SARS-CoV-2 variant typing using real-time reverse transcription-polymerase chain reaction-based assays in Addis Ababa, Ethiopia.

Objectives: This study aimed to determine the SARS-CoV-2 variants in the first four COVID-19 waves using polymerase chain reaction (PCR)-based variant detection in Addis Ababa, Ethiopia. Methods: A cross-sectional study was conducted using repository nasopharyngeal samples stored at the Ethiopian Public Health Institute COVID-19 testing laboratory. Stored positive samples were randomly selected from the first four waves based on their sample collection date. A total of 641 nasopharyngeal samples were selected and re-tested for SARS-CoV-2. RNA was extracted using nucleic acid purification instrument. Then, SARS-CoV-2 detection was carried out using 10 µl RNA and 20 µl reverse transcription-PCR fluorescent mix. Cycle threshold values <38 were considered positive. Results: A total of 374 samples qualified for B.1.617 Lineage and six spike gene mutation variant typing kits. The variant typing kits identified 267 (71.4%) from the total qualifying samples. Alpha, Beta, Delta, and Omicron were dominantly identified variants from waves I, II, III, and IV, respectively. From the total identified positive study samples, 243 of 267 (91%) of variants identified from samples had cycle threshold values <30. Conclusions: The study data demonstrated that reverse transcription-PCR-based variant typing can provide additional screening opportunities where sequencing opportunity is inaccessible. The assays could be implemented in laboratories performing SARS-CoV-2 molecular testing.

Substantial Diversity in Cocirculating Omicron Lineages in Hospital Setting, Porto Alegre, Brazil.

We describe substantial variant diversity among 23 detected SARS-CoV-2 Omicron lineage viruses cocirculating among healthcare workers and inpatients (272 sequenced samples) from Porto Alegre, Brazil, during November 2022-January 2023. BQ.1 and related lineages (61.4%) were most common, followed by BE.9 (19.1%), first described in November 2022 in the Amazon region.

Performance of Reverse Transcription Loop-Mediated Isothermal Amplification (RT-LAMP) Targeting the RNA Polymerase Gene for the Direct Detection of SARS-CoV2 in Nasopharyngeal Swabs.

In 2020, a global pandemic caused by SARS-CoV-2 was declared. Different institutes proposed diagnostic molecular methods to detect the virus in clinical samples. This study aims to validate and standardize the use of a loop-mediated isothermal amplification (LAMP)-based methodology targeting the viral RP gene, as a faster and low-cost diagnostic method for SARS-CoV-2 infections. The results obtained with RT-LAMP (Reverse Transcriptase) were compared to the results of real-time polymerase chain reaction (RT-PCR) to assess its sensitivity and specificity. In total, 115 samples (nasopharyngeal samples) were used for detecting SARS-CoV-2 by RT-LAMP, with 43 positives and 72 negatives. The study showed a positive predictive value (PPV) of 90.7% and a negative predictive value (VPN) of 100%. The LAMP assay also demonstrated a high sensitivity of 90.7% and a specificity of 100% (confidence interval 77.9-97.4%) when using the lower detection limit of 40 copies/µL. The RT-LAMP described here has the potential to detect even the new variants of SARS-CoV-2, suggesting that it may not be significantly affected by gene mutations. The RT-LAMP targeting the RP viral region is faster and less expensive than other molecular approaches, making it an alternative for developing countries.

Validation of a MALDI-TOF MS Method for SARS-CoV-2 Detection on the Bruker Biotyper and Nasopharyngeal Swabs: A Brazil-UK Collaborative Study.

