scholarly journals Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Bacterial Gastroenteritis

2015 ◽  
Vol 28 (1) ◽  
pp. 3-31 ◽  
Author(s):  
Romney M. Humphries ◽  
Andrea J. Linscott
Keyword(s):  
Clinical Microbiology ◽  
Clinical Manifestations ◽  
Laboratory Diagnosis ◽  
Invasive Disease ◽  
Stool Culture ◽  
Content Type ◽  
Specimen Collection ◽  
Primary Means ◽  
Bacterial Gastroenteritis ◽  
Stool Cultures

SUMMARY Bacterial gastroenteritis is a disease that is pervasive in both the developing and developed worlds. While for the most part bacterial gastroenteritis is self-limiting, identification of an etiological agent by bacterial stool culture is required for the management of patients with severe or prolonged diarrhea, symptoms consistent with invasive disease, or a history that may predict a complicated course of disease. Importantly, characterization of bacterial enteropathogens from stool cultures in clinical laboratories is one of the primary means by which public health officials identify and track outbreaks of bacterial gastroenteritis. This article provides guidance for clinical microbiology laboratories that perform stool cultures. The general characteristics, epidemiology, and clinical manifestations of key bacterial enteropathogens are summarized. Information regarding optimal specimen collection, transport, and processing and current diagnostic tests and testing algorithms is provided. This article is an update of Cumitech 12A (P. H. Gilligan, J. M. Janda, M. A. Karmali, and J. M. Miller, Cumitech 12A, Laboratory diagnosis of bacterial diarrhea, 1992).

scholarly journals Whole-Genome Characterization of Bacillus cereus Associated with Specific Disease Manifestations

2017 ◽  
Vol 86 (2) ◽  
Author(s):  
T. Chang ◽  
J. W. Rosch ◽  
Z. Gu ◽  
H. Hakim ◽  
C. Hewitt ◽  
...  
Keyword(s):  
Bacillus Cereus ◽  
Clinical Manifestations ◽  
Invasive Disease ◽  
Whole Genome ◽  
Skin Infections ◽  
Virulence Determinants ◽  
Bacterial Strains ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Superficial Skin

ABSTRACTBacillus cereusremains an important cause of infections, particularly in immunocompromised hosts. While typically associated with enteric infections, disease manifestations can be quite diverse and include skin infections, bacteremia, pneumonia, and meningitis. Whether there are any genetic correlates of bacterial strains with particular clinical manifestations remains unknown. To address this gap in understanding, we undertook whole-genome analysis ofB. cereusstrains isolated from patients with a range of disease manifestations, including noninvasive colonizing disease, superficial skin infections, and invasive bacteremia. Interestingly, strains involved in skin infection tended to form a distinct genetic cluster compared to isolates associated with invasive disease. Other disease manifestations, despite not being exclusively clustered, nonetheless had unique genetic features. The unique features associated with the specific types of infections ranged from traditional virulence determinants to metabolic pathways and gene regulators. These data represent the largest genetic analysis to date of pathogenicB. cereusisolates with associated clinical parameters.

scholarly journals Complete Genome Sequences of Eight Methicillin-Resistant Staphylococcus aureus Strains Isolated from Patients in Japan

2019 ◽  
Vol 8 (47) ◽  
Author(s):  
Miyako Hikichi ◽  
Miki Nagao ◽  
Kazunori Murase ◽  
Chihiro Aikawa ◽  
Takashi Nozawa ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Soft Tissue ◽  
Complete Genome ◽  
Methicillin Resistant Staphylococcus Aureus ◽  
Clinical Manifestations ◽  
Invasive Disease ◽  
Genome Sequences ◽  
Methicillin Resistant ◽  
Content Type ◽  
Mrsa Strains

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing nosocomial infections, and the clinical manifestations of MRSA range from asymptomatic colonization of the nasal mucosa to soft tissue infection to fulminant invasive disease. Here, we report the complete genome sequences of eight MRSA strains isolated from patients in Japan.

