Culture Of Clinical Specimens Research Articles

Hematuria Due to Possible Histoplasma-Associated Urinary Bladder Pseudotumor With Negative Serologic and Urine Antigen Testing

Abstract Histoplasma capsulatum is a ubiquitous dimorphic fungus causing multiple infectious syndromes, ranging from subclinical to severe disseminated disease. We present an unusual case of hematuria due to pedunculated urinary bladder mass in an immunocompetent host. Although the gold standard for diagnosis of histoplasmosis is through demonstration of characteristic yeast forms on histopathologic examination of infected tissue, or observation of typical mycelial growth in culture of clinical specimens, investigational multiplex polymerase chain reaction of formalinized tissue was helpful in this case due to conflicting serologic testing, equivocal morphologic findings on histopathologic examination and, surprisingly, a negative urine Histoplasma antigen despite anatomically proximal location within the urinary bladder. Although antigen immunoassay and serology are commonly used proxy diagnostics in Histoplasma-associated disease, varying performance characteristics in certain disease states, such as cases of locally proliferative infection mimicking neoplastic growth similar to this report, may lead to elusive diagnosis.

Resistance pattern of isolated microorganisms from 783 clinical specimen cultures in patients admitted to Yasuj Educational Hospitals, Iran

BackgroundInfectious diseases are still one of the leading causes of morbidity and mortality in resource-limited settings. Serious infection caused mostly by gram-negative pathogens causes significant morbidity. According to the Centers for Disease Control and Prevention, antimicrobial resistance kills over 700,000 people worldwide. Antibiotic resistance is on the rise, and as a consequence, serious public health issues are arising. The present study investigated isolated clinical samples from Yasuj teaching hospitals to determine the antimicrobial resistance profile to various antibiotics.Materials and methodsMicrobial isolates regarding cultures from urine, blood, wound, abdominal tap, throat, stool, cerebrospinal fluid, endotracheal tube, sputum, skin lesion, nasal, and mouth secretion were collected from patients admitted to hospitals affiliated with Yasuj teaching hospitals. Antibiotic susceptibility profiles were determined by using the Kirby-Bauer disc diffusion method. Data were tabulated and analyzed with SPSS version 26.0.ResultsA total of 783 samples were evaluated in our study, with an average of 30.6 years and 54.5% female patients. Most of the bacterial isolates were gram-negative (64.2%). The majority of cultures were Escherichia coli (49.9%), mainly among urine samples (64.2%). The frequency distribution of norfloxacin antibiotic resistance was more common in internal medicine (66.7%), infectious (63.6%), and emergency wards (58.8%). The frequency distribution of penicillin antibiotic resistance was statistically significant in different wards. All cases of oxacillin were resistant.ConclusionOur data showed a high level of antibiotic resistance among bacterial isolates in our center. Considering widespread empirical antibiotic therapy in Iran, the rate of increasing resistance to common antibiotics prescribed for ambulatory and hospitalized patients is concerning. We recommend providing more strict guidelines and policies to control the overuse and overprescription of antimicrobials by health policy-making organizations.

Multiplex real-time PCR using SYBR Green: Unspecific intercalating dye to detect antimicrobial resistance genes of Streptococcus pneumoniae in cerebrospinal fluid.

