Microbiological Cause Research Articles

Model development and simulation for predicting risk of foaming in anaerobic digestion systems

Although there is not a complete agreement on the causes of foaming in anaerobic digestion, experts and operators do have valuable empirical knowledge of key factors. Based on this knowledge, a model for calculating the risk of foaming in anaerobic digestion systems due to microbiological causes has been developed. Organic loading rate, variation in organic loading rate, and the presence of filamentous microorganisms in the activated sludge system, used as a feed source for the digester, have been selected as the inputs of a knowledge-based model designed to provide as output the risk of foaming in an anaerobic digester. The performance of the model is demonstrated by means of a case study using the IWA Benchmark Simulation Model No. 2 as a framework, where risk of foaming is used as a new evaluation criterion. The simulated results of an open-loop configuration and two closed-loop control strategies illustrate the usefulness of this knowledge-based approach as a means of estimating the risk of foaming in anaerobic digestion.

Bicalutamide-induced Interstitial Lung Disease

Androgen deprivation therapy, which is the standard treatment for metastatic prostate cancer, includes nonsteroidal antiandrogenic drugs, such as flutamide, nilutamide and bicalutamide. Of them, bicalutamide rarely induces interstitial pneumonia. We report a case of bicalutamide-induced interstitial pneumonia. A 68-year old male diagnosed with prostate cancer and multiple bone metastases presented with dry cough and low grade fever for 3 days. He had taken bicalutamide (50 mg/day) for 13 months. High resolution computed tomography revealed ground glass opacity in his right upper lung. The laboratory studies showed no eosinophilia in the serum and bronchoalveolar lavage fluid. Despite the use of antimicrobial agents for 2 weeks, the extent of the lung lesions increased to the left upper and right lower lung. He had no environmental exposure, collagen vascular disease and microbiological causes. Under the suspicion of bicalutamide-induced interstitial pneumonia, bicalutamide was stopped and prednisolone (1 mg/kg/ day) was initiated. The symptoms and radiologic abnormalities were resolved with residual minimal fibrosis.

Respiratory infections in the immunocompromised host

There are a wide range of pathogens that affect the respiratory tract in patients with abnormal immune system; typically this is referred to as pneumonia. In general, these infections can be divided into community-acquired pathogens and opportunistic pathogens. The clinical presentation and microbiologic causes of pneumonia in the different immunocompromised hosts will be reviewed. Special attention will be paid to the community respiratory viruses, Pneumocystis carinii pneumonia (PCP), and tuberculosis.

Cluster of necrotizing enterocolitis in a neonatal intensive care unit: New Mexico, 2007

BackgroundAlthough the cause of necrotizing enterocolitis (NEC) is unknown, infection control practices have been shown to play an important role in containing many outbreaks. We investigated the etiology of a cluster of NEC in a level 3 neonatal intensive care unit and monitored for new cases following the implementation of enhanced infection control measures.MethodsInvestigators performed a chart and laboratory review for neonates with a diagnosis of NEC during January 1, 2007, to February 13, 2007, to identify risk factors. Enhanced environmental cleaning, cohorting of infants and nurses, and increased attention to hand hygiene were instituted. Commercial feeding products in the unit were tested for bacterial contamination. Close monitoring for new cases continued for 2 months following the identification of the cluster.ResultsEleven cases of NEC were identified during the study period. Patients had a median of 5 disease risk factors (range, 3-8). Four distinct pathogens were detected in blood or stool specimens from 4 different patients. One sample of human milk fortifier (HMF) tested contained a colony count of Bacillus cereus at the US Food and Drug Administration's upper microbiologic limit for contamination. Seven (65%) patients received HMF before symptom onset, and 9 (82%) patients received 1 or more types of liquid formula. Only 1 new case was identified during the period of close monitoring.ConclusionA microbiologic cause was not identified, and, although the cluster might have resolved spontaneously, enhanced infection control and changing batches of HMF might have played a role in controlling this outbreak.