scholarly journals Genomic Serotyping, Clinical Manifestations, and Antimicrobial Resistance of Nontyphoidal Salmonella Gastroenteritis in Hospitalized Children in Ho Chi Minh City, Vietnam

2020 ◽  
Vol 58 (12) ◽  
Author(s):  
Vu Thuy Duong ◽  
Hao Chung The ◽  
Tran Do Hoang Nhu ◽  
Ha Thanh Tuyen ◽  
James I. Campbell ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Genome Sequencing ◽  
Clinical Manifestations ◽  
Bacterial Pathogen ◽  
Multidrug Resistant ◽  
Stool Culture ◽  
Ho Chi Minh City ◽  
Content Type ◽  
Serovar Typhimurium ◽  
Tertiary Hospitals

ABSTRACT Nontyphoidal Salmonella (NTS) are among the most common etiological agents of diarrheal diseases worldwide and have become the most commonly detected bacterial pathogen in children hospitalized with diarrhea in Vietnam. Aiming to better understand the epidemiology, serovar distribution, antimicrobial resistance (AMR), and clinical manifestation of NTS gastroenteritis in Vietnam, we conducted a clinical genomics investigation of NTS isolated from diarrheal children admitted to one of three tertiary hospitals in Ho Chi Minh City. Between May 2014 and April 2016, 3,166 children hospitalized with dysentery were recruited into the study; 478 (∼15%) children were found to be infected with NTS by stool culture. Molecular serotyping of the 450 generated genomes identified a diverse collection of serogroups (B, C1, C2 to C3, D1, E1, G, I, K, N, O, and Q); however, Salmonella enterica serovar Typhimurium was the most predominant serovar, accounting for 41.8% (188/450) of NTS isolates. We observed a high prevalence of AMR to first-line treatments recommended by WHO, and more than half (53.8%; 242/450) of NTS isolates were multidrug resistant (MDR; resistant to ≥3 antimicrobial classes). AMR gene detection positively correlated with phenotypic AMR testing, and resistance to empirical antimicrobials was associated with a significantly longer hospitalization (0.91 days; P = 0.04). Our work shows that genome sequencing is a powerful epidemiological tool to characterize the serovar diversity and AMR profiles in NTS. We propose a revaluation of empirical antimicrobials for dysenteric diarrhea and endorse the use of whole-genome sequencing for sustained surveillance of NTS internationally.

scholarly journals Stool Culture for Diagnosis of Pulmonary Tuberculosis in Children

2017 ◽  
Vol 55 (12) ◽  
pp. 3355-3365 ◽  
Author(s):  
Elisabetta Walters ◽  
Anne-Marie Demers ◽  
Marieke M. van der Zalm ◽  
Andrew Whitelaw ◽  
Megan Palmer ◽  
...  
Keyword(s):  
Drug Susceptibility ◽  
Stool Culture ◽  
Smear Microscopy ◽  
Diagnostic Study ◽  
Content Type ◽  
Molecular Tests ◽  
Specimen Collection ◽  
Increased Sensitivity ◽  
Low Sensitivity ◽  
Respiratory Specimens

ABSTRACTBacteriological confirmation ofMycobacterium tuberculosisis achieved in the minority of young children with tuberculosis (TB), since specimen collection is resource intensive and respiratory secretions are mostly paucibacillary, leading to limited sensitivity of available diagnostic tests. Although molecular tests are increasingly available globally, mycobacterial culture remains the gold standard for diagnosis and determination of drug susceptibility and is more sensitive than molecular methods for paucibacillary TB. We evaluated stool culture as an alternative to respiratory specimens for the diagnosis of suspected intrathoracic TB in a subgroup of 188 children (median age, 14.4 months; 15.4% HIV infected) enrolled in a TB diagnostic study at two local hospitals in Cape Town, South Africa. One stool culture was compared to overall bacteriological confirmation by stool Xpert and by Xpert and culture of multiple respiratory specimens. After decontamination/digestion with NALC (N-acetyl-l-cysteine)-NaOH (1.25%), concentrated fluorescent smear microscopy, Xpert MTB/RIF, and liquid culture were completed for all specimens. Culture contamination of stool specimens was high at 41.5%. Seven of 90 (7.8%) children initiating TB treatment were stool culture positive forM. tuberculosis. Excluding contaminated cultures, the sensitivity of stool culture versus confirmed TB was 6/25 (24.0%; 95% confidence interval [CI] = 9.4 to 45.1%). In addition, stool culture detected TB in 1/93 (1.1%) children with “unconfirmed TB.” Testing the same stool by Xpert increased sensitivity to 33.3% (95% CI = 18.0 to 51.8%). In conclusion, stool culture had low sensitivity forM. tuberculosisdetection in children with intrathoracic TB. Reducing culture contamination through improved laboratory protocols may enable more reliable estimates of its diagnostic utility.

