Development and performance evaluation of a recombinase polymerase amplification assay for the rapid detection of group B streptococcus

Automated Microfluidic Nucleic Acid Detection Platform-Integrated RPA-T7-Cas13a for Pathogen Diagnosis

There is a growing urgent need for point-of-care testing (POCT) devices that integrate sample pretreatment and nucleic acid detection in a rapid, economical, and non-labor-intensive way. Here, we have developed an automated, portable nucleic acid detection system employing microfluidic chips integrating rotary valve-assisted sample pretreatment and recombinase polymerase amplification (RPA)-T7-Cas13a into one-step nucleic acid detection. The RPA and clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a were integrated into a single-chamber reaction. As a validation model, we used this method to detect Group B streptococci (GBS) DNA and achieved a detection sensitivity of 8 copies/reaction, which is 6 times more sensitive than gold-standard polymerase chain reactions (PCRs). Dual specific recognition of RPA with CRISPR/Cas13a makes our method ultraspecific, with correct detection of Group B streptococci from 8 kinds of pathogenic bacteria. For the 16 positive and 24 negative clinical GBS samples, our assay achieved 100% accuracy compared to the PCR technique. The whole procedure can be automatically completed within 30 min, providing a more robust, sensitive, and accurate molecular diagnostic tool for POCT.

Do NAAT-Based Methods Increase the Diagnostic Sensitivity of Streptococcus agalactiae Carriage Detection in Pregnant Women?

The aim of the study was to evaluate particular polymerase chain reaction primers targeting selected representative genes and the influence of a preincubation step in a selective broth on the sensitivity of group B Streptococcus (GBS) detection by nucleic acid amplification techniques (NAAT). Research samples were vaginal and rectal swabs collected in duplicate from 97 pregnant women. They were used for enrichment broth culture-based diagnostics, bacterial DNA isolation, and amplification, using primers based on species-specific 16S rRNA, atr and cfb genes. To assess the sensitivity of GBS detection, additional isolation of samples preincubated in Todd-Hewitt broth with colistin and nalidixic acid was performed and then subjected to amplification again. The introduction of the preincubation step increased the sensitivity of GBS detection by about 33-63%. Moreover, NAAT made it possible to identify GBS DNA in an additional six samples that were negative in culture. The highest number of true positive results compared to the culture was obtained with the atr gene primers, as compared to cfb and 16S rRNA primers. Isolation of bacterial DNA after preincubation in enrichment broth significantly increases the sensitivity of NAAT-based methods applied for the detection of GBS from vaginal and rectal swabs. In the case of the cfb gene, the use of an additional gene to ensure the appropriate results should be considered.

Development of a Rapid and Efficient RPA-CRISPR/Cas12a Assay for Mycoplasma pneumoniae Detection

Mycoplasma pneumoniae (MP) is a one of most common pathogen in causing respiratory infection in children and adolescents. Rapid and efficient diagnostic methods are crucial for control and treatment of MP infections. Herein, we present an operationally simple, rapid and efficient molecular method for MP identification, which eliminates expensive instruments and specialized personnel. The method combines recombinase polymerase amplification (RPA) with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated proteins (Cas) 12a-based detection, with an optimal procedure less than 1 h from sample to result including DNA extraction (25 min), RPA reaction (39°C for 15-20 min), CRISPR/Cas12a detection (37°C for 10 min) and visual detection by naked eyes (2 min). This diagnostic method shows high sensitivity (two copies per reaction) and no cross-reactivity against other common pathogenic bacteria. Preliminary evaluation using 201 clinical samples shows sensitivity of 99.1% (107/108), specificity of 100% (93/93) and consistency of 99.5% (200/201), compared with real-time PCR method. The above data demonstrate that our developed method is reliable for rapid diagnosis of MP. In conclusion, the RPA-CRISPR/Cas12a has a great potential to be as a useful tool for reliable and quick diagnosis of MP infection, especially in primary hospitals with limited conditions.