Meningitis caused by Streptococcus pneumoniae is still a disease of great impact on Public health, which requires immediate diagnosis and treatment. However, the culture of clinical specimens is often negative and antibiotic susceptibility testing (AST) must be performed with isolated strains. Multiplex real-time polymerase chain reaction (qPCR) has high sensitivity and specificity, produces faster results to identify the pathogen, and it can also be an important tool to identify resistance antibiotic genes earlier than AST, especially in the absence of an isolated strain. This study developed a multiplex qPCR assay, using SYBR Green as a nonspecific dye, to detect antibiotic resistance genes to predict pneumococcal susceptibility/resistance in cerebrospinal fluid (CSF) samples from meningitis patients. From 2017 to 2020, CSF samples were cultured and analyzed by qPCR to detect the main three bacteria causing meningitis. Isolated and reference strains were applied in SYBR Green qPCR multiplex to detect pbp2b, ermB, and mef genes, and the results were compared with the AST. Pneumococcal-positive CSF samples (lytA-positive gene) without isolated strains were also tested to evaluate the antimicrobial susceptibility profile in the region from 2014 to 2020. From the received 873 CSF samples; 263 were cultivated, 149 were lytA-positive in the qPCR, and 25 produced viable isolated pneumococci strains, which were evaluated by AST. Melting temperature for each gene and the acceptance criteria were determined (pbp2b: 78.24-79.86; ermB: 80.88-82.56; mef: 74.85-76.34 ºC). A total of 48/51 strains presented a genetic profile in agreement with the AST results. Resistant strains to erythromycin and clindamycin were ermB-positive, and two were also mef-positive, indicating both resistance mechanisms were present. In the retrospective study of the genetic profile of resistance, 82 lytA-positive CSF samples plus 4 strains were applied in the SYBR Green qPCR multiplex: 51% of samples presented the wild genotype (pbp2b positive and ermB/mef negative); 15% were negative for all the three evaluated, indicating pneumococci resistant to penicillin; and 17% represented the multidrug-resistant pneumococci (pbp2b negative and ermB positive or pbp2b negative and ermB and mef positive). Therefore, SYBR Green qPCR multiplex proved to be a reliable tool to identify resistance genes in S. pneumoniae and would be less expensive than multiplex qPCR using specific probes. This could be easily introduced into the routine of diagnostic laboratories and provide a strong presumption of pneumococcal resistance, especially in the absence of isolated strains.

Recovery and Its Dynamics of Filamentous Fungi from Clinical Specimen Cultures: An Extensive Study.

ABSTRACTThe culture method remains vital in diagnosing fungal infections, but extensive data-based evaluation of the method, especially for filamentous fungi (molds), is minimal. The purpose of this study was to characterize mold recoveries from fungal cultures and the impact of media and incubation duration. Clinical specimens for fungal cultures were submitted primarily from the eastern and central United States, and mold isolation data were prospectively collected and analyzed. A total of 1,821 molds in 59 genera were isolated from 1,687 positive specimens, accounting for approximately 5.6% of our cohort of 30,000 fungal cultures. Within 2 weeks, nearly 90% of molds and 97.3% of Aspergillus fumigatus complex were recovered (>95% confidence interval [CI]). All Mucorales fungi were recovered within 11 days of incubation. The recovery peak time was day 3 for Mucorales fungi, day 4 for hyaline molds, day 5 for dematiaceous molds, and day 7 for Onygenales fungi. The recovery of Histoplasma capsulatum and Trichophyton species in the fourth week of incubation reveals that a 3-week incubation time is insufficient. Inhibitory mold agar was the best medium for recovering all mold types among all tested specimen types, yielding nearly 78% of mold growth overall, indicating the necessity of selective medium for fungal cultures.IMPORTANCE Fungal culture is the gold standard method of diagnosing fungal infections, but important information, such as the impact of media and incubation times on fungal recovery, is not well documented. This study addressed these gaps using extensive data-based evaluation focused on molds. We identified the best medium types and incubation times for better fungal culture practice. We analyzed 1,821 molds from 1,687 positive specimens in our cohort of approximately 30,000 fungal cultures. Mold recovery peaked between 3 and 7 days of incubation, dependent upon the type of mold. Some well-defined fungal pathogens, such as Histoplasma capsulatum and Trichophyton species, were isolated in the fourth week of incubation. Inhibitory mold agar was identified as the best medium for recovering all mold types among all tested specimen sources. As we are aware, this is the largest study of fungal culture methods and supports 4 weeks of incubation for optimal mold recovery.