scholarly journals Role of Serum Mycoplasma pneumoniae IgA, IgM, and IgG in the Diagnosis of Mycoplasma pneumoniae-Related Pneumonia in School-Age Children and Adolescents

2016 ◽  
Vol 24 (1) ◽  
Author(s):  
Wei-Ju Lee ◽  
Eng-Yen Huang ◽  
Chih-Min Tsai ◽  
Kuang-Che Kuo ◽  
Yi-Chuan Huang ◽  
...  
Keyword(s):  
Children And Adolescents ◽  
Mycoplasma Pneumoniae ◽  
Immunoglobulin A ◽  
Fold Increase ◽  
Laboratory Diagnosis ◽  
Diagnostic Value ◽  
Immunoglobulin M ◽  
School Age Children ◽  
School Age ◽  
Content Type

ABSTRACT Mycoplasma pneumoniae is an important causative pathogen of community-acquired pneumonia in children. Rapid and reliable laboratory diagnosis of M. pneumoniae infection is important so that appropriate antibiotic treatment can be initiated to reduce the misuse of drugs and resistance rates. Anti-M. pneumoniae immunoglobulin M (IgM) is an indicator of recent primary infection but can persist for several months after initial infection. It has been suggested that anti-M. pneumoniae immunoglobulin A (IgA) can be a reliable indicator for recent M. pneumoniae infection in adults. We investigated the clinical diagnostic value of M. pneumoniae IgA in school-age children and adolescents with M. pneumoniae-related pneumonia. Eighty children with pneumonia and seropositive for M. pneumoniae IgM or with a 4-fold increase of anti-M. pneumoniae immunoglobulin G (IgG) were enrolled from May 2015 to March 2016. The titers of M. pneumoniae IgA, IgM, and IgG, the clinical features, and laboratory examinations of blood, C-reactive protein, and liver enzymes were analyzed. The initial positivity rates for M. pneumoniae IgM and IgA upon admission to the hospital were 63.6 and 33.8%, respectively. One week after admission, the cumulative positivity rates for M. pneumoniae IgM and IgA increased to 97.5 and 56.3%, respectively. Detection of M. pneumoniae IgM was more sensitive than detection of M. pneumoniae IgA for the diagnosis of M. pneumoniae-related pneumonia in school-age children and adolescents; however, paired sera are necessary for a more accurate diagnosis.

scholarly journals Control of Mucosal Candidiasis in the Zebrafish Swim Bladder Depends on Neutrophils That Block Filament Invasion and Drive Extracellular-Trap Production

2017 ◽  
Vol 85 (9) ◽  
Author(s):  
Remi L. Gratacap ◽  
Allison K. Scherer ◽  
Brittany G. Seman ◽  
Robert T. Wheeler
Keyword(s):  
Invasive Disease ◽  
Extracellular Dna ◽  
Epithelial Barrier ◽  
Infection Model ◽  
Swim Bladder ◽  
Spatiotemporal Resolution ◽  
Zebrafish Model ◽  
Content Type ◽  
Mucosal Candidiasis ◽  
Disease Pressure