We developed a MALDI-TOF mass spectrometry method for the detection of the SARS-CoV-2 virus in saliva-gargle samples using Shimadzu MALDI-TOF mass spectrometers in the UK. This was validated in the USA to CLIA-LDT standards for asymptomatic infection detection remotely via sharing protocols, shipping key reagents, video conferencing, and data exchange. In Brazil, more so than in the UK and USA, there is a need to develop non-PCR-dependent, rapid, and affordable SARS-CoV-2 infection screening tests that also identify variant SARS-CoV-2 and other virus infections. In addition, travel restrictions necessitated remote collaboration with validation on the available clinical MALDI-TOF-the Bruker Biotyper (microflex® LT/SH)-and on nasopharyngeal swab samples, as salivary gargle samples were not available. The Bruker Biotyper was shown to be almost log103 more sensitive at the detection of high molecular weight spike proteins. A protocol for saline swab soaks out was developed, and duplicate swab samples collected in Brazil were analyzed by MALDI-TOF MS. The swab collected sample spectra that varied from that of saliva-gargle in three additional mass peaks in the mass region expected for IgG heavy chains and human serum albumin. A subset of clinical samples with additional high mass, probably spike-related proteins, were also found. Further, spectral data comparisons and analysis, subjected to machine learning algorithms in order to resolve RT-qPCR positive from RT-qPCR negative swab samples, showed 56-62% sensitivity, 87-91% specificity, and a 78% agreement with RT-qPCR scoring for SARS-CoV-2 infection.

Otopathogens in the middle ear and nasopharynx of children with recurrent acute otitis media.

OBJECTIVE: This study aimed to describe the microbiology of the middle ear and nasopharynx, determining the prevalence of Streptococcus pneumoniae, Haemophilus influenzae and Moraxella catarrhalis in a group of children vaccinated with pneumococcal conjugate vaccine (PCV) who underwent ventilation tube insertion for recurrent acute otitis media. METHODS: We analyzed 278 middle ear effusion and 139 nasopharyngeal samples obtained from 139 children who underwent myringotomy and ventilation tube insertion for recurrent acute otitis media between June 2017 and June 2021. The children's ages ranged from 9 months to 9 years, 10 months, with a median of 21 months. The patients had no signs of acute otitis media or respiratory tract infection and were not on antibiotic therapy at the time of the procedure. The middle ear effusion and nasopharyngeal samples were collected with an Alden-Senturia aspirator and a swab, respectively. Bacteriological studies and multiplex PCR were performed for the detection of the three pathogens. Direct molecular determination of pneumococcal serotypes was performed by real-time PCR. The chi-square test was used to verify associations between categorical variables and measures of strength of association based on prevalence ratios, considering a 95% confidence interval a 5% significance level. RESULTS: Vaccination coverage was 77.7% with the basic regimen plus booster dose and 22.3% with the basic regimen alone. Middle ear effusion culture identified H. influenzae in 27 children (19.4%), S. pneumoniae in 7 (5.0%), and M. catarrhalis in 7 (5.0%). PCR detected H. influenzae in 95 children (68.3%), S. pneumoniae in 52 (37.4%), and M. catarrhalis in 23 (16.5%), a three-to seven-fold increase compared to culture. In the nasopharynx, culture isolated H. influenzae in 28 children (20.1%), S. pneumoniae in 29 (20.9%), and M. catarrhalis in 12 (8.6%). PCR identified H. influenzae in 84 children (60.4%), S. pneumoniae in 58 (41.7%), and M. catarrhalis in 30 (21.5%), a two-to three-fold increase in detection. The most common pneumococcal serotype was 19A, both in the ears and the nasopharynx. In the ears, of the 52 children who had pneumococcus, 24 (46.2%) had serotype 19A. In the nasopharynx, of the 58 patients who had pneumococcus, 37 (63.8%) had serotype 19A. Of all 139 children, 53 (38.1%) had polymicrobial samples (more than 1 of the 3 otopathogens) in the nasopharynx. Of the 53 children who had polymicrobial samples in the nasopharynx, 47 (88.7%) also had 1 of the 3 otopathogens in the middle ear, mainly H. influenzae (40%-75.5%), especially when it was found in the nasopharynx in conjunction with S. pneumoniae. CONCLUSION: The prevalence of bacteria in a group of Brazilian children immunized with the PCV who required ventilation tube insertion for recurrent acute otitis media was similar to that reported in other parts of the world after the advent of PCV. H. influenzae was the most frequent bacteria, both in the nasopharynx and the middle ear, while S. pneumoniae serotype 19A was the most common pneumococcus in the nasopharynx and middle ear. Polymicrobial colonization of the nasopharynx was strongly associated with detection of H. influenzae in the middle ear.

Staphylococcus argenteus Infections, Brazil.

In 2015, two new species related to the Staphylococcus aureus were proposed. We describe five isolates of the new species Staphylococcus argenteus cultured from human cases of bacteremia and skin and soft tissue infections. This is the first report of S. argenteus, from South America, causing community-acquired and nosocomial infections.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil.

