Development of real-time PCR assays for detection of the Streptococcus milleri group from cystic fibrosis clinical specimens by targeting the cpn60 and 16S rRNA genes

Streptococcus intermedius: an underestimated pathogen in brain infection?

Streptococcus intermedius is an oral commensal organism belonging to the Streptococcus anginosus group (SAG). S. intermedius causes periodontitis as well as invasive, pyogenic infection of the central nervous system, pleural space or liver. Compared with other SAG organisms, S. intermedius has a higher mortality as well as a predilection for intracranial infection, suggesting it is likely to possess virulence factors that mediate specific interactions with the host resulting in bacteria reaching the brain. The mechanisms involved are not well described. Intracranial suppuration (ICS) due to S. intermedius infection can manifest as an abscess within the brain parenchyma, or a collection of pus (empyema) in the sub- or extra-dural space. These infections necessitate neurosurgery and prolonged antibiotic treatment and are associated with a considerable burden of morbidity and mortality. The incidence of ICS is increasing in several settings, with SAG species accounting for an increasing proportion of cases. There is a paucity of published literature regarding S. intermedius pathogenesis as well as few published genomes, hampering molecular epidemiological research. This perspective evaluates what is known about the clinical features and pathogenesis of ICS due to S. intermedius and explores hypothetical explanations why the incidence of these infections may be increasing.

Uncommon Streptococcus Constellatus Meningitis Leading to Pulmonary Abscess and Brainstem Infarct in an Immunocompetent Patient

BACKGROUND Except for neonates, streptococci other than Streptococcus pneumoniae are a rare cause of acute bacterial meningitis. Streptococcus constellatus is a member of the Streptococcus anginosus group of gram-positive streptococci. It is a commensal microbe of the mucosae of the oral cavity, gastrointestinal tract, and urogenital tract. Rarely, it becomes pathogenic and causes contiguous or distant infections after mucosal damage. This report describes a 19-year-old immunocompetent man who developed bacterial meningitis, lung abscess, and brainstem infarct secondary to Streptococcus constellatus. CASE REPORT A 19-year-old immunocompetent man presented to the Emergency Department with a 4-week history of headache and neck pain. He was febrile on arrival. Physical examination revealed ataxia, upper-limb discoordination, and a positive Brudzinski sign. Cerebrospinal fluid and blood cultures were positive for Streptococcus constellatus, identified by matrix-assisted laser desorption ionization - time of flight mass spectrometry. Computed tomography of the chest demonstrated a lung abscess measuring 7×3.5×3 cm. A magnetic resonance imaging scan of the head revealed a 1.8×0.7 cm acute infarct in the right pons. The patient was treated initially with intravenous ceftriaxone and vancomycin before culture and sensitivity results, in addition to intravenous dexamethasone. After culture and sensitivities resulted, antibiotics were transitioned to a 4-week course of intravenous penicillin. The patient survived with no neurological consequences upon discharge. CONCLUSIONS Streptococcus constellatus should be suspected as an etiological agent for bacterial meningitis and other rare complications such as brainstem infarction and lung abscess, even in immunocompetent patients.

Proton pump inhibitors alter gut microbiota by promoting oral microbiota translocation: a prospective interventional study

BACKGROUND

The mechanism by which proton pump inhibitors (PPIs) alter gut microbiota remains to be elucidated. We aimed to learn whether PPI induced gut microbiota alterations by promoting oral microbial translocation.

METHODS

Healthy adult volunteers were randomly assigned: PP group (n=8, 40 mg esomeprazole daily for seven days) and PM group (n=8, 40 mg esomeprazole along with chlorhexidine mouthwash after each meal for seven days). Fecal and saliva samples were analysed using 16S ribosomal RNA sequencing. Mouse models were introduced to confirm the findings in vivo, while the effect of pH on oral bacteria proliferation activity was investigated in vitro.