Evaluation of the Autof MS1000 mass spectrometer in the identification of clinical isolates

BackgroundTo evaluate the accuracy and performance of the Autof MS1000 mass spectrometer in bacteria and yeast identification, 2342 isolates were obtained from microbial cultures of clinical specimens (e.g. blood, cerebrospinal fluid, respiratory tract samples, lumbar puncture fluid, wound samples, stool, and urine) collected in 2019 in Henan Provincial People’s Hospital. Repetitive strains from the same patient were excluded. We tested the Autof MS1000 and Bruker Biotyper mass spectrometry systems and the classical biochemical identification system VITEK 2/API 20C AUX. Inconsistencies in strain identification among the three systems were identified by 16S rDNA and gene sequencing.ResultsAt the species level, the Autof MS1000 and Bruker Biotyper systems had isolate identification accuracies of 98.9 and 98.5%, respectively. At the genus level, the Autof MS1000 and Bruker Biotyper systems were 99.7 and 99.4% accurate, respectively. The instruments did not significantly differ in identification accuracy at either taxonomic level. The frequencies of unreliable identification were 1.1% (26/2342) for the Autof MS1000 and 1.5% (34/2342) for the Bruker Biotyper. In vitro experiments demonstrated that the coincidence rate of the Autof MS1000 mass spectrometer in the identification of five types of bacteria was > 93%, the identification error rate was < 3%, and the no identification rate was 0. This indicates that the Autof MS1000 system is acceptable for identification.ConclusionsThe Autof MS1000 mass spectrometer can be utilised to identify clinical isolates. However, an upgradation of the database is recommended to correctly identify rare strains.

Continuous ambulatory peritoneal dialysis-associated Histoplasma capsulatum peritonitis: a case report and literature review

BackgroundFungal peritonitis (FP) is a rare complication of peritoneal dialysis. We herein describe the second case in Asia of Histoplasma capsulatum peritonitis associated with continuous ambulatory peritoneal dialysis (CAPD).Case presentationAn 85-year-old woman with end-stage renal disease (ESRD) who had been on CAPD for 3 years and who had a history of 3 prior episodes of peritonitis presented with intermittent abdominal pain for 2 weeks and high-grade fever for 3 days. Elevated white blood cell (WBC) count and rare small oval budding yeasts were found in her peritoneal dialysis (PD) fluid. From this fluid, a white mold colony was observed macroscopically after 7 days of incubation, and numerous large, round with rough-walled tuberculate macroconidia along with small smooth-walled microconidia were observed microscopically upon tease slide preparation, which is consistent with H. capsulatum. The peritoneal dialysis (PD) catheter was then removed, and it also grew H. capsulatum after 20 days of incubation. The patient was switched from CAPD to hemodialysis. The patient was successfully treated with intravenous amphotericin B deoxycholate (AmBD) for 2 weeks, followed by oral itraconazole for 6 months with satisfactory result. The patient remains on hemodialysis and continues to be clinically stable.ConclusionH. capsulatum peritonitis is an extremely rare condition that is associated with high morbidity and mortality. Demonstration of small yeasts upon staining of PD fluid, and isolation of slow growing mold in the culture of clinical specimen should provide important clues for diagnosis of H. capsulatum peritonitis. Prompt removal of the PD catheter and empirical treatment with amphotericin B or itraconazole is recommended until the culture results are known.

Mupirocin and Chlorhexidine Genotypic Resistance Found in Staphylococcus aureus Isolated From Young Infants Below 90 Days Old: A Genetic Basis for Eradication Failure.