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Etiology of meningitis among adults in three quaternary hospitals in Mozambique, 2016-2017: The role of HIV.

BACKGROUND: Meningitis remains an important cause of morbi-mortality in adults in sub-Saharan Africa. Data on the etiological investigation of meningitis in adults in Mozambique is limited and most studies were conducted in southern Mozambique. Identification of the etiology of meningitis in adults are crucial to guide prevention and treatments strategies. In this study, we determine the burden of fungal and bacterial meningitis among adults at the three largest hospitals in Mozambique. METHOD: We performed analysis of data from the routine sentinel surveillance system for meningitis in Mozambique from January 2016 to December 2017. Cerebrospinal fluid (CSF) samples were collected from eligible adults (≥18 years old) who met World Health Organization (WHO) case definition criteria for Meningitis. All samples were tested by cryptococcal antigen (CrAg) lateral flow assay (LFA), culture and triplex real-time polymerase chain reaction (qPCR) assay and all patients were tested for human immunodeficiency virus (HIV) using the national algorithm for HIV testing. RESULTS: Retrospective analysis of 1501 CSF samples from adults clinically suspected of meningitis revealed that 10.5% (158/1501) were positive for bacterial and fungal meningitis. Of these 158 confirmed cases, the proportion of Cryptococcal meningitis and pneumococcal meningitis was38.6% (95% CI: 31.0% to 46.7%) and 36.7% (95% CI: 29.2% to 44.7%), respectively. The other bacterial agents of meningitis identified include Neisseria meningitidis (8.9%; 14/158), Escherichia coli (6.3%; 10/158), Haemophilus influenzae (5.1%; 8/158) and S. aureus (4.4%; 7/158), which represent (24.7%; 39/158) of the total confirmed cases. CONCLUSION: Altogether, our findings show a high burden of Cryptococcal meningitis among adults in Mozambique, especially in people living with HIV, followed by pneumococcal meningitis. Our findings suggest that rollout of CrAg Lateral Flow Assay in the health system in Mozambique for early detection of cryptococcus neoformans is necessary to improve overall patient care.

Genomic epidemiology reveals the impact of national and international restrictions measures on the SARS-CoV-2 epidemic in Brazil.

Brazil has experienced some of the highest numbers of COVID-19 cases and deaths globally and from May 2021 made Latin America a pandemic epicenter. Although SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, important gaps remain in our understanding of virus transmission dynamics at the national scale. Here, we describe the genomic epidemiology of SARS-CoV-2 using near-full genomes sampled from 27 Brazilian states and a bordering country - Paraguay. We show that the early stage of the pandemic in Brazil was characterised by the co-circulation of multiple viral lineages, linked to multiple importations predominantly from Europe, and subsequently characterized by large local transmission clusters. As the epidemic progressed under an absence of effective restriction measures, there was a local emergence and onward international spread of Variants of Concern (VOC) and Variants Under Monitoring (VUM), including Gamma (P.1) and Zeta (P.2). In addition, we provide a preliminary genomic overview of the epidemic in Paraguay, showing evidence of importation from Brazil. These data reinforce the usefulness and need for the implementation of widespread genomic surveillance in South America as a toolkit for pandemic monitoring that provides a means to follow the real-time spread of emerging SARS-CoV-2 variants with possible implications for public health and immunization strategies.

Genomic epidemiology of the SARS-CoV-2 epidemic in Brazil

The high numbers of COVID-19 cases and deaths in Brazil have made Latin America an epicentre of the pandemic. SARS-CoV-2 established sustained transmission in Brazil early in the pandemic, but important gaps remain in our understanding of virus transmission dynamics at a national scale. We use 17,135 near-complete genomes sampled from 27 Brazilian states and bordering country Paraguay. From March to November 2020, we detected co-circulation of multiple viral lineages that were linked to multiple importations (predominantly from Europe). After November 2020, we detected large, local transmission clusters within the country. In the absence of effective restriction measures, the epidemic progressed, and in January 2021 there was emergence and onward spread, both within and abroad, of variants of concern and variants under monitoring, including Gamma (P.1) and Zeta (P.2). We also characterized a genomic overview of the epidemic in Paraguay and detected evidence of importation of SARS-CoV-2 ancestor lineages and variants of concern from Brazil. Our findings show that genomic surveillance in Brazil enabled assessment of the real-time spread of emerging SARS-CoV-2 variants.