RESULTS

Taxon-based analysis indicated that PPI administration increased Streptococcus abundance in gut microbiota (P<0.001), and the increased species of Streptococcus were found to be from the oral site or oral/nasal sites, in which Streptococcus anginosus was identified as the significantly changed species (P<0.004). Microbial source tracker revealed that PPI significantly increased the contribution of oral bacteria to gut microbiota (P=0.026), and no significant difference was found in PM group (P=0.467). Compared to the baseline, there was a 42-fold increase in gut abundance of Streptococcus anginosus in PP group (P=0.002), and the times decreased to 16-fold in PM group (P=0.029). Mouse models showed that combination of PPI and Streptococcus anginosus significantly increased the gut abundance of Streptococcus anginosus compared with using PPI or Streptococcus anginosus only. Furthermore, Streptococcus anginosus cannot survive in vitro at a pH lower than 5.

CONCLUSIONS

PPIs altered gut microbiota by promoting oral-originated Streptococcus translocation into gut.

The Clinical View on Streptococcus anginosus Group – Opportunistic Pathogens Coming Out of Hiding

Three distinct streptococcal species: Streptococcus anginosus, Streptococcus intermedius, and Streptococcus constellatus, belonging to the Streptococcus anginosus group (SAG), also known as Streptococcus milleri group, have been attracting clinicians and microbiologists, not only as oral commensals but also as opportunistic pathogens. For years they have been simply classified as so called viridans streptococci, and distinct species were not associated with particular clinical manifestations. Therefore, description of SAG members are clearly underrepresented in the literature, compared to other medically relevant streptococci. However, the increasing number of reports of life-threatening infections caused by SAG indicates their emerging pathogenicity. The improved clinical data generated with the application of modern molecular diagnostic techniques allow for precise identification of individual species belonging to SAG. This review summarizes clinical reports on SAG infections and systematizes data on the occurrence of individual species at the site of infection. We also discuss the issue of proper microbiological diagnostics, which is crucial for further clinical treatment.

Facial Palsy as Initial Symptom in Glycine Receptor Antibody Positive Progressive Encephalomyelitis With Rigidity and Myoclonus: A Case Report

Progressive encephalomyelitis with rigidity and myoclonus (PERM) is a rare and disabling syndrome characterized by painful spasms, myoclonic jerks, hyperekplexia, brainstem signs, and dysautonomia, which is considered to be a severe form of stiff person spectrum disorder (SPSD) and is mostly associated with glycine receptor antibodies. The PERM has an acute or subacute course, with complex and varied initial symptoms mainly manifest as stiffness and pain. The authors present the case of a male patient admitted for intractable stiffness and paroxysmal myoclonus of the lower extremities preceded by a 5-day history of facial weakness. After admission, his symptoms deteriorated rapidly. He developed progressive generalized hypertonia and painful spasms, which quickly spread to the upper extremities, and he suffered frequent paroxysmal myoclonus. Serum and cerebrospinal fluid (CSF) were tested by a cell-based assay, and both were positive for glycine receptor antibodies (GlyR-Abs). The patient developed complications, such as crushed teeth, lumbar vertebral compression fractures, and psoas major muscle abscess, during rapid disease progression, although he responded well after being treated with intravenous methylprednisolone and immunoglobulin. This report of PERM, initiated as facial palsy followed by acute progression, helps to expand the clinical spectrum of this rare autoimmune disorder and raise awareness of the prevention of complications.

Empyema caused by Streptococcus constellatus: a case report and literature review

Background

Streptococcus constellatus is a member of Streptococcus anginosus group (SAG) that tends to cause pyogenic infections in various sites. However, Streptococcus constellatus is easily ignored by routine clinical laboratory tests for its prolonged anaerobic culture environment.

Case presentation

A 71-year-old man was admitted to our hospital due to productive cough, fever, chest pain and shortness of breath for 3 weeks. Chest computed tomography showed patchy opacities and right-sided pleural effusion, so a chest tube was inserted and purulent and hemorrhagic fluid was aspirated. The routine etiological examinations of the pleural effusion were all negative, and next-generation sequencing (NGS) detected Streptococcus constellatus. Intravenous piperacillin-tazobactam 4.5 g every 8 h was used accordingly. The patient recovered and subsequent chest computed tomography confirmed the improvement.

Conclusions

We reported a case of empyema secondary to Streptococcus constellatus infection, which was identified by NGS, instead of bacterial culture. This case highlights the utility of NGS in detecting pathogens negative in traditional bacterial tests.