To investigate the genetic characteristics associated with eradication failure of Staphylococcus aureus in infants below 90 days old. S. aureus isolated from clinical specimen cultures (blood, surgical tissue, or drainage, pus, etc.) and routine screening cultures in the neonatal intensive care unit (nasal and axillary skin swab) from patients below 90 days old were collected prospectively for 1 year, from August 2017 to July 2018. The isolates underwent typing and screening for genes associated with chlorhexidine (qacA/B), quaternary ammonium (smr), and mupirocin resistance (iles mutation, mupA, mupB), as well as Panton-Valentine leukocidin (PVL) toxin. During the study period, 40 nonduplicate isolates were included for analyses, of which 70.0% were methicillin-resistant S. aureus (MRSA). Mupirocin resistance was found in 25% of the total isolates; 17.4% of the colonizers; and 35.3% of the pathogens (P = 0.196). Chlorhexidine resistance gene was found in 3 MRSA isolates colonized in the nares of preterm infants. All isolates harbored the disinfectant quaternary ammonium compound (QAC) resistance gene. PVL toxin gene was found in 57.5%, and the presence of PVL gene among colonizers and pathogens was similar (69.6% vs. 41.2%, P = 0.072). Mupirocin, chlorhexidine, and QAC-resistant MRSAs harboring the PVL toxin gene were found in the nasal carriages of preterm infants. In this highly vulnerable patient population, one-fourth of the isolates harbored mupirocin-resistant genes, and all were resistant to QAC disinfectants. These strains are associated with persistence in both carriage and environmental reservoirs within the hospitals.

Salmonellosis Outbreak After a Large-Scale Food Event in Virginia, 2017.

The Virginia Department of Health (VDH) identified an outbreak of Salmonella serotype Javiana infections in Virginia after a chili and chowder cook-off with 11 competitors and about 2500 attendees on September 30, 2017. The objectives of this study were to assess the extent of the outbreak and identify the most likely source of exposure. To identify people with suspected Salmonella infection, VDH used press releases and social media posts to recruit event attendees to take an online survey about foods eaten at the cook-off and any gastrointestinal (GI) symptoms experienced. VDH defined a case as reported GI illness that occurred within 1 week after eating food from the cook-off. Confirmed cases required a clinical specimen culture positive for Salmonella. Probable cases reported diarrhea or related clinical symptoms. "Not ill" people did not report GI illness. Investigators calculated unadjusted relative risks of illness and performed stratified analysis to address potential confounding. Available food samples were tested for Salmonella. Environmental health specialists interviewed food handlers and inspected restaurants where 3 competitors had prepared food. Of 438 survey responses, 171 (39%) met the case definition. Of all chilies and chowders consumed, Chowder A was associated with the highest relative risk of illness (8.9; 95% CI, 5.7-13.7). A Chowder A sample tested positive for Salmonella serotype Javiana. The environmental investigation did not identify an original contamination source but did find deficiencies in maintaining safe cooking temperatures. Epidemiologic and laboratory findings indicated that Chowder A was the most likely cause of outbreak. Recommendations to prevent future outbreaks include preparation of all food on-site to ensure safe temperatures during food preparation and service.

Antimicrobial resistance pattern of Acinetobacter; a multicenter study, comparing European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Clinical and Laboratory Standards Institute (CLSI); evaluation of susceptibility testing methods for polymyxin

Introduction: Acinetobacter species in clinical isolates cause severe infections including meningitis, bloodstream infection, ventilator-associated pneumonia, and surgical site infections. Objectives: In the present study, we evaluated Acinetobacter drug resistance using both European Committee on Antimicrobial Susceptibility Testing (EUCAST) and the Clinical and Laboratory Standards Institute (CLSI) antimicrobial susceptibility test methods. Materials and Methods: Clinical specimens of 128 patients who were admitted in three referral tertiary care teaching hospitals were enrolled in 2014. Blood and other sterile fluid samples, endotracheal secretion, ulcer, urine and other clinical specimen cultures were included, and microbial resistance of Acinetobacter isolates was determined and compared with disk diffusion and E-test antimicrobial susceptibility methods, using both the EUCAST and CLSI standards. Cohen’s kappa coefficient was also reported. Results: The highest percentage of resistance (96.9%) was found for meropenem and imipenem antimicrobials, and the lowest resistance (82.8%) was found for amikacin. The highest kappa agreement coefficient was for ciprofloxacin (kappa coefficient = 0.783), and the lowest kappa was for amikacin (kappa coefficient = 0.21). Conclusion: According to the results, it is better to consider amikacin as a choice in combination with another effective antimicrobial for treatment of drug resistant Acinetobacter.