Evaluation of alternative RNA extraction methods for detection of SARS-CoV-2 in nasopharyngeal samples using the recommended CDC primer-probe set.

Background: The efficiency of isolation and purification of the viral genome is a critical step to the accuracy and reliability of RT-qPCR to detect SARS-CoV-2. However, COVID-19 testing laboratories were overwhelmed by a surge in diagnostic demand that affected supply chains especially in low and middle-income facilities. Objectives: Thus, this study compares the performance of alternative methods to extraction and purification of viral RNA in samples of patients diagnosed with COVID-19. Study design: Nasopharyngeal swabs were submitted to three in-house protocols and three commercial methods; viral genome was detected using the primer-probe (N1 and N2) described by CDC and viral load of samples were determined. Results: The in-house protocols resulted in detection of virus in 82.4 to 86.3% of samples and commercial methods in 94.1 to 98%. The disagreement results were observed in samples with low viral load or below the estimated limit of detection of RT-qPCR. Conclusion: The simplified methods proposed might be less reliable for patients with low viral load and alternative commercial methods showed comparable performance.

An unusual presentation of disseminated histoplasmosis in a non-HIV patient from Vietnam.

BACKGROUND: Histoplasmosis is a systemic infection caused by the dimorphic fungus Histoplasma capsulatum, naturally found in nitrogen-rich soil, whose main transmission route is the inhalation of conidia. Up to 95% of histoplasmosis cases are asymptomatic or transient, and the remaining 5% of cases have pathological manifestations in the lungs, bone marrow, liver, spleen, intestine, mucous membranes, and rarely on the skin. This mycosis has been reported from many endemic areas, mainly in immunosuppressed patients, such as HIV-positive patients, and its disseminated form is rarely reported. CASE REPORT: Histoplama capsulatum was isolated and identified by means of microscopy, culture characteristics and nested PCR from the cutaneous lesions of a non-HIV patient from Vietnam. The patient improved significantly with systemic itraconazole treatment. CONCLUSIONS: Disseminated histoplasmosis with cutaneous involvement in non-HIV patients is an extremely unusual presentation.

Occurrence of Infected Free-Living Amoebae in Cooling Towers of Southern Brazil.

This study determined the occurrence of potentially pathogenic free-living amoebae (FLA) and bacteria associated with amoebae in air-conditioning cooling towers in southern Brazil. Water samples were collected from 36 cooling systems from air-conditioning in the state of Rio Grande do Sul, Brazil. The organisms were identified using polymerase chain reaction (PCR) and sequencing automated. The results showed that these aquatic environments, with variable temperature, are potential "hot spots" for emerging human pathogens like free-living amoebae and bacteria associated. In total, 92% of the cooling-tower samples analyzed were positive for FLA, and Acanthamoeba was the dominant genus by culture and PCR. Amoebal isolates revealed intracellular bacteria in 39.3% of them and all were confirmed as members of the genus Pseudomonas. The results obtained show the important role of cooling towers as a source of amoebae-associated pathogens.

Surveillance of impact of PCV-10 vaccine on pneumococcal meningitis in Mozambique, 2013 - 2015.

BACKGROUND: Vaccination using the 10-valent conjugate vaccine (PCV-10) was introduced into the Extended Program on Immunization in Mozambique in March 2013, however its impact on pediatric pneumococcal meningitis is unknown. In this study, we assessed for the first time the impact of PCV10 on the burden of pneumococcal meningitis in children less than 5 years of age at the three largest hospitals in Mozambique. METHOD: Between March 2013 and December 2015, a total of 744 cerebrospinal fluid (CSF) samples were collected from eligible children, of which 160 (21.5%) were positive for S. pneumoniae. Of these, only 86 samples met the criteria for serotyping and were subsequently serotyped using sequential multiplex PCR (SM-PCR), but 17 samples were non-typable. RESULTS: The proportion of cases of pneumococcal meningitis decreased from 33.6% (124 of 369) in 2013 to 1.9% (3 of 160) in 2015 (p < 0.001). The relative frequency of PCV10 serotype cases also decreased from 84.2% (48 of 57) in 2013 to 0% (0 of 3) in 2015 (p = 0.006). Between 2013 and 2015, serotype coverage of PCV-10 and PCV13 vaccine formulations was 66.7% and 81.2%, respectively. CONCLUSION: Altogether, our findings shows that introduction of PCV-10 immunization resulted in rapid decline of pneumococcal meningitis children less than 5 years old in Mozambique. This decline was accompanied by substantial changes in the pattern of circulating pneumococcal serotypes.