Shotgun whole genome sequencing of drug-resistance Streptococcus anginosus strain 47S1 isolated from a patient with pharyngitis in Saudi Arabia

BACKGROUND

Streptococcus anginosus is an emergence opportunistic pathogen that colonize the human upper respiratory tract (URT), S. anginosus alongside with S. intermedius and S. constellatus, members of S. anginosus group, are implicated in several human infections. However, our understanding this bacterium to the genotype level with determining the genes associated with pathogenicity and antimicrobial resistance (AMR) is scarce. S. anginosus 47S1 strain was isolated from sore throat infection, the whole genome was characterized and the virulence & AMR genes contributing in pathogenicity were investigated.

METHODOLOGY

The whole genome of 47S1 was sequenced by Illumina sequencing technology. Strain 47S1 genome was de novo assembled with different strategies and annotated via PGAP, PROKKA and RAST pipelines. Identifying the CRISPR-Cass system and prophages sequences was performed using CRISPRloci and PhiSpy tools respectively. Prediction the virulence genes were performed with the VFDB database. AMR genes were detected in silico using NCBI AMRFinderPlus pipeline and CARD database and compared with in vitro AST findings.

RESULTS

β-hemolytic strain 47S1 was identified with conventional microbiology techniques and confirmed by the sequences of 16S rRNA gene. Genome of 47S1 comprised of 1981512 bp. Type I-C CRISPR-Cas system and 4 prophages were detected among the genome of 47S1. Several virulence genes were predicted, most of these genes are found in other pathogenic streptococci, mainly lmb, pavA, htrA/degP, eno, sagA, psaA and cpsI which play a significant role in colonizing, invading host tissues and evade form immune system. In silico AMR findings showed that 47S1 gnome harbors (tetA, tetB &tet32), (aac(6')-I, aadK &aph(3')-IVa), fusC, and PmrA genes that mediated-resistance to tetracyclines, aminoglycosides, fusidic acid, and fluoroquinolone respectively which corresponds with in vitro AST obtained results. In conclusion, WGS is a key approach to predict the virulence and AMR genes, results obtained in this study may contribute for a better understanding of the opportunistic S. anginosus pathogenicity.

From Normal Flora to Brain Abscesses: A Review of Streptococcus intermedius

Streptococcus intermedius is a β-hemolytic Gram-positive member of the Streptococcus anginosus group (SAG). Despite being a part of the normal microbiota, it is one of the most common pathogens associated with brain and liver abscesses and thoracic empyema, increasing as a result the morbidity and mortality rates in affected patients. Though there are numerous published case reports on S. intermedius infections, it is still understudied compared to other SAG members. Our knowledge of the genomic factors contributing to its dissemination to the brain and abscess development is also limited to few characterized genes. In this review, we summarize our current knowledge on S. intermedius identification methods, virulence factors, and insight provided by the whole-genome and correlate patients’ metadata, symptoms, and disease outcome with S. intermedius infections in 101 recent case reports obtained from PubMed. This combined information highlights the gaps in our understanding of S. intermedius pathogenesis, suggesting future research directions to unveil the factors contributing to abscess development.

A New Highly Sensitive and Specific Real-Time PCR Assay Targeting the Malate Dehydrogenase Gene of Kingella kingae and Application to 201 Pediatric Clinical Specimens

Kingella kingae is a significant pediatric pathogen responsible for bone and joint infections, occult bacteremia, and endocarditis in early childhood. Past efforts to detect this bacterium using culture and broad-range 16S rRNA gene PCR assays from clinical specimens have proven unsatisfactory; therefore, by the late 2000s, these were gradually phased out to explore the benefits of specific real-time PCR tests targeting the groEL gene and the RTX locus of K. kingae However, recent studies showed that real-time PCR (RT-PCR) assays targeting the Kingella sp. RTX locus that are currently available for the diagnosis of K. kingae infection lack specificity because they could not distinguish between K. kingae and the recently described Kingella negevensis species. Furthermore, in silico analysis of the groEL gene from a large collection of 45 K. kingae strains showed that primers and probes from K. kingaegroEL-based RT-PCR assays display a few mismatches with K. kingae groEL variations that may result in decreased detection sensitivity, especially in paucibacillary clinical specimens. In order to provide an alternative to groEL- and RTX-targeting RT-PCR assays that may suffer from suboptimal specificity and sensitivity, a K. kingae-specific RT-PCR assay targeting the malate dehydrogenase (mdh) gene was developed for predicting no mismatch between primers and probe and 18 variants of the K. kingae mdh gene from 20 distinct sequence types of K. kingae This novel K. kingae-specific RT-PCR assay demonstrated high specificity and sensitivity and was successfully used to diagnose K. kingae infections and carriage in 104 clinical specimens from children between 7 months and 7 years old.