ASAS Centennial Paper: A century of pioneers and progress in meat science in the United States leads to new frontiers

Discoveries, understanding, and innovations in meat science during the last century have led to revolutionary changes in meat and poultry production, processing, marketing, and consumption. American Society of Animal Science members have made key contributions in most, if not all, categories of advancement. The first US university meat science program was begun in Minnesota in 1905. Use of mechanical refrigeration in the meatpacking industry, improved transportation and packaging, and home refrigeration provided more flexibility, variety, and consistency in meat and meat products in the early 1900s. Cooperative meat research was begun by 27 universities in 1925, with a focus on the observational characterization of carcass traits and composition, meat quality attributes, and causes of the wide variation in these variables. Scientific study of genetic, nutritional, and environmental influences on the growth, physiology, and postmortem biochemistry of muscle often used muscle-comparative investigations. Rigor mortis, cold shortening and thaw rigor, postmortem muscle metabolism, postmortem tenderization and tenderness variation, and postmortem myoglobin and lipid oxidation were studied vigorously in the 1960s and beyond, defining the biochemical bases for associated outcomes in fresh and processed products. Value-added benefits resulted from implementation of electrical stimulation, boxed beef and modified-atmosphere packaging, restructuring technologies, collagen recovery, and muscle profiling work. Isolation, purification, and definition of the primary structure and biophysical properties of the myofribillar and cytoskeletal proteins in muscle aided the understanding of contraction and postmortem changes. The role of Ca-dependent proteases in meat tenderness and muscle growth is being clarified. The chemistry of meat curing, meat emulsion formation, fermentation, and other processing methods led to new technologies, new meat products, and new benchmarks in product shelf life and quality. Meat safety assurance and our ability to manage the microbiological causes of food-borne illness and spoilage are imminently important now and in the future.

Pulmonary and Blood Stream Infections in Adult Living Donor and Cadaveric Liver Transplant Patients

Infectious complications occur in approximately 50% of cadaveric liver transplant (CDLT) recipients. Living-donor liver transplantation (LDLT) is an established alternative to shorten the waiting time. Currently, the incidence of pulmonary infections after LDLT and the microbiologic causes are unknown. In the present cohort study, we compared the incidence and profiles of pulmonary and blood stream infections (BSI) between LDLT and CDLT recipients. We hypothesized a lower incidence in LDLT recipients. The clinical course of 55 LDLT recipients consecutively transplanted between January 2003 and December 2006 was analyzed. The 173 CDLT recipients who were transplanted in the same period served as a control group. Patients were treated in a single Intensive Care Unit, applying standardized postoperative care. Mean model for end-stage liver disease score did not differ between LDLT and CDLT recipients (14.2 vs. 13.3). The overall incidence of pulmonary and BSI for both groups was 8% and 24%, respectively. Pulmonary infections were experienced by 18% of LDLT versus 5% of CDLT recipients (P=0.005) and BSI occurred in 33% of LDLT versus 21% of CDLT recipients (P=0.1). In contrast to our hypothesis, LDLT recipients experienced significantly more pulmonary infections and a trend toward increased higher incidence of BSI. These findings emphasize the need for future research on the causative agents and prevention of infection in LDLT recipients. The observation that patients with pulmonary infection had a significantly reduced 1-year survival rate underscores the importance of our observations.

The patient with possible pneumonia

Abstract Community-acquired pneumonia (CAP) is part of a spectrum of lower respiratory tract infection (LRTI) and is commoner in the winter months and in more deprived populations. Despite modern antibiotics, pneumonia remains the second commonest cause of death in the UK after ischaemic heart disease. Streptococcus pneumoniae is the commonest confirmed microbiological cause of CAP, with Mycoplasma pneumoniae the second commonest during epidemic years. Although most patients with CAP will have lung crackles or bronchial breathing, distinguishing pneumonia from non-pneumonic LRTI can be difficult and chest X-ray confirmation is often required. All patients with CAP should undergo an initial severity assessment using the CURB-65 score before deciding on management, and respiratory rate is the most important clinical sign in assessing severity. Patients with severe pneumonia as defined by CURB-65 should receive broad spectrum intravenous antibiotics immediately, covering all suspected organisms, including Streptococcus pneumoniae . Those with no markers of severity can be treated safely at home with oral antibiotics. CRP should fall by 50% in 4 days; if not, reconsider the diagnosis and look for complications such as empyema. Clearance of the pneumonic consolidation takes on average 6 weeks and follow-up chest X-ray is usually unnecessary except in those at increased risk of malignancy, such as smokers and those aged over 65 years.