Serotype distribution and antimicrobial resistance of Streptococcus pneumoniae in children with acute bacterial meningitis in Mozambique: implications for a national immunization strategy.

BACKGROUND: S. pneumoniae is the leading cause of acute bacterial meningitis (ABM) in children. Vaccination using the 10-valent conjugate vaccine (PCV-10) was recently introduced into the National Immunization Program in Mozambique, but data on serotype coverage of this vaccine formulation are scarce. In this study, we investigated the serotype distribution and antimicrobial resistance of isolates of S. pneumoniae causing ABM in children < 5 years at the two largest hospitals in Mozambique. METHODS: Between March 2013 and March 2014, a total of 352 cerebrospinal fluid (CSF) samples were collected from eligible children, of which 119 (33.8 %) were positive for S. pneumoniae. Of these, only 50 samples met the criteria for serotyping and were subsequently serotyped using sequential multiplex PCR (SM-PCR), but 15 samples were non-typable. RESULTS: The most common serotypes of S. pneumoniae were 1 (18.2 %), 5 (15.2 %), 14 (12.1 %), 9 V (12.1 %), 23 F (9.1 %), 6A (9.1 %), 4 (9.1 %) and 6B (6.1 %). Serotypes 1, 5, 9 V, 6A and 12 were mostly prevalent in Northern Mozambique, while serotypes 23 F, 4, 6B, 3 and 15B were predominant in Southern. Serotype coverage of PCV-10 and PCV-13 vaccine formulations were 81.8 % and 93.9 %, respectively. Serotypes 1, 3, 4, 6B, 14, 23 F were resistant to penicillin and sensitive to ceftriaxone. CONCLUSIONS: Our findings shows that changing the current in use PCV-10 vaccine formulation to PCV-13 formulation might increase substantially the protection against invasive strains of S. pneumoniae as the PCV-10 vaccine formulation does not cover the serotypes 3 and 6A, which are prevalent in Mozambique.

Frequency of Pathogenic Paediatric Bacterial Meningitis in Mozambique: The Critical Role of Multiplex Real-Time Polymerase Chain Reaction to Estimate the Burden of Disease.

BACKGROUND: In Sub-Saharan Africa, including Mozambique, acute bacterial meningitis (ABM) represents a main cause of childhood mortality. The burden of ABM is seriously underestimated because of the poor performance of culture sampling, the primary method of ABM surveillance in the region. Low quality cerebrospinal fluid (CSF) samples and frequent consumption of antibiotics prior to sample collection lead to a high rate of false-negative results. To our knowledge, this study is the first to determine the frequency of ABM in Mozambique using real-time polymerase chain reaction (qPCR) and to compare results to those of culture sampling. METHOD: Between March 2013 and March 2014, CSF samples were collected at 3 regional hospitals from patients under 5 years of age, who met World Health Organization case definition criteria for ABM. Macroscopic examination, cytochemical study, culture, and qPCR were performed on all samples. RESULTS: A total of 369 CSF samples were collected from children clinically suspected of ABM. qPCR showed a significantly higher detection rate of ABM-causing pathogens when compared to culture (52.3% [193/369] versus 7.3% [27/369], p = 0.000). The frequency of Streptococcus pneumoniae, Haemophilus influenzae, group B Streptococci, and Neisseria meningitidis were 32.8% (121/369), 12.2%, (45/369), 3.0% (16/369) and 4.3% (11/369), respectively, significantly higher compared to that obtained on culture (p < 0.001 for each). CONCLUSION: Our findings demonstrate that culture is less effective for the diagnosis of ABM than qPCR. The common use of culture rather than qPCR to identify ABM results in serious underestimation of the burden of the disease, and our findings strongly suggest that qPCR should be incorporated into surveillance activities for ABM. In addition, our data showed that S. pneumoniae represents the most common cause of ABM in children under 5 years of age.