ABSTRACT Candida albicans is a ubiquitous mucosal commensal that is normally prevented from causing acute or chronic invasive disease. Neutrophils contribute to protection in oral infection but exacerbate vulvovaginal candidiasis. To dissect the role of neutrophils during mucosal candidiasis, we took advantage of a new, transparent zebrafish swim bladder infection model. Intravital microscopic tracking of individual animals revealed that the blocking of neutrophil recruitment leads to rapid mortality in this model through faster disease progression. Conversely, artificial recruitment of neutrophils during early infection reduces disease pressure. Noninvasive longitudinal tracking showed that mortality is a consequence of C. albicans breaching the epithelial barrier and invading surrounding tissues. Accordingly, we found that a hyperfilamentous C. albicans strain breaches the epithelial barrier more frequently and causes mortality in immunocompetent zebrafish. A lack of neutrophils at the infection site is associated with less fungus-associated extracellular DNA and less damage to fungal filaments, suggesting that neutrophil extracellular traps help to protect the epithelial barrier from C. albicans breach. We propose a homeostatic model where C. albicans disease pressure is balanced by neutrophil-mediated damage of fungi, maintaining this organism as a commensal while minimizing the risk of damage to host tissue. The unequaled ability to dissect infection dynamics at a high spatiotemporal resolution makes this zebrafish model a unique tool for understanding mucosal host-pathogen interactions.

scholarly journals Masking of β(1-3)-Glucan in the Cell Wall of Candida albicans from Detection by Innate Immune Cells Depends on Phosphatidylserine

2014 ◽  
Vol 82 (10) ◽  
pp. 4405-4413 ◽  
Author(s):  
Sarah E. Davis ◽  
Alex Hopke ◽  
Steven C. Minkin ◽  
Anthony E. Montedonico ◽  
Robert T. Wheeler ◽  
...  
Keyword(s):  
Cell Wall ◽  
Candida Albicans ◽  
De Novo ◽  
Invasive Disease ◽  
Innate Immune ◽  
Dependent Manner ◽  
Content Type ◽  
Immune Effector ◽  
Host Interactions ◽  
Innate Immune Effector

ABSTRACTThe virulence ofCandida albicansin a mouse model of invasive candidiasis is dependent on the phospholipids phosphatidylserine (PS) and phosphatidylethanolamine (PE). Disruption of the PS synthase geneCHO1(i.e.,cho1Δ/Δ) eliminates PS and blocks thede novopathway for PE biosynthesis. In addition, thecho1Δ/Δ mutant's ability to cause invasive disease is severely compromised. Thecho1Δ/Δ mutant also exhibits cell wall defects, and in this study, it was determined that loss of PS results in decreased masking of cell wall β(1-3)-glucan from the immune system. In wild-typeC. albicans, the outer mannan layer of the wall masks the inner layer of β(1-3)-glucan from exposure and detection by innate immune effector molecules like the C-type signaling lectin Dectin-1, which is found on macrophages, neutrophils, and dendritic cells. Thecho1Δ/Δ mutant exhibits increases in exposure of β(1-3)-glucan, which leads to greater binding by Dectin-1 in both yeast and hyphal forms. The unmasking of β(1-3)-glucan also results in increased elicitation of TNF-α from macrophages in a Dectin-1-dependent manner. The role of phospholipids in fungal pathogenesis is an emerging field, and this is the first study showing that loss of PS inC. albicansresults in decreased masking of β(1-3)-glucan, which may contribute to our understanding of fungus-host interactions.