Quantitative PCR for detection and discrimination of the bloodborne pathogen Staphylococcus epidermidis in platelet preparations using divIVA and icaA as target genes

Bacterial contamination of blood components is the major microbiological cause of transfusion-associated morbidity, with Staphylococcus epidermidis being the most frequently isolated organism from contaminated platelet preparations (PPs). We have recently shown that S. epidermidis forms biofilms during platelet storage, which might account for reported missed detection during routine screening. In this study, we developed a highly sensitive and specific multiplex quantitative PCR (QPCR) assay to detect S. epidermidis in PPs at levels of 10(2)-10(3) cfu/mL. A specific primer pair and hydrolysis probe were designed to amplify an internal region of the cell division divIVA gene that is unique to S. epidermidis. In addition, an internal sequence of the virulence gene icaA, which is involved in the synthesis of the S. epidermidis biofilm matrix, was selected to allow for differentiation of potentially biofilm-forming S. epidermidis isolates. A conserved region of the 8 alleles of the HLA-DQalpha1 locus present in residual white blood cells in PPs was selected as an internal control for the assay. The specificity of this assay was confirmed, as other staphylococcal species that were tested with the optimized parameters were not detected. This QPCR assay could be adaptable for the detection of other bloodborne bacterial pathogens.

Infective endocarditis in patients with congenitally malformed hearts: characterization of the syndrome in a developing country

Cardiac surgery for correction or palliation of congenital cardiac disease in infancy and childhood remains a privilege that is rarely accessible to two-thirds of the world's population. This imbalance has created a unique spectrum of illness in patients with underlying congenital cardiac disease and complicating infective endocarditis in developing countries, including Pakistan. In this study, we characterize endocarditis as seen in such patients presenting in Karachi. We reviewed retrospectively patients admitted to Aga Khan University with underlying congenitally malformed hearts and endocarditis between 1991 and 2004. We identified 48 patients with endocarditis according to the modified Duke Criterions, with just over half the cases (54%) classified as definite endocarditis. Of the patients, 23 (49%) patients were more than 16 years old. Uncorrected left-to-right-shunts, tetralogy of Fallot, and congenital mitral valvar disease were the most common underlying defects. Patients with cyanotic defects, particularly of the complex type, were underrepresented (4%). Only 11 (22.9%) of the patients had a previous palliative or corrective surgery. In one-third of the patients (16), streptococcal species were identified as the microbiologic cause of endocarditis, and 22 (45.8%) had culture-negative endocarditis. In contrast, Staphylococcus aureus and enterococci caused endocarditis in only one patient each. There were no differences in mortality or complications between cyanotic and acyanotic congenital defects. Surgery was performed in nine (18.7%) patients with endocarditis, and of these, 13 (27.1%) died. In contrast to the developed world, endocarditis in the developing countries, such as Pakistan, complicates uncorrected left-to-right shunts and tetralogy of Fallot, probably because patients with complex cyanotic defects fail to survive long after birth due to the lack of available surgery. Almost half of patients had culture-negative endocarditis, likely related to several factors.

Acute childhood diarrhoea in northern Ghana: epidemiological, clinical and microbiological characteristics.