Development of a quantitative PCR assay for monitoring Streptococcus agalactiae colonization and tissue tropism in experimentally infected tilapia

Streptococcus agalactiae has become one of the most important emerging pathogens in the aquaculture industry and has resulted in large economic losses for tilapia farms in China. In this study, three pairs of specific primers were designed and tested for their specificities and sensitivities in quantitative real-time polymerase chain reactions (qPCRs) after optimization of the annealing temperature. The primer pair IGS-s/IGS-a, which targets the 16S-23S rRNA intergenic spacer region, was finally chosen, having a detection limit of 8.6 copies of S. agalactiae DNA in a 20 μL reaction mixture. Bacterial tissue tropism was demonstrated by qPCR in Oreochromis niloticus 5 days post-injection with a virulent S. agalactiae strain. Bacterial loads were detected at the highest level in brain, followed by moderately high levels in kidney, heart, spleen, intestines, and eye. Significantly lower bacterial loads were observed in muscle, gill and liver. In addition, significantly lower bacterial loads were observed in the brain of convalescent O. niloticus 14 days post-injection with several different S. agalactiae strains. The qPCR for the detection of S. agalactiae developed in this study provides a quantitative tool for investigating bacterial tissue tropism in infected fish, as well as for monitoring bacterial colonization in convalescent fish.

Real-time polymerase chain reaction for microbiological diagnosis of parapneumonic effusions in Canadian children

Community-acquired pneumonia with parapneumonic effusion/empyema is not uncommon in children and can cause serious illness; there -fore, the timely optimization of antimicrobial therapy is essential in this situation. The aim of this study was to determine whether using real-time polymerase chain reaction of pleural fluids to identify the causative organism improves the process of microbiological diagnosis in the context of community-acquired pneumonia with parapneumonic effusion/empyema. This technique was compared with traditional culture methods for microbiological diagnosis.

BACKGROUND:

Community-acquired pneumonia (CAP) complicated by parapneumonic effusion/empyema is an infectious syndrome commonly encountered by physicians caring for children in Canada.

OBJECTIVE:

To investigate the incremental benefit of novel molecular testing for the microbiological diagnosis of pediatric CAP complicated by parapneumonic effusion/empyema in Canada.

METHODS:

A convenience sample of pleural fluid from 56 children who had been admitted to hospital in Ontario with CAP complicated by parapneumonic effusion between 2009 and 2011 was examined. Multiple uniplex real-time polymerase chain reaction (PCR) testing was performed on these pleural fluids and compared with traditional culture-based testing of blood and pleural fluid samples.

RESULTS:

Molecular methods detected a pathogen in 82% of cases, whereas traditional cultures of blood and pleural fluids detected a pathogen in only 25%. The majority of parapneumonic effusions were associated with pneumococcal infection; Streptococcus pneumoniae was detected in 62% of the samples using molecular methods but in only 14% of samples using culture-based methods. Streptococcus pyogenes, detected in 16% of samples using PCR, was the second most common pathogen found. No patients were found to have empyema caused by Staphylococcus aureus.

DISCUSSION:

The results showed that multiple uniplex real-time PCR performed substantially better than traditional culture methods for microbiological diagnosis of CAP complicated by effusion/ empyema. S pneumoniae and S pyogenes were found to be responsible for the majority of infections. The approach detected pathogens in a similar proportion of pleural fluid samples as previously reported nested PCR assays; furthermore, the real-time closed-well approach also minimized the risk of nonspecificity due to cross-contamination relative to nested PCR.

CONCLUSIONS:

Real-time PCR for the detection of bacterial DNA in pleural fluids has the potential to better define the microbiological cause of pediatric CAP. This approach could help clinicians provide targeted antimicrobial therapy.

Development of a panel of seven duplex real-time PCR assays for detecting 13 streptococcal superantigens

BACKGROUND

Streptococcal superantigens (SAgs) are the major virulence factors of infection in humans for group A Streptococcus (GAS) bacteria. A panel consisting of seven duplex real-time PCR assays was developed to simultaneously detect 13 streptococcal SAgs and one internal control which may be important in the control of GAS-mediated diseases.

