Salmonella enterica remains a leading cause of food-borne diseases worldwide. Serotype information is important in food safety and public health activities to reduce the burden of salmonellosis. In ...the current study, two methods were used to determine serotypes of 111 strains of Salmonella isolated from poultry feces in Burkina Faso. First, Salmonella Multiplex Assay for Rapid Typing (SMART) Polymerase Chain Reaction (PCR) was used to determine the serovars of the S. enterica isolates. Second, serovar prediction based on whole genome sequencing (WGS) data was performed using SeqSero 2.0.
Among the 111 Salmonella isolates, serotypes for 17 (15.31%) isolates were identified based on comparison to a panel of representative SMART codes previously determined for the 50 most common serovars in the United States. Forty-four (44) new SMART codes were developed for common and uncommon serotypes. A total of 105 (94.59%) isolates were serotyped using SeqSero 2.0 for serovar prediction based on WGS data.
We determined that SeqSero 2.0 was more comprehensive for identifying Salmonella serotypes from Burkina Faso than SMART PCR.
Introduction Non-perennial rivers and streams are increasingly present, in part because of climate change, even in the temperate climate. However, how the loss of connectivity and complete drying ...affect microphytobenthos in general and diatom communities in particular has gone mostly unstudied. Methods With this paper, we aim to close this gap, identifying diatom biodiversity through manual digital microscopy and rbcL amplicon sequencing, to observe a) which method is better suited to it and b) how the ecotone flow-pool-dry affects diatom diversity under duress. Three karstic, non-perennial rivers and streams with a gradient from natural to anthropogenically disturbed were sampled under flooding conditions and after a long and intense drought in 2022. Results Our results show that digital microscopy shows a higher diversity and species richness than amplicon sequencing. We posit that this might be due to a reduced pool of subaerophile taxa having been sequenced and being part of the reference database. Furthermore, the effect of drying only resulted in a reduction in diversity after this drought, although the biofilm was still alive under these conditions. Discussion To use amplicon sequencing for non-perennial river diatom diversity monitoring, the reference databases will have to be adapted to such systems, as most rivers may be subjected to drying regularly in the future.
An early and accurate diagnosis followed by prompt treatment is pre-requisite for the management of any disease. Malaria diagnosis is routinely performed by microscopy and rapid diagnostic tests ...(RDTs) in the field settings; however, their performance may vary across regions, age and asymptomatic status. Owing to this, we assessed the diagnostic performance of conventional and advanced molecular tools for malaria detection in low and high malaria-endemic settings. We performed mass blood surveys in low and high endemic regions of two North-Eastern districts from the states of Assam and Meghalaya. A total of 3322 individuals were screened for malaria using RDT, microscopy and PCR and measures of diagnostic accuracy were estimated. Out of 3322 individuals, 649 (19.5%) were detected with malaria parasite. Asymptomatic were 86.4% (2872/3322), of which 19.4% (557/2872) had
Plasmodium
infection. The sensitivity and specificity of microscopy were 42.7% and 99.3%, and RDT showed 49.9% and 90.4%, respectively, considering PCR as standard. RDT (AUC: 0.65 vs 0.74;
p
= 0.001) and microscopy (AUC: 0.64 vs 0.76;
p
< 0.0001) performances were significantly lower in low compared to high endemic areas. True positive rate was lower in asymptomatics but true negative rate was found similar to symptomatic individuals. The conventional diagnostic tools (RDT and microscopy) had detected malaria in children with nearly twofold greater sensitivity than in the adults (
p
< 0.05). To conclude, asymptomatics, adults and low malaria-endemic regions require major attention due to mediocre performance of conventional diagnostic tools in malaria detection.
Leishmaniasis is one of the most common vector-borne parasitic diseases in Iran.
Leishmania
species identification is necessary for epidemiological aspects, precise prognosis, control and treatment ...of the disease. We systematically searched all the studies, reports, and documentation related to species identification and geographical distribution of causative agents of cutaneous (CL), mucosal (ML), and visceral leishmaniasis (VL) using DNA-based molecular diagnostic techniques in Iran. International databases including PubMed, ScienceDirect, Embase, Google Scholar, Scopus, and Web of Science were systemically searched for English articles and Iran's databases including SID, IranMedex and Magiran were searched for Persian reports and articles. Searches were performed from 1999 to 2019 (20 years). The current review was conducted using the keywords: cutaneous leishmaniasis, visceral leishmaniasis,
Leishmania
species, Human, Molecular, PCR, and Iran. The study quality was evaluated using the NOS checklist. This meta-analysis procedure was accomplished using STATA, version 2.7.9. Of the 3,426 records identified in the initial search, 154 articles met inclusion criteria and qualified for the systematic review and meta-analysis. In subgroup analysis, the pooled frequency of causative agents of CL isolates was 67.3% (95% CI: 59.51–74.67%) for
L. major
and 32.1% (95% CI: 24.72–39.87%) for
L. tropica
. In addition, the pooled frequency of causative agents of VL isolates was 97.1% (95% CI: 94.6–98.8%) for
L. infantum
and 2.9% (95% CI: 1.12–5.37%) for
L. tropica
. The findings of this study showed that the main causative agents of CL and VL in Iran are
L. major
and
L. infantum
, respectively. Moreover, kinetoplast DNA (kDNA) and internal transcriber spacer (ITS) were the most used markers for identifying
Leishmania
species. The current study provides valuable data to encourage and direct researchers as well as public health managers in the comprehensive leishmaniasis control and prevention planning in Iran.