BackgroundAcute diarrhoea is a major cause of childhood morbidity and mortality in sub-Saharan Africa. Its microbiological causes and clinico-epidemiological aspects were examined during the dry season 2005/6 in Tamale, urban northern Ghana.MethodsStool specimens of 243 children with acute diarrhoea and of 124 control children were collected. Patients were clinically examined, and malaria and anaemia were assessed. Rota-, astro-, noro- and adenoviruses were identified by (RT-) PCR assays. Intestinal parasites were diagnosed by microscopy, stool antigen assays and PCR, and bacteria by culturing methods.ResultsWatery stools, fever, weakness, and sunken eyes were the most common symptoms in patients (mean age, 10 months). Malaria occurred in 15% and anaemia in 91%; underweight (22%) and wasting (19%) were frequent. Intestinal micro-organisms were isolated from 77% of patients and 53% of controls (P < 0.0001). The most common pathogens in patients were rotavirus (55%), adenovirus (28%) and norovirus (10%); intestinal parasites (5%) and bacteria (5%) were rare. Rotavirus was the only pathogen found significantly more frequently in patients than in controls (odds ratio 7.7; 95%CI, 4.2–14.2), and was associated with young age, fever and watery stools. Patients without an identified cause of diarrhoea more frequently had symptomatic malaria (25%) than those with diagnosed intestinal pathogens (12%, P = 0.02).ConclusionRotavirus-infection is the predominant cause of acute childhood diarrhoea in urban northern Ghana. The abundance of putative enteropathogens among controls may indicate prolonged excretion or limited pathogenicity. In this population with a high burden of diarrhoeal and other diseases, sanitation, health education, and rotavirus-vaccination can be expected to have substantial impact on childhood morbidity.

Nocardiose postopératoire à Nocardia otitidiscaviarum : pièges et retard de diagnostic

Nocardiosis is an uncommon infection, which is exceptionally present as a postoperative event. A case of postoperative pulmonary and cerebro-meningeal infection caused by Nocardia otitidiscaviarum after a leg amputation in a diabetic patient is reported. Diagnosis has been delayed and the clinical, radiological and microbiological causes of this delay are assessed from a quality of care management point of view. Recommendations are proposed regarding physicians' role and optimized microbiological procedures for recognition of slowly growing nocardial strains.

Subtotal resection of clavicle for chronic, recurrent, multifocal osteomyelitis in children

Chronic, recurrent, multifocal osteomyelitis (CRMO) is an obscure disease of bone, occurring in children. It appears to be an inflammatory condition with no obvious microbiological cause. Current treatments of antibiotics and anti-inflammatory medication appear to have limited success. This case report looks at two separate cases of CRMO where partial resection of the affected bone—the clavicle—leads to complete resolution of symptoms and regrowth of the excised bone.

The management of acute bronchitis in children

Acute bronchitis is one of the most common infections reported in children under 5 years of age, and is a leading cause of hospitalisation. In general practice, confusion surrounds the clinical diagnosis of acute bronchitis, especially when distinguishing it from asthma. The microbiological causes are mostly known, but the contribution of each is much less clear, and they are non-specific in their clinical expression in individual cases. Viral pathogens, particularly respiratory syncytial virus and rhinoviruses are cited as the leading agents in the development of serious episodes, but other pathogens may also be important. This article covers a range of issues surrounding acute bronchitis, including epidemiology and pathogenesis, as well as the management, prevention and treatment of disease in children.

Bloodstream infections in a secondary and tertiary care hospital setting

Bloodstream infections (BSI) occurring in community and health-care settings vary with the patient group and treatment of underlying medical conditions. We studied the clinical infectious syndromes occurring in patients with positive blood cultures routinely obtained at a regional secondary and tertiary care hospital. BSI were categorized as either community-acquired (C-BSI), or health-care-associated (H-BSI) acquired either as a (i) non-inpatient (outpatient) or (ii) hospital inpatient. Clinical information was collected prospectively during the 1-year study. There were 193 C-BSI and 230 H-BSI. The large majority of C-BSI were caused by bacterial pathogens susceptible to narrow-spectrum antibiotics, particularly in children. Cefuroxime was active against 90% of C-BSI isolates and 46% of H-BSI isolates, excluding anaerobes. Of all H-BSI, the 35% occurring in outpatients had a similar source, microbiological cause and bacterial susceptibilities to the inpatients. H-BSI were infrequently due to enterococci (4%), Candida (3%) or methicillin-resistant Staphylococcus aureus (0.4%). No BSI were due to vancomycin-resistant enterococci or extended-spectrum beta-lactamase producing Enterobacteriaciae. I.v. catheters, predominantly central lines, were the source of 60% of all H-BSI, mostly in haematology-oncology or neonatal patients. Mortality at 1 month was 12% overall for both C-BSI and H-BSI, varying markedly by underlying disease and increasing age (for C-BSI). In this population, C-BSI have remained susceptible to narrow-spectrum antibiotics, whereas H-BSI due to multiresistant organisms were rare. Obtaining a history of recent medical procedures is important for community patients presenting with a BSI.