METHODS

Primer and probe sequences were selected based on the highly conserved region from an alignment of nucleotide sequences of the 13 streptococcal SAgs. The reaction conditions of the duplex real-time PCR were optimized and the specificity of the duplex assays was evaluated using SAg positive strains. The limit of detection of the duplex assays was determined by using 10-fold serial dilutions of the DNA of 13 streptococcal SAgs and compared to a conventional polymerase chain reaction (PCR) method for evaluating the duplex assays sensitivity.

RESULTS

Using the duplex assays, we were able to differentiate between 13 SAgs from Streptococcus strains and other non-Streptococcus bacteria without cross-reaction. On the other hand, the limit of detection of the duplex assays was at least one or two log dilutions lower than that of the conventional PCR.

CONCLUSIONS

The panel was highly specific (100%) and the limit of detection of these duplex groups was at least ten times lower than that obtained by using a conventional PCR method.

Usefulness of PCR-HRMA in identification of non-fermentative Gram-negative rods recovered from patients suffering from cystic fibrosis or chronic obstructive pulmonary disease

Adequate treatment of microbial infections requires rapid and accurate identification of the etiological agent. In routine diagnostics, identification of bacteria conventionally relies on phenotypic testing, which can be hindered by phenotypic variations. Therefore, genotyping techniques should perform faster and more accurately. Recently, the technique of high-resolution melting analysis (HRMA) of PCR amplicons promises to provide a convenient and economic tool of genotypic identification. In our study, we performed prospective routine testing of a PCR-HRMA system that was recently published in a proof-of-the-principle study. The system was evaluated by analysing 275 clinical isolates of bacteria acquired from 65 patients suffering from cystic fibrosis or chronic obstructive pulmonary disease. Our results show that its routine use may result in partial worsening of its discriminatory power; however, it still outmatched conventional phenotyping in the group of non-fermentative Gram-negative rods. Moreover, when supplemented by rapid, simple and economic oxidase test, it can be even simplified for more economic performance.

Effects of extracellular DNA and DNA-binding protein on the development of a Streptococcus intermedius biofilm

AIMS

The aim of this study was to clarify the effects of homologous and heterologous extracellular DNAs (eDNAs) and histone-like DNA-binding protein (HLP) on Streptococcus intermedius biofilm development and rigidity.

METHODS AND RESULTS

Formed biofilm mass was measured with 0·1% crystal violet staining method and observed with a scanning electron microscope. The localizations of eDNA and extracellular HLP (eHLP) in formed biofilm were detected by staining with 7-hydoxyl-9H-(1,3-dichloro-9,9-dimethylacridin-2-one) and anti-HLP antibody without fixation, respectively. DNase I treatment (200 U ml(-1)) markedly decreased biofilm formation and cell density in biofilms. Colocalization of eHLP and eDNA in biofilm was confirmed. The addition of eDNA (up to 1 μg ml(-1)) purified from Strep. intermedius, other Gram-positive bacteria, Gram-negative bacteria, or human KB cells into the Strep. intermedius culture increased the biofilm mass of all tested strains of Strep. intermedius, wild-type, HLP-downregulated strain and control strains. In contrast, the addition of eDNA (>1 μg ml(-1)) decreased the biofilm mass of all Strep. intermedius strains.

CONCLUSIONS

These findings demonstrated that eDNA and eHLP play crucial roles in biofilm development and its rigidity.

SIGNIFICANCE AND IMPACT OF THE STUDY

eDNA- and HLP-targeting strategies may be applicable to novel treatments for bacterial biofilm-related infectious diseases.