Pathogenic mechanism, detection methods and clinical significance of group B Streptococcus

Group B Streptococcus (GBS) is the main pathogen of perinatal infection. It can lead to adverse pregnancy, maternal infection, premature delivery, abortion, stillbirth and a series of adverse maternal and infant outcomes such as neonatal sepsis, meningitis or pneumonia during delivery. In order to reduce the infection of perinatal pregnant and the adverse pregnancy outcome, more attention should be paid in the clinical practice, screening efforts, universal detection of GBS infection for pregnant women and preventive treatment for the possible mother infant infection. In this study, the biological characteristics, immunophenotype, major pathogenic mechanism, laboratory test methods and clinical significance of GBS are summarized.

Molecular diagnostic assays for the detection of common bacterial meningitis pathogens: A narrative review

Bacterial meningitis is a major global cause of morbidity and mortality. Rapid identification of the aetiological agent of meningitis is essential for clinical and public health management and disease prevention given the wide range of pathogens that cause the clinical syndrome and the availability of vaccines that protect against some, but not all, of these. Since microbiological culture is complex, slow, and often impacted by prior antimicrobial treatment of the patient, molecular diagnostic assays have been developed for bacterial detection. Distinguishing between meningitis caused by Neisseria meningitidis (meningococcus), Streptococcus pneumoniae (pneumococcus), Haemophilus influenzae, and Streptococcus agalactiae and identifying their polysaccharide capsules is especially important. Here, we review methods used in the identification of these bacteria, providing an up-to-date account of available assays, allowing clinicians and diagnostic laboratories to make informed decisions about which assays to use.

Nucleic acid visualization assay for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) by targeting the UpE and N gene

Since its first emergence in 2012, cases of infection with Middle East respiratory syndrome coronavirus (MERS-CoV) have continued to occur. At the end of January 2020, 2519 laboratory confirmed cases with a case-fatality rate of 34.3% have been reported. Approximately 84% of human cases have been reported in the tropical region of Saudi Arabia. The emergence of MERS-CoV has highlighted need for a rapid and accurate assay to triage patients with a suspected infection in a timely manner because of the lack of an approved vaccine or an effective treatment for MERS-CoV to prevent and control potential outbreaks. In this study, we present two rapid and visual nucleic acid assays that target the MERS-CoV UpE and N genes as a panel that combines reverse transcription recombinase polymerase amplification with a closed vertical flow visualization strip (RT-RPA-VF). This test panel was designed to improve the diagnostic accuracy through dual-target screening after referencing laboratory testing guidance for MERS-CoV. The limit of detection was 1.2×101 copies/μl viral RNA for the UpE assay and 1.2 copies/μl viral RNA for the N assay, with almost consistent with the sensitivity of the RT-qPCR assays. The two assays exhibited no cross-reactivity with multiple CoVs, including the bat severe acute respiratory syndrome related coronavirus (SARSr-CoV), the bat coronavirus HKU4, and the human coronaviruses 229E, OC43, HKU1 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Furthermore, the panel does not require sophisticated equipment and provides rapid detection within 30 min. This panel displays good sensitivity and specificity and may be useful to rapidly detect MERS-CoV early during an outbreak and for disease surveillance.

Group B Streptococcus colonisation and their antimicrobial susceptibility among pregnant women attending antenatal clinics in tertiary care hospitals in the Western Province of Sri Lanka