Valid data on prenatal cell-free DNA-based screening tests for copy number variations and microdeletions are still insufficient. We aimed to compare different methodological approaches concerning the ...achieved diagnostic accuracy measurements and positive predictive values. For this systematic review, we searched the Scopus and PubMed databases and backward citations for studies published between 2013 and 4 February 2022 and included articles reporting the analytical and clinical performance of cfDNA screening tests for CNVs and microdeletions. Of the 1810 articles identified, 32 met the criteria. The reported sensitivity of the applied tests ranged from 20% to 100%, the specificity from 81.62% to 100%, and the PPV from 3% to 100% for cases with diagnostic or clinical follow-up information. No confirmatory analysis was available in the majority of cases with negative screening results, and, therefore, the NPVs could not be determined. NIPT for CNVs and microdeletions should be used with caution and any developments regarding new technologies should undergo strict evaluation before their implementation into clinical practice. Indications for testing should be in correlation with the application guidelines issued by international organizations in the field of prenatal diagnostics.
Environmental matrices and food products are hypothesized to be sources of Cronobacter spp. The severity of neonatal infections, increasing number of cases in elderly and immunocompromised ...individuals, as well as isolation of Cronobacter spp. from clinical materials demands that more attention should be paid to Cronobacter spp. detection and occurrence of the bacteria in food products. Here, a total of 175 samples of ready‐to‐eat vegetables, frozen vegetables, and sprouted seeds were collected during a period of 1 year and examined for the presence of Cronobacter spp. using a cultivation method with two different sample preparations and real‐time polymerase chain reaction (qPCR). In total, Cronobacter spp. were detected in 22.3% of tested samples using cultivation. In comparison, direct qPCR detected Cronobacter spp. in 37.7% of these samples (p < 0.01; Fisher's exact test) and the numbers of genome equivalents per gram reached 108 in some samples of sprouts. Cronobacter spp. were isolated from 51.4%, 37.2%, and 5.2% samples of sprouts, frozen vegetables, and cut green leaves/salads, respectively. Using qPCR, the most frequently contaminated sample types were sprouts (91.4%) and frozen vegetables (60.5%), whereas the rate of positivity for cut green leaves/salads was, in comparison, only 8.2% (p < 0.01; χ2‐test for independence).
Practical Application
This study provided valuable information on the occurrence of Cronobacter spp. in ready‐to‐eat vegetables using cultivation and qPCR. Cronobacter spp. are emerging opportunistic pathogens that can be present in food of plant origin. Cronobacter spp. were isolated from sprouts, frozen vegetables, and cut green leaves/salads, and the numbers of genome equivalents per gram reached 108 in some samples of sprouts.
BACKGROUND: Early treatment is critical to reducing tuberculous meningitis (TBM) related morbidity and mortality. Diagnosis based on cerebrospinal fluid (CSF) culture is impractical due to slow ...turnaround times, while microscopy has poor sensitivity. Enhanced detection methods are essential
to guide early treatment initiation, especially in vulnerable young children.METHODS: We assessed the diagnostic accuracy of the GenoType® MTBDRplus and Xpert® MTB/RIF assays on CSF collected from paediatric meningitis suspects prospectively enrolled
at Tygerberg Hospital, Cape Town, South Africa. Fluorescent auramine-O microscopy, liquid culture for Mycobacterium tuberculosis, GenoType and Xpert assays were performed on all CSF samples.RESULTS: Of 101 meningitis suspects, 55 were diagnosed with TBM and 46 served as non-TBM
controls. Using a pre-defined TBM case definition as reference standard, sensitivities and specificities were 4% and 100% for fluorescent microscopy, 22% and 100% for culture, 33% and 98% for GenoType, 26% and 100% for Xpert, 22% and 100% for microscopy and culture combined and 49% and 98%
for GenoType and Xpert combined. Culture, GenoType and Xpert combined performed best, with 56% sensitivity and 98% specificity.CONCLUSION: Although commercial nucleic-acid amplification tests performed on CSF revealed incrementally improved diagnostic accuracy, providing rapid microbiological confirmation, they cannot serve as a rule-out test.