Taxonomy of the Anginosus group of the genus Streptococcus and description of Streptococcus anginosus subsp. whileyi subsp. nov. and Streptococcus constellatus subsp. viborgensis subsp. nov

The Anginosus group of the genus Streptococcus has been the subject of much taxonomic confusion, which has hampered the full appreciation of its clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Anginosus group, with special attention to β-haemolytic, Lancefield group C strains, using multilocus sequence analysis (MLSA) combined with 16S rRNA gene sequence and phenotypic analyses. Phylogenetic analysis of concatenated sequences of seven housekeeping genes previously used for examination of viridans streptococci distinguished seven distinct and coherent clusters in the Anginosus group. Analyses of 16S rRNA gene sequences and phenotypic characters supported the MLSA clustering and currently recognized taxa of the Anginosus group. Single gene analyses showed considerable allele sharing between species, thereby invalidating identification based on single-locus sequencing. Two novel clusters of β-haemolytic, Lancefield group C strains within the Streptococcus constellatus and Streptococcus anginosus species and isolated from patients with sore throat showed sufficient phylogenetic distances from other clusters to warrant status as novel subspecies. The novel cluster within S. anginosus was identified as the previously recognized DNA homology cluster, DNA group 2. The names S. anginosus subsp. whileyi subsp. nov. (type strain CCUG 39159(T) = DSM 25818(T) = SK1267(T)) and S. constellatus subsp. viborgensis subsp. nov. (type strain SK1359(T) = CCUG 62387(T) = DSM 25819(T)) are proposed.

Direct sampling of cystic fibrosis lungs indicates that DNA-based analyses of upper-airway specimens can misrepresent lung microbiota

Recent work using culture-independent methods suggests that the lungs of cystic fibrosis (CF) patients harbor a vast array of bacteria not conventionally implicated in CF lung disease. However, sampling lung secretions in living subjects requires that expectorated specimens or collection devices pass through the oropharynx. Thus, contamination could confound results. Here, we compared culture-independent analyses of throat and sputum specimens to samples directly obtained from the lungs at the time of transplantation. We found that CF lungs with advanced disease contained relatively homogenous populations of typical CF pathogens. In contrast, upper-airway specimens from the same subjects contained higher levels of microbial diversity and organisms not typically considered CF pathogens. Furthermore, sputum exhibited day-to-day variation in the abundance of nontypical organisms, even in the absence of clinical changes. These findings suggest that oropharyngeal contamination could limit the accuracy of DNA-based measurements on upper-airway specimens. This work highlights the importance of sampling procedures for microbiome studies and suggests that methods that account for contamination are needed when DNA-based methods are used on clinical specimens.

Development and validation of a real-time TaqMan assay for the detection and enumeration of Pseudomonas fluorescens ATCC 13525 used as a challenge organism in testing of food equipments

Pseudomonas fluorescens ATCC 13525 is used as the challenge organism to evaluate the efficacy of the clean-in-place (CIP) process of food equipment (automatic ice-maker) as per NSF/ANSI Standard 12. Traditional culturing methodology is presently used to determine the concentration of the challenge organism, which takes 48 h to confirm the cell density. Storage of the challenge preparation in the refrigerator might alter the cell density as P. fluorescens is capable of growing at 4 °C. Also, background organism can grow on the Pseudomonas F agar (PFA) used for the recovery of P. fluorescens thus affecting the results of the test. Real-time TaqMan assay targeting the cpn60 gene was developed for the enumeration and the identification of P. fluorescens because of its specificity, accuracy, and shorter turnaround time. The TaqMan primer-probe pair developed using the Allele ID® 7.0 probe design software was highly specific and sensitive for the target organism. The sensitivity of the assay was 10 colony forming units (CFU)/mL. The assay was also successful in determining the concentration of the challenge preparation within 2 h. Based on these observations, TaqMan assay targeting the cpn60 gene can be efficiently used for strain level identification and enumeration of bacteria.

PRACTICAL APPLICATION

Pseudomonas fluorescens ATCC 13525 is used as a challenge organism in the efficacy testing of clean-in-place process of food equipments. Currently, culturing technique is used for its identification and estimation, which is not only time-consuming but also prone to error. Real-time TaqMan assay is more specific, sensitive, and accurate along with a shorter turnaround time compared to culturing techniques, thereby increasing the overall quality of the testing methodology to evaluate the clean-in-place process critical for the food industry to protect public health and safety.

The Streptococcus milleri population of a cystic fibrosis clinic reveals patient specificity and intraspecies diversity

The genetic relatedness of Streptococcus milleri group isolates from the airways of cystic fibrosis patients was determined by using pulsed-field gel electrophoresis. This study reveals no evidence for patient-to-patient transmission in our patient population; however, within individual patients, complex inter- and intraspecies diversity and dynamics can be observed.