The proportion of Group B Streptococcus (GBS) colonisation in pregnant women >35 weeks of gestation was 18% and 49% by culture and real-time PCR respectively in selected hospitals from the Western Province of Sri Lanka. A Descriptive cross-sectional study was conducted from January to April 2019. Two low vaginal and rectal swabs were collected from 100 pregnant women. Identification of GBS was done by culture and real-time PCR. GBS isolates were found to be sensitive to penicillin, ampicillin, cefotaxime, vancomycin, while 5 and 4 isolates out of 18 were resistant to erythromycin and clindamycin, respectively. Further, there was a significant association between GBS colonisation and a history of vaginal discharge and unemployment.IMPACT STATEMENTWhat is already known on this subject? Prevalence of GBS colonisation in the vagina and rectum of pregnant women in developing countries ranges from 8.5% to 22%. The Conventional method of culture has been considered the gold standard for diagnosis, however, the culture method does not give positive results for all cases of GBS. Polymerase chain reaction (PCR) has been found to be more sensitive for the detection of GBS than culture. In Sri Lanka, ante-natal screening for GBS is not practiced as the prevalence of GBS is still unlcear due to non-availably of data. Only a few scattered studies have been conducted using culture in Sri Lanka. Thus there is an urgent need to determine the magnitude of the GBS colonisers of ante-natal women in order to set up guidelines for screening and management of GBS.What do the results of this study add? In this study, the overall GBS colonisation rate which was detected using both culture and PCR was 50% in Western Province of Sri Lanka. That was a high figure when compared to the figures which were detected previously in Sri Lanka using only conventional culture methods. The risk factors for GBS colonisation were found to have a significant relationship with the history of abnormal vaginal discharge. Further, it was found that when Candida species coexisted with GBS, the existence of GBS was enhanced. Penicillin remains the antibiotic of choice for GBS.What are the implications of these findings for clinical practice and/or further research? This study emphasises the importance of establishing national policies for screening of pregnant women of >35 weeks of gestation to reduce the risk of neonatal infection. Further, it gives an insight into the options of antibiotics that can be used for treatment of these GBS colonisers from Sri Lanka.

Influence of design probe and sequence mismatches on the efficiency of fluorescent RPA

Recombinase polymerase amplification (RPA) is an isothermal amplification technique. Because of its short detection cycle and high specificity, it has been applied in various fields. However, the design of probe on the efficiency of RPA is not well understood and the effect of sequence mismatches of oligonucleotides on the performance of RPA is rarely discussed. In this study, we found that different primers with the same probe have a slight effect on the efficiency of fluorescent RPA, and different probes with the same amplified region have a great influence on the efficiency of fluorescent RPA. We summarized the design rules of probes suitable for fluorescent RPA by analyzing the experimental data. The rule is that the best distance between fluorescent groups in the probe is 1-2 bases, and the G content should be reduced as far as possible. In addition, we verified this rule by designing a series of probes. Furthermore, we found the base mismatches of the probe had a significant effect on RPA, which can lead to false positives and can change the amplification efficiency. However, 1-3 mismatches covering the center of the primer sequence only affect the amplification efficiency of RPA, not its specificity. And with an increase in the number of primer mismatches, the efficiency of RPA will decrease accordingly. This study suggests that the efficiency of fluorescent RPA is closely related to the probe. We recommend that when designing a fluorescent probe, one must consider the presence of closely related non-targets and specific bases.

Review: a comprehensive summary of a decade development of the recombinase polymerase amplification

RPA is a versatile complement or replacement of PCR, and now is stepping into practice.

SERS-Based Lateral Flow Strip Biosensor for Simultaneous Detection of Listeria monocytogenes and Salmonella enterica Serotype Enteritidis

Rapid, sensitive, point-of-care detection of bacteria is extremely important in food safety. To address this requirement, we developed a new surface-enhanced Raman scattering (SERS)-based lateral flow (LF) strip biosensor combined with recombinase polymerase amplification (RPA) for simultaneous detection of Listeria monocytogenes and Salmonella enterica serotype Enteritidis. Au^MBA@Ag core-shell nanoparticles were used in this SERS-LF. Highly sensitive quantitative detection is achieved by measuring the characteristic peak intensities of SERS tags. Under optimal conditions, the SERS intensities of MBA at 1077 cm^-1 on test lines are used to measure S. Enteritidis (y = 1980.6x - 539.3, R² = 0.9834) and L. monocytogenes (y = 1696.0x - 844, R² = 0.9889), respectively. The limit of detection is 27 CFU/mL for S. Enteritidis and 19 CFU/mL for L. monocytogenes. Significantly, this SERS-LF has high specificity and applicability in the detection of L. monocytogenes and S. Enteritidis in food samples. Therefore, the SERS-LF is a feasible method for the rapid and quantitative detection of a broad range of bacterial pathogens in real food samples.