The Diagnosis and Clinical Manifestations of Activated Protein C Resistance: A Case Report and Review of the Literature

1996 ◽  
Vol 1 (4) ◽  
pp. 275-280 ◽  
Author(s):  
Howard Daniel Hoerl ◽  
Aldo Tabares ◽  
Kandice Kottke-Marchant
Keyword(s):  
Case Report ◽  
Protein C ◽  
Activated Protein C ◽  
Clinical Manifestations ◽  
Factor V Leiden ◽  
Laboratory Diagnosis ◽  
Factor V ◽  
Review Of The Literature ◽  
Activated Protein C Resistance ◽  
Genetic Anomaly

Activated protein C resistance (APCR) is a recently discovered, medically important cause of venous thrombosis. More than 95% of cases are due to factor V Leiden (FVL), a mutated form of factor V that is resistant to degradation by activated protein C. The prevalence of this disorder, which is inherited in an autosomal dominant fashion, is approximately 5% among asymptomatic people of European heritage. In addition, 20 to 60% of patient cohorts with previous thrombosis demonstrate APCR, making it the most common known genetic cause of abnormal thrombophilia. Current laboratory techniques available for diagnosis include functional assays, such as the APC ratio, as well as DNA-based tests that detect the specific genetic anomaly responsible for FVL. A case report is presented, along with a review of the literature highlighting epidemiology, pathogenesis, clinical features and methods for laboratory diagnosis.

scholarly journals Complete Genome Sequence of Serotype III Streptococcus agalactiae Sequence Type 17 Strain 874391

2017 ◽  
Vol 5 (42) ◽  
Author(s):  
Matthew J. Sullivan ◽  
Brian M. Forde ◽  
Darren W. Prince ◽  
Deepak S. Ipe ◽  
Nouri L. Ben Zakour ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Streptococcus Agalactiae ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Historical Context ◽  
Invasive Disease ◽  
Sequence Type ◽  
Content Type ◽  
Disproportionate Number

ABSTRACT Here we report the complete genome sequence of Streptococcus agalactiae strain 874391. This serotype III isolate is a member of the hypervirulent sequence type 17 (ST-17) lineage that causes a disproportionate number of cases of invasive disease in humans and mammals. A brief historical context of the strain is discussed.

scholarly journals Evaluation of a Turbidimetric β-D-Glucan Test for Detection of Pneumocystis jirovecii Pneumonia

2018 ◽  
Vol 56 (7) ◽  
pp. e00286-18 ◽  
Author(s):  
Karl Dichtl ◽  
Ulrich Seybold ◽  
Johannes Wagener
Keyword(s):  
Sensitivity And Specificity ◽  
Test Performance ◽  
Laboratory Diagnosis ◽  
Turnover Time ◽  
Pneumocystis Jirovecii ◽  
Pneumocystis Jirovecii Pneumonia ◽  
Content Type ◽  
Increased Risk ◽  
Turbidimetric Assay ◽  
Respiratory Specimens

ABSTRACT Currently, diagnosis of Pneumocystis jirovecii pneumonia (PJP) relies on analysis of lower respiratory specimens, either by microscopy or quantitative real-time PCR (qPCR). Thus, bronchoscopy is required, which is associated with increased risk of respiratory failure. We assessed the value of noninvasive serologic β-d-glucan (BDG) testing for laboratory diagnosis of PJP using a newly available turbidimetric assay. We identified 73 cases of PJP with positive qPCR results from lower respiratory specimens for Pneumocystis and serology samples dating from 1 week before to 4 weeks after qPCR. In addition, 25 sera from controls with suspected PJP but specimens negative for Pneumocystis by qPCR were identified. Sera were tested with a turbidimetric BDG assay (Fujifilm Wako Chemicals Europe GmbH, Neuss, Germany), using an 11-pg/ml cutoff. Sensitivity and specificity were calculated based on qPCR test results as a reference. The turbidimetric BDG assay identified 63/73 patients with positive or slightly positive qPCR tests for an overall sensitivity of 86%; after exclusion of cases with only slightly positive qPCR results, sensitivity was 91%. No correlation between serum BDG levels and respiratory specimen DNA levels was found. Serologic BDG testing was negative in 25/25 controls with negative qPCR for a specificity of 100% using the predefined cutoff. In 22/25 samples (88%), no BDG was detected. Serologic BDG testing using the turbidimetric assay showed high sensitivity and specificity compared to qPCR of lower respiratory specimens for the diagnosis of PJP. Both turnover time and test performance will allow clinicians to delay or in some cases forego bronchoscopy.

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