A Single-Nucleotide-Polymorphism-Based Multilocus Genotyping Assay for Subtyping Lineage I Isolates of Listeria monocytogenes

Listeria monocytogenes is a facultative intracellular pathogen responsible for food-borne disease with high mortality rates in humans and is the leading microbiological cause of food recalls. Lineage I isolates of L. monocytogenes are a particular public health concern because they are responsible for most sporadic cases of listeriosis and the vast majority of epidemic outbreaks. Rapid, reproducible, and sensitive methods for differentiating pathogens below the species level are required for effective pathogen control programs, and the CDC PulseNet Task Force has called for the development and validation of DNA sequence-based methods for subtyping food-borne pathogens. Therefore, we developed a multilocus genotyping (MLGT) assay for L. monocytogenes lineage I isolates based on nucleotide variation identified by sequencing 23,251 bp of DNA from 22 genes distributed across seven genomic regions in 65 L. monocytogenes isolates. This single-well assay of 60 allele-specific probes captured 100% of the haplotype information contained in approximately 1.5 Mb of comparative DNA sequence and was used to reproducibly type a total of 241 lineage I isolates. The MLGT assay provided high discriminatory power (Simpson's index value, 0.91), uniquely identified isolates from the eight listeriosis outbreaks examined, and differentiated serotypes 1/2b and 4b as well as epidemic clone I (ECI), ECIa, and ECII. In addition, the assay included probes for a previously characterized truncation mutation in inlA, providing for the identification of a specific virulence-attenuated subtype. These results demonstrate that MLGT represents a significant new tool for use in pathogen surveillance, outbreak detection, risk assessment, population analyses, and epidemiological investigations. DNA sequences were deposited in the GenBank database under accession numbers DQ 812146 to DQ 812517, DQ 843664 to DQ 844598, and AY 512391 to AY 512502.

The effects of low pH and palliative liming on beech litter decomposition in acid-sensitive streams

The decomposition of allochthonous leaf litter is retarded by stream acidification, but few studies have evaluated whether this effect can be offset by liming – the palliative addition of calcium carbonate either to streams or their catchments. We assessed the response of litter decomposition to pH and experimental liming in Welsh upland streams. Small-mesh (<335 μm) litter-bags containing common beech (Fagus sylvatica L.) were submerged in main river sites along the River Wye, and in replicate acid, circumneutral and experimentally limed tributaries (all n = 3) for 20 days. Beech decomposition was inhibited in acid tributaries and main river sites compared to circumneutral tributaries. Despite having only moderately increased pH relative to acid streams, limed sites had increased decomposition rates that were indistinguishable from naturally circumneutral streams. Decomposition rates increased highly significantly with pH across all 12 sites studied, and values were near identical to those in more prolonged experiments elsewhere. There were no significant variations in shredder numbers with decomposition rate, and no evidence that sites with faster decomposition had smaller shredder proportions. Although based on short-term observations and leaves from just one tree species, these results are consistent with the well-known retardation at low pH of some aspect microbial decomposition (e.g. by hyphomycete fungi). They are among the first to suggest that stream liming to combat acidification might reverse such impacts of low pH. Further data are required on the microbiological causes and ecological consequences of altered detrital processing in acid-sensitive and limed streams.

La Listeria monocytogenes, un agente patógeno transmitido por los alimentos que también sirve de indicador de higiene

In the past 25 years, Listeria monocytogenes has become increasingly important as a food-associated pathogen. Most European Union countries have an annual incidence of human listeriosis of between two and ten reported cases per million. Because of its high case fatality rate, listeriosis ranks among the most frequent causes of death due to food-borne illness. Listeria monocytogenes infections are responsible for the highest hospitalisation rates (91%) amongst known food-borne pathogens and have been linked to sporadic episodes and large outbreaks of human illness worldwide. The ability to persist in food-processing environments and multiply under refrigeration temperatures makes L. monocytogenes a significant threat to public health. Listeria monocytogenes contamination is one of the leading microbiological causes of food recalls, mainly of meat, poultry, seafood and dairy products. Prevention and control measures are based on hazard analysis and critical control point programmes throughout the food industry, and on specific recommendations for high-risk groups. Understanding how these micro-organisms adapt their cellular physiology to overcome stress is important in controlling L. monocytogenes in food environments.