Diagnosis of severe community-acquired pneumonia caused by Acinetobacter baumannii through next-generation sequencing: a case report

BackgroundAcinetobacter baumannii is a gram-negative aerobic bacillus that is commonly causes of hospital-acquired infections. Community-acquired pneumonia caused by Acinetobacter baumannii (CAP-Ab) is rare but fatal if diagnosis and treatment are delayed. Conventional culture of clinical specimens is the main method for clinical diagnosis of A. baumannii infections which may suffer from limited positive rate and is time consuming. Timely and precise diagnosis of CAP-Ab remains challenging.Case presentationA 66-year-old man with 24 h history of acute fever and dyspnea was admitted to our hospital. He was diagnosed as severe community acquired pneumonia (CAP), septic shock, respiratory failure and acute kidney injury. Next-generation sequencing (NGS) was performed on the patient’s sputum and blood, which identified numerous A. baumannii nucleotide sequences in the sample of sputum and led to the rapid diagnosis and treatment of community acquired pneumonia caused by A. baumannii. This result was confirmed by subsequent sputum culture.ConclusionsThis case described that the successful application of the next generation sequencing assisting the speedy diagnosis of A. baumannii infection provides a new idea for the timely diagnosis of CAP-Ab and highlights that NGS is a promising tool in rapid etiological diagnosis of acute and severe infectious diseases.

Clinical Epidemiology of 7126 Melioidosis Patients in Thailand and the Implications for a National Notifiable Diseases Surveillance System.

BackgroundNational notifiable diseases surveillance system (NNDSS) data in developing countries are usually incomplete, yet the total number of fatal cases reported is commonly used in national priority-setting. Melioidosis, an infectious disease caused by Burkholderia pseudomallei, is largely underrecognized by policy-makers due to the underreporting of fatal cases via the NNDSS.MethodsCollaborating with the Epidemiology Division (ED), Ministry of Public Health (MoPH), we conducted a retrospective study to determine the incidence and mortality of melioidosis cases already identified by clinical microbiology laboratories nationwide. A case of melioidosis was defined as a patient with any clinical specimen culture positive for B. pseudomallei. Routinely available microbiology and hospital databases of secondary care and tertiary care hospitals, the national death registry, and NNDSS data were obtained for analysis.ResultsA total of 7126 culture-confirmed melioidosis patients were identified from 2012 to 2015 in 60 hospitals countrywide. The total number of cases diagnosed in Northeast, Central, South, East, North, and West Thailand were 5475, 536, 374, 364, 358, and 19 cases, respectively. The overall 30-day mortality was 39% (2805/7126). Only 126 (4%) deaths were reported to the NNDSS. Age, presentation with bacteremia and pneumonia, prevalence of diabetes, and 30-day mortality differed by geographical region (all P < .001). The ED at MoPH has agreed to include the findings of our study in the next annual report of the NNDSS.ConclusionsMelioidosis is an important cause of death in Thailand nationwide, and its clinical epidemiology may be different by region. In developing countries, NNDSS data can be supplemented by integrating information from readily available routine data sets.

Ventilator-associated pneumonia diagnosis: a prioritization exercise based on multi-criteria decision analysis.

