recovery. Infections can affect a variety of organs with gastrointestinal and urinary tract diseases being the most common. When disseminated infection occurs, reported mortality rates are as high as 60%. The responses to treatment in immunocompromised patients have generally been disappointing. New molecular diagnostic techniques have meant that adenoviral infections can now be detected early, often before symptoms have developed. Clinicians now screen for adenovirus infection to allow early initiation of treatment. It is hoped that this approach, together with effective antiviral therapy, will reduce the deaths from this common virus in high-risk children.