This study aimed to reveal the genetic diversity and phylogenetic relationship between intra- and inter-breeds of Zavot cattle raised locally in and around Kars province, Türkiye. A total of 209 ...Zavot (ZAV)
n
= 49, Eastern Anatolian Red (EAR)
n
= 40, Simmental (SIM)
n
= 40, Brown-Swiss (BS)
n
= 40, and Holstein (HOLS)
n
= 40 non-related cattle without any clinical health problems were evaluated. Using the standard phenol–chloroform method, deoxyribonucleic acid (DNA) was isolated from blood samples and amplified by multiplex polymerase chain reaction (PCR) using 19 bovine-specific microsatellite markers. A capillary electrophoresis process was applied to the denatured PCR products. A total of 274 different alleles were identified, with an average of 10.29 and an average of effective alleles of 5.38. According to the genetic distance matrix between populations, the largest genetic distance was found between ZAV-HOLS (0.358) populations, while ZAV-EAR populations were located at the same roots. The largest
F
ST
value (0.072) was found among ZAV-HOLS populations. According to the factorial correspondence analysis (FCA) graph, each population was located separately but also showed a mixture, especially the ZAV, EAR, and BS populations. The average polymorphism information content (PIC) values were the lowest (0.44) for the BM2113 marker and the highest (0.92) for the TGLA53 marker. In conclusion, ZAV cattle bred in the Kars region were found to be completely separate from the BS and SIM breeds which were claimed to have contributed to the formation of the ZAV breed. Since currently the native breeds, which are symbolic of the region, inbreeding cannot be prevented, an increase in studies devoted to the protection of these breeds and the establishment of pure herds will be useful for the future of native cattle in Türkiye.
•This is the first report of ddPCR assays for Babesia microti and B. duncani.•The B. microti assay detected parasitemia as early as 3 days of hamster infection.•The assays were 100% specific when ...compared with other blood-borne pathogens.•ddPCR may become a useful tool in the diagnosis of Babesia in human blood.
Babesia spp. are obligate protozoan parasites of red blood cells. Transmission to humans occurs through bites from infected ticks or blood transfusion. Infections with B. microti account for the majority of the reported cases of human babesiosis in the USA. A lower incidence is caused by the more recently described species B. duncani. The current gold standard for detection of Babesia is microscopic examination of blood smears. Recent PCR-based assays, including real-time PCR, have been developed for B. microti. On the other hand, molecular assays that detect and distinguish between B. microti and B. duncani infections are lacking. Closely related species of Babesia can be differentiated due to sequence variation within the internal transcribed spacer (ITS) regions of nuclear ribosomal RNAs. In the present study, we targeted the ITS regions of B. microti and B. duncani to develop sensitive and species-specific droplet digital PCR (ddPCR) assays. The assays were shown to discriminate B. microti from B. duncani and resulted in limits of detection of ~10 gene copies. Moreover, ddPCR for these species were useful in DNA extracted from blood of experimentally infected hamsters, detecting infections of low parasitemia that were negative by microscopic examination. In summary, we have developed sensitive and specific quantitative ddPCR assays for the detection of B. microti and B. duncani in blood. Our methods could be used as sensitive approaches to monitor the progression of parasitemia in rodent models of infection as well as serve as suitable molecular tests in blood screening.
The co-infection of different influenza A virus enable viral gene re-assortments especially in pigs that serve as mixing vessel with the possibility of emergence of novel subtypes. Such re-assortants ...pose serious public health threat, as epitomised by the emergence of pandemic influenza in 2009. In Nigeria, there is mixture of animal species and highly populated densities that can increase the risk of influenza virus endemicity, genetic reshuffling and emergence of future pandemic influenza viruses. Thus, this study was aimed at determining influenza virus disease burden in pigs. This study was a cross sectional molecular surveillance of influenza virus. A total of 194 pig nasal samples from reported cases and randomly sampled were collected from pig farms in Ojo and Ikorodu in Lagos State between October, 2015 and April, 2016. The samples were investigated for the presence of influenza virus matrix gene by Reverse Transcriptase Polymerase Chain Reaction and detected by gel electrophoresis. P-values were calculated using Chi-square and Fisher’s exact tests. The result showed that 25 (12.9%) samples were positive for influenza A virus, out of which, 20 (80%) were samples from Ojo while 5 (20%) were samples from Ikorodu. Epidemiological parameters for the sampled locations, methods either as reported case or randomised, and sex compared were significant at 95% confidence interval. This study determined influenza viral burden in pigs with a molecular prevalence of 12.9% to influenza A. It further confirmed the sub-clinical and clinical circulation of Influenza A virus in pigs in Ojo and Ikorodu in Lagos. Therefore, the detection of influenza A virus in commercial pigs in Nigeria accentuates the importance of continuous surveillance and monitoring of the virus in order to prevent the advent of virulent strains that may spread to Pig-handlers and the community at large.
PDF