The aim was to provide global experts ranking on priorities in diagnostic tools for VAP in clinical practice. A multiple criteria decision analysis (MCDA) was performed to identify diagnosis tools for VAP diagnosis. Priority factors were identified after literature review. An international, multidisciplinary expert panel reviewed variables and ranked diagnostic tools. Experts from ten European hospitals participated. Regarding bedside clinical practices, seven required chest X-ray use in all patients, whereas six reported the use of blood cultures and endotracheal aspirate in all patients. Invasive techniques were routinely performed in seven sites. CRP, PCT, and Gram stains were performed in all patients by 5, 2, and 8, respectively. Impact on patient outcomes, safety, and impact on the decision to start antibiotic therapy were ranked as the top three relevant concerns (7.7/10, 7/10, and 6.9/10, respectively). Chest X-ray was ranked as the most important imaging technique to diagnose VAP (score 251.7). Apart from blood cultures, endotracheal aspirate culture was identified as the main collection method for the microbiological testing (scores of 274.8 and 246.8, respectively). Mini-BAL was the preferred invasive technique with a score of 208. Top three biomarkers were CRP (score 184.3), PCT (181.3), and WBC (166.4). Gram stain (192.5) was prioritized among laboratory diagnostic techniques. Using MCDA, it is recommended to perform a combination of diagnostic techniques including images (chest X-ray), culture of clinical specimens (blood cultures and endotracheal aspirate), and biomarkers (CRP or PCT) for VAP diagnosis at the bedside. Gram stain was ranked as the preferred laboratory technique.Electronic supplementary materialThe online version of this article (10.1007/s10096-019-03720-x) contains supplementary material, which is available to authorized users.

High prevalence of multidrug resistant Enterobacteriaceae among residents of long term care facilities in Amsterdam, the Netherlands.

IntroductionThe aim of this study was to determine the rate of asymptomatic carriage and spread of multidrug-resistant micro-organisms (MDRO) and to identify risk factors for extended spectrum beta-lactamase-producing Enterobacteriaceae (ESBL-E) carriage in 12 long term care facilities (LTCFs) in Amsterdam, the Netherlands.Materials and methodsFrom November 2014 to august 2015, feces and nasal swabs from residents from LTCFs in Amsterdam, the Netherlands were collected and analyzed for presence of multidrug-resistant Gram-negative bacteria (MDRGN), including ESBL-E, carbapenemase-producing Enterobacteriaceae (CPE), colistin-resistant Enterobacteriaceae and methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE). Logistic regression analysis was performed to assess associations between variables and ESBL-carriage.ResultsIn total, 385 residents from 12 LTCFs (range 15–48 residents per LTCF) were enrolled. The prevalence of carriage of MDRGN was 18.2% (range among LTCFs 0–47%) and the prevalence of ESBL-E alone was 14.5% (range among LTCFs: 0–34%). Of 63 MDRGN positive residents, 50 (79%) were ESBL-E positive of which 43 (86%) produced CTX-M. Among 44 residents with ESBL-E positive fecal samples of whom data on contact precautions were available at the time of sampling, only 9 (20%) were already known as ESBL-E carriers. The prevalence for carriage of MRSA was 0.8% (range per LTCF: 0–7%) and VRE 0%. One CPE colonized resident was found. All fecal samples tested negative for presence of plasmid mediated resistance for colistin (MCR-1). Typing of isolates by Amplified Fragment Length Polymorphism (AFLP) showed five MDRGN clusters, of which one was found in multiple LTCFs and four were found in single LTCFs, suggesting transmission within and between LTCFs. In multivariate analysis only the presence of MDRO in the preceding year remained a risk factor for ESBL-E carriage.ConclusionsThe ESBL-carriage rate of residents in LTCFs is nearly two times higher than in the general population but varies considerably among LTCFs in Amsterdam, whereas carriage of MRSA and VRE is low. The majority (80%) of ESBL-E positive residents had not been detected by routine culture of clinical specimens at time of sampling. Current infection control practices in LTCFs in Amsterdam do not prevent transmission. Both improvement of basic hygiene, and funding for laboratory screening, should allow LTCFs in Amsterdam to develop standards of care to prevent transmission of ESBL-E.