Extracellular accumulation of bioactive substances; Interleukin-1β (IL-1β) and plasminogen activator inhibitor-1 (PAI-1) in stored blood units and relation to bacterial contamination

Bacterial contamination of blood and its cellular components remains an unresolved problem in transfusion medicine and is considered to be the most common microbiological cause of transfusion associated morbidity and mortality.The present work was designed to explore the levels of two bioactive compounds interleukin-1 β (IL-1 β) and plasminogen activator inhibitor-1 (PAI-1) in stored blood units and their relation to bacterial contamination of these units.This study was conducted on 112 blood units obtained from blood bank of Mansoura University Children Hospital. Sequential blood samples were obtained both immediately at donation and after 10 days for measurement of IL-1 β and PAI-1 and for bacterial culture by BACTEC 9050 system.There was statistically significant increase in both IL-1 β and PAI-1 (P = 0.0001) after 10 days of blood units storage. Bacteriological culture revealed no growth in 68% and positive growth in 32% of blood units. The commonest isolated organism was Staphylococcus aureus (15%) followed by Staphylococcus epidermedis (13%) then Yersinia sp. and Enterobacter sp. (2%) for each.From the present study we could conclude that stored blood units contain platelets and WBCs derived bioactive substances PAI-1 and IL-1 β which increase with the duration of blood storage. Furthermore, the extended duration of storage carries the danger of blood contamination by bacteria. Automated blood culture system seems to be helpful in identification of bacterial contamination of blood units. We recommend fresh blood transfusion as early as possible and the practice of Leucofiltration to avoid blood transfusion complications.

Traitement antifongique des candidoses systémiques en réanimation

Hospital-acquired infections secondary to Candida have undergone a considerable recrudescence in the last decade. They still represent a substantial mortality rate, particularly in ICU patients. Their bad prognosis is mainly due to delay in treatment because of the difficulties involved in diagnosis. Clear indications for treatment resulting from an international consensus have not yet been established. The therapeutic regimen includes Amphotericin B, 5-fluorocytosin, azoles (fluconazole, itraconazole), and recently, new antifungals, mainly voriconazole and caspofungin. The use of amphotericin B is restricted because of its renal toxicity and the difficulty involved in its administration. Fluconazole use is still limited because of the possible development of fungal resistance especially in case of severe infection or of previous exposure to the drug. Indeed, the emergence of fluconazole resistance in Candida albicans as well as the frequency of other naturally resistant Candida species, such as Candida krusei, seems to have increased considerably since the introduction of fluconazole at the beginning of the 1990s'. However, since the appearance of new standardized and reasonably reliable methods to measure resistance, this worrisome rise in resistance seems to be the result of the absence of standard definition criteria rather than a microbiological cause. Furthermore, the interaction between the yeast and the host is so complex that the microbiological resistance has a low predictive value, if at all, for clinical resistance. Fluconazole should be the first choice for all patients without a documented or highly suspected resistance. Amphotericin B should be reserved for particular indications such us intracranial infections. The treatment should be adjusted according to the clinical evolution and the results of sensitivity tests.

Recurrent Pregnancy Loss

Recurrent pregnancy loss is a profound personal tragedy to couples seeking parenthood and a formidable clinical challenge to their physicians. Although spontaneous abortion occurs in approximately 15 to 20% of clinically diagnosed pregnancies of reproductive-aged women, recurrent pregnancy loss occurs in approximately 1 to 2% of this same population.[1] Great strides have been made in characterizing the incidence and diversity of this heterogeneous disorder, and a definite cause of pregnancy loss can be established in approximately two thirds of couples after a thorough evaluation.[2] A complete evaluation will include investigations into genetic, endocrinologic, anatomic, immunologic, microbiologic, thrombophilic, and iatrogenic causes (Table [1]). The occurrence of recurrent pregnancy losses may induce significant emotional distress and in some cases intensive supportive care may be necessary. Successful outcomes will occur in more than two thirds of all couples.[3]