Recombinase polymerase amplification: Basics, applications and recent advances

Recombinase polymerase amplification (RPA) is a highly sensitive and selective isothermal amplification technique, operating at 37-42°C, with minimal sample preparation and capable of amplifying as low as 1-10 DNA target copies in less than 20 min. It has been used to amplify diverse targets, including RNA, miRNA, ssDNA and dsDNA from a wide variety of organisms and samples. An ever increasing number of publications detailing the use of RPA are appearing and amplification has been carried out in solution phase, solid phase as well as in a bridge amplification format. Furthermore, RPA has been successfully integrated with different detection strategies, from end-point lateral flow strips to real-time fluorescent detection amongst others. This review focuses on the different methodologies and advances related to RPA technology, as well as highlighting some of the advantages and drawbacks of the technique.

Group B Streptococcus detection in pregnant women via culture and PCR methods

INTRODUCTION:

Group B Streptococcus (GBS), a source of neonatal infection, colonizes the gastrointestinal and genitourinary tracts of pregnant women. Routine screening for maternal GBS in late pregnancy and consequent intrapartum antibiotic prophylaxis have reduced the incidence of early-onset GBS neonatal infection. The aim of this study was to evaluate the performance of PCR, compared to culture (gold standard), in GBS colonization screening of pregnant women, and to establish the prevalence of GBS colonization among this population.

METHODS:

Vaginal introitus and perianal samples were collected from 204 pregnant women, between the 35th and 37th weeks of pregnancy, at the Obstetrics and Gynecology Unit of the University of Caxias do Sul General Hospital between June 2008 and September 2009. All samples were cultured after enrichment in a selective medium and then assayed by culture and PCR methods.

RESULTS:

The culture and PCR methods yielded detection rates of vaginal/perianal GBS colonization of 22.5% and 26%, respectively (sensitivity 100%; specificity 95.6%; positive and negative predictive values 86.8% and 100%, respectively). A higher prevalence of GBS colonization was detected in the combined vaginal and perianal samples by both culture and PCR assay analyses.

CONCLUSIONS:

PCR is a faster and more efficient method for GBS screening, allowing for optimal identification of women who should receive intrapartum antibiotic prophylaxis to prevent newborn infection.

Group B streptococcal PCR testing in comparison to culture for diagnosis of late onset bacteraemia and meningitis in infants aged 7-90 days: a multi-centre diagnostic accuracy study

The aim of this study was to compare an in-house real-time PCR assay, with bacterial culture as the reference, for the diagnosis of late onset group B Streptococcal (GBS) disease. This was a retrospective review. All children aged 7-90 days presenting to four paediatric centres that had a blood or CSF sample tested by GBS PCR were included. Of 7,686 blood and 2,495 cerebrospinal fluid (CSF) samples from patients of all ages received for PCR testing, 893 and 859 samples were eligible for the study, respectively. When compared to culture, the sensitivity of blood PCR was 65% (13/20) in comparison to the CSF PCR test which was 100% (5/5). Ten of 23 PCR-positive blood samples and 17 of 22 PCR-positive CSF samples were culture negative. The median threshold Ct values for culture-positive/PCR-positive CSF samples was lower than that of culture-negative/PCR-positive CSF samples (p = 0.08). Clinical details of 17 available cases that were culture negative/PCR positive were reviewed; seven were deemed to be definite cases, eight were probable and two were possible. The results showed that detection of GBS by PCR is useful for CSF samples from infants aged 7-90 days with suspected meningitis; however, analysis of blood samples by PCR is of limited value as a routine screening test for late onset GBS sepsis and should not replace bacterial culture.