Consumo de antimicrobianos e o impacto na resistência bacteriana em um hospital público do estado do Pará, Brasil, de 2012 a 2016

OBJECTIVE: To evaluate the profile of antibiotic consumption and its impact on bacterial resistance in a university hospital in Para State, Northern Brazil, from 2012 to 2016. MATERIALS AND METHODS: A total of 279 blood cultures from adult patients, both sexes, admitted to wards and Intensive Care Unit (ICU), were selected for further analysis of clinical specimen culture results. RESULTS: Primary bloodstream infections accounted for 60.2% of the total. Gram-negative bacilli (GNB) were the most frequent microorganisms (51.3%), of which the fermenters were resistant to ceftazidime (83.0%) and cefepime (76.1%). Staphylococcus aureus resistance to clindamycin and oxacillin reached 57.4% and 48.9%, respectively. There was a statistically significant reduction in overall consumption of piperacillin + tazobactam and vancomycin. In ICU, there was reduction in ceftriaxone, oxacillin, piperacillin + tazobactam and vancomycin consumption and increase in amikacin and meropenem consumption (all statistically significant). Fermentative GNB and S. aureus showed a positive and nonlinear correlation between the increase of resistance rates and cefepime and oxacillin consumption, respectively. CONCLUSION: Antimicrobial consumption and its impact on bacterial resistance varied over the study period, highlighting the positive and nonlinear correlation between increased cefepime and oxacillin consumption and the recrudescence of fermenting BGN strains and resistant S. aureus strains, respectively.

Culture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona.

Between 2000 and 2017, a total of 236 Legionella species isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, all Legionellapneumophila isolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging to L. pneumophila serogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113 L. pneumophila clinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens for Legionella spp. reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches.IMPORTANCE Culture of clinical specimens from patients with Legionnaires' disease is rarely performed, restricting our understanding of the diversity and ecology of Legionella Culture of Legionella from patient specimens in Arizona revealed a greater proportion of non-serogroup 1 Legionellapneumophila isolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.

New technologies in microbiology and their potential impact on paediatric practice

Reliable microbiological diagnosis of infections for almost 50–60 years has been limited to culture of clinical specimens for bacteria, fungi, virus, microscopy for parasites and on rare occasion cultivation of...

Canadian Public Health Laboratory Network position statement: Non-culture based diagnostics for gastroenteritis and implications for public health investigations.

As clinical laboratories transition to using culture-independent detection test (CIDT) panels for cases of acute gastroenteritis, culture of clinical specimens is becoming less common. The reduction in bacterial cultures available for public health activities is expected to hinder surveillance and outbreak response by public health laboratories at the local, provincial, national and international levels. These recommendations are intended to serve as guidelines for the implementation of CIDT panels in frontline laboratories in Canada. The United States of America has already seen a significant reduction in culture of stool specimens despite the Association of Public Health Laboratories recommendation to perform reflex culture on positive CIDT specimens. Priority public health organisms addressed in these Canadian guidelines include Shiga toxin-producing Escherichia coli, Shigella and Salmonella and, under regional circumstances, other organisms such as Campylobacter jejuni/coli and Yersinia enterocolitica. These recommendations suggest active engagement between primary diagnostic laboratories and provincial public health laboratories to determine the workflow and protocols for reflex or parallel culture. Consequently, notifiable disease definitions will also need modification, with consultation of all stakeholders. Stakeholders need to work together to enhance recovery of bacterial isolates with best practices used for stool transport and storage.

Clinical and microbiological characteristics of Pantoea agglomerans infection in children.