Performance of the Vitek 2 system software version 5.03 in the bacterial identification and antimicrobial susceptibility test: evaluation study of clinical and reference strains of Gram-positive cocci.

INTRODUCTION: The genera Enterococcus, Staphylococcus and Streptococcus are recognized as important Gram-positive human pathogens. The aim of this study was to evaluate the performance of Vitek 2 in identifying Gram-positive cocci and their antimicrobial susceptibilities. METHODS: One hundred four isolates were analyzed to determine the accuracy of the automated system for identifying the bacteria and their susceptibility to oxacillin and vancomycin. RESULTS: The system correctly identified 77.9% and 97.1% of the isolates at the species and genus levels, respectively. Additionally, 81.8% of the Vitek 2 results agreed with the known antimicrobial susceptibility profiles. CONCLUSION: Vitek 2 correctly identified the commonly isolated strains; however, the limitations of the method may lead to ambiguous findings.

MULTIPLEX SYBR® GREEN-REAL TIME PCR (qPCR) ASSAY FOR THE DETECTION AND DIFFERENTIATION OF Bartonella henselae AND Bartonella clarridgeiae IN CATS / PCR em Tempo Real (qPCR) multiplex utilizando SYBR® Green para a detecção e diferenciação de Bartonella henselae e Bartonella clarridgeiae em gatos

A novel SYBR® green-real time polymerase chain reaction (qPCR) was developed to detect two Bartonella species, B. henselae and B. clarridgeiae, directly from blood samples. The test was used in blood samples obtained from cats living in animal shelters in Southern Brazil. Results were compared with those obtained by conventional PCR targeting Bartonella spp. Among the 47 samples analyzed, eight were positive using the conventional PCR and 12 were positive using qPCR. Importantly, the new qPCR detected the presence of both B. henselae and B. clarridgeiae in two samples. The results show that the qPCR described here may be a reliable tool for the screening and differentiation of two important Bartonella species.

Um novo teste baseado na reação em cadeia da polimerase em tempo real (qPCR) com SYBR ® Green foi desenvolvido para detectar duas espécies de Bartonella, B. henselae e B. clarridgeiae, diretamente em amostras de sangue. Este teste foi utilizado em amostras de sangue obtidas de gatos que vivem em abrigos de animais do sul do Brasil. Os resultados foram comparados aos obtidos pelo PCR convencional utilizado para a detecção de Bartonella spp. Das 47 amostras analisadas, oito foram positivas no PCR convencional e 12 foram positivas para qPCR. A reação de qPCR, permitiu a detecção da presença simultânea de B. henselae e B. clarridgeiae em duas destas amostras. Os resultados mostram que a qPCR aqui descrita pode ser uma ferramenta confiável para a detecção e diferenciação de duas espécies importantes de Bartonella spp.

Multiplex SYBR® green-real time PCR (qPCR) assay for the detection and differentiation of Bartonella henselae and Bartonella clarridgeiae in cats.

A novel SYBR® green-real time polymerase chain reaction (qPCR) was developed to detect two Bartonella species, B. henselae and B. clarridgeiae, directly from blood samples. The test was used in blood samples obtained from cats living in animal shelters in Southern Brazil. Results were compared with those obtained by conventional PCR targeting Bartonella spp. Among the 47 samples analyzed, eight were positive using the conventional PCR and 12 were positive using qPCR. Importantly, the new qPCR detected the presence of both B. henselae and B. clarridgeiae in two samples. The results show that the qPCR described here may be a reliable tool for the screening and differentiation of two important Bartonella species.

Novel real-time PCR assays using TaqMan minor groove binder probes for identification of fecal carriage of Streptococcus bovis/Streptococcus equinus complex from rectal swab specimens.

Real-time PCR based on the recN and gyrB genes was developed to detect four Streptococcus bovis/Streptococcus equinus complex (SBEC) subspecies from rectal swab specimens. The overall prevalence was 35.2%: Streptococcus gallolyticus subsp. gallolyticus (11.1%), S. gallolyticus subsp. pasteurianus (13%), Streptococcus infantarius subsp. coli (20.4%), and S. infantarius subsp. infantarius (11.1%). To conclude, these real-time PCR assays provide a reliable molecular method to detect SBEC pathogenic subspecies from rectal swab specimens.