Pantoea agglomerans is an environmental Gram-negative bacterium that rarely is responsible for the infections in humans but it is often a causative factor of a number of occupational diseases. This study evaluated the clinical and microbiological characteristics and pathogenicity of P. agglomerans in children. We retrospectively reviewed microbiological test results for all children (1 month old to 18 years old) who were admitted to our pediatric hospital between January 2000 to June 2015 and had positive clinical specimen cultures for P. agglomerans. Isolates were identified using conventional tests and the BBL Crystal E/NF ID or MALDI-TOF MS systems. Antibiotic susceptibilities were evaluated using the Kirby-Bauer disc diffusion method. We identified fifteen positive cultures from 14 patients with confirmed infections. The positive specimens included pus, urine, tracheal aspirate, blood, and central venous line samples that yielded P. agglomerans. The median patient age was 8.8 years (range: 1.5 months to 16.5 years), and all patients had underlying comorbidities. Five patients had medical devices, and two devices were removed. The most common P. agglomerans infections involved wound infections (35.7%), pneumonia (21.4%), and urinary tract infections (21.4%). Three patients had concomitant infections (Enterococcus faecium, Pseudomonas aeruginosa, and Aspergillus fumigatus). Five patients had anemia. Three patients (21.4%) died, and all three had carbapenem-resistant P. agglomerans that was detected after the first week of hospitalization; two cases involved pneumonia, which was ineffectively treated. P. agglomerans infections may be life-threatening, especially in young patients with pneumonia. Hospital-acquired P. agglomerans may have different pathogenicity and clinical features, compared to community-acquired P. agglomerans, although further studies are needed to understand the drug-resistance patterns in this bacterium.

Laboratory Diagnostics for Histoplasmosis.

The diagnosis of histoplasmosis is based on a multifaceted approach that includes clinical, radiographic, and laboratory evidence of disease. The gold standards for laboratory diagnosis include demonstration of yeast on pathological examination of tissue and isolation of the mold in the culture of clinical specimens; however, antigen detection has provided a rapid, noninvasive, and highly sensitive method for diagnosis and is a useful marker of treatment response. Molecular methods with improved sensitivity on clinical specimens are being developed but are not yet ready for widespread clinical use. This review synthesizes currently available laboratory diagnostics for histoplasmosis, with an emphasis on complexities of testing and performance in various clinical contexts.

Clinical characteristics of Q fever and etiology of community-acquired pneumonia in a tropical region of southern Taiwan: a prospective observational study.

BackgroundThe clinical characteristics of Q fever are poorly identified in the tropics. Fever with pneumonia or hepatitis are the dominant presentations of acute Q fever, which exhibits geographic variability. In southern Taiwan, which is located in a tropical region, the role of Q fever in community-acquired pneumonia (CAP) has never been investigated.Methodology/Principal FindingsDuring the study period, May 2012 to April 2013, 166 cases of adult CAP and 15 cases of acute Q fever were prospectively investigated. Cultures of clinical specimens, urine antigen tests for Streptococcus pneumoniae and Legionella pneumophila, and paired serologic assessments for Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Q fever (Coxiella burnetii) were used for identifying pathogens associated with CAP. From April 2004 to April 2013 (the pre-study period), 122 cases of acute Q fever were also included retrospectively for analysis. The geographic distribution of Q fever and CAP cases was similar. Q fever cases were identified in warmer seasons and younger ages than CAP. Based on multivariate analysis, male gender, chills, thrombocytopenia, and elevated liver enzymes were independent characteristics associated with Q fever. In patients with Q fever, 95% and 13.5% of cases presented with hepatitis and pneumonia, respectively. Twelve (7.2%) cases of CAP were seropositive for C. burnetii antibodies, but none of them had acute Q fever. Among CAP cases, 22.9% had a CURB-65 score ≧2, and 45.8% had identifiable pathogens. Haemophilus parainfluenzae (14.5%), S. pneumoniae (6.6%), Pseudomonas aeruginosa (4.8%), and Klebsiella pneumoniae (3.0%) were the most common pathogens identified by cultures or urine antigen tests. Moreover, M. pneumoniae, C. pneumoniae, and co-infection with 2 pathogens accounted for 9.0%, 7.8%, and 1.8%, respectively.ConclusionsIn southern Taiwan, Q fever is an endemic disease with hepatitis as the major presentation and is not a common etiology of CAP.