Identification of Bacteria and Viruses Associated with Patients with Acute Febrile Illness in Khon Kaen Province, Thailand.

The majority of cases of undifferentiated acute febrile illness (AFI) in the tropics have an undefined etiology. In Thailand, AFI accounts for two-thirds of illnesses reported to the Ministry of Public Health. To characterize the bacterial and viral causes of these AFIs, we conducted molecular pathogen screening and serological analyses in patients who sought treatment in Chum Phae Hospital, Khon Kaen province, during the period from 2015 to 2016. Through integrated approaches, we successfully identified the etiology in 25.5% of cases, with dengue virus infection being the most common cause, noted in 17% of the study population, followed by scrub typhus in 3.8% and rickettsioses in 6.8%. Further investigations targeting viruses in patients revealed the presence of Guadeloupe mosquito virus (GMV) in four patients without other pathogen co-infections. The characterization of four complete genome sequences of GMV amplified from AFI patients showed a 93-97% nucleotide sequence identity with GMV previously reported in mosquitoes. Nucleotide substitutions resulted in amino acid differences between GMV amplified from AFI patients and mosquitoes, observed in 37 positions. However, these changes had undergone purifying selection pressure and potentially had a minimal impact on protein function. Our study suggests that the GMV strains identified in the AFI patients are relatively similar to those previously reported in mosquitoes, highlighting their potential role associated with febrile illness.

Identification of bacteria associated with canine otitis externa based on 16S rDNA high-throughput sequencing.

Bacteria are regarded as predisposing and perpetuating factors causing otitis externa (OE), whereas auricular anatomy is a predisposing factor. This study aims to investigate bacterial populations in the external auditory canals of healthy dogs and dogs with OE. Four categories of ear swabs included healthy erect-ear dogs, erect-ear dogs with OE, healthy pendulous-ear dogs and pendulous-ear dogs with OE. After bacterial DNA extraction, 16S rDNAs were amplified using specific primers within a V3/V4 region. Following DNA library construction, high-throughput sequencing was performed on MiSeq (Illumina). CLC Microbial Genomics Module was used to determine the rarefaction curve, bacterial classification, relative abundance, richness and diversity index. The results demonstrated that healthy dogs had higher bacterial richness and diversity than the dogs with OE. Comparable with culture-dependent methods described previously, this study revealed predominant Corynebacterium spp., Pseudomonas spp., Staphylococcus spp., and Proteus spp. in OE cases. Furthermore, high-throughput sequencing might disclose some potential emerging pathogens including Tissierella spp., Acinetobacter spp., and Achromobacter spp., which have not been reported in previous canine OE cases. Nevertheless, larger sample sizes are further required for an extensive evidence-based investigation.

Development of a simplified and cost-effective sample preparation method for genotyping of human papillomavirus by next-generation sequencing.

High-risk human papillomavirus (HPV) infection is the most common cause of cervical cancer, but low-risk HPV strains can sometimes also be involved. Although HPV genotyping techniques used in clinical diagnosis cannot detect low-risk HPV, next-generation sequencing (NGS) can detect both types. However, DNA library preparation is complicated and expensive. The aim of this study was to develop a simplified, cost-effective sample preparation procedure for HPV genotyping based on next-generation sequencing (NGS). After DNA extraction, a first round of PCR was performed using modified MY09/11 primers specific for the L1 region of the HPV genome, followed by a second round of PCR to add the indexes and adaptors. Then, the DNA libraries were purified and quantified, and high-throughput sequencing was performed using an Illumina MiSeq platform. The sequencing reads were compared with reference sequences for HPV genotyping. The limit of detection for HPV amplification was 100 copies/µl. Analysis of the correlation of pathological cytology with the HPV genotype in individual clinical samples showed that HPV66 was the most common genotype found in the normal stage, whereas HPV16 was the main genotype found in low-grade squamous intraepithelial lesions, high-grade squamous intraepithelial lesions, and cervical cancer. This NGS method can detect and identify several HPV genotypes with 92% accuracy and 100% reproducibility, and it shows potential as a simplified and cost-effective technique for large-scale HPV genotyping in clinical samples.

Classification of salivary bacteriome in asymptomatic COVID-19 cases based on long-read nanopore sequencing.

The coronavirus (COVID-19) global pandemic has impacted the health of almost everyone, including changes in their salivary microbiota. Since 2019, there has been an increase in the number of new COVID-19 cases in Thailand. Therefore, COVID-19 active case finding is important for early detection and epidemic control. Moreover, the dynamic changes of salivary bacteriome in asymptomatic COVID-19 cases are largely unknown. This research aimed to investigate and compare the salivary bacteriome and the co-infectious bacterial pathogens in the asymptomatic COVID-19 positive group to the negative group, based on novel nanopore sequencing. This cohort was a cross-sectional study including saliva samples collected from 82 asymptomatic participants (39 COVID-19 positive and 43 COVID-19 negative cases). All samples were sequenced for the full-length bacterial 16S rDNA. The alpha and beta diversity analyses were not significantly different between groups. The three major species in salivary bacteriome including Veillonella parvula, Streptococcus mitis, and Prevotella melaninogenica were observed in both groups. Interestingly, Lautropia mirabilis was a significantly enriched species in the saliva of the asymptomatic COVID-19-positive cases based on linear discriminant analysis effect size (LEfSe) analysis. The results suggested that L. mirabilis was a co-infectious agent in the asymptomatic COVID-19 group. However, the potential role of L. mirabilis should be validated in further experimental studies.

Genome Assembly and Genome Annotation of Leishmania martiniquensis Isolated from a Leishmaniasis Patient in Thailand.

Leishmaniasis is a parasitic disease caused by Leishmania spp. with worldwide distribution. Autochthonous leishmaniasis has been reported to result from the infection by Leishmania martiniquensis in Thailand. This species was isolated in culture and subjected to high-throughput whole-genome sequencing. A total of 30.8 Mb in 36 chromosomes of the whole genome was assembled, annotated, and characterized. The L. martiniquensis under study was shown to segregate into the same clade and thus closely related to the previously identified L. martiniquensis (LU_Lmar_1.0), as determined by phylogenetic analysis of their genomic sequences along with those of representative kinetoplastid species. The total number of open reading frames genomewide predicts 8,209 protein-coding genes, of which 359 are putative virulence factors, including two previously known, e.g., cysteine proteinase C and superoxide dismutase B1. The results obtained from this study will be useful for further annotation and comparison with other Leishmania martiniquensis in the future.

Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients.

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of clinical manifestations from asymptomatic, mild infections to severe illness involving organ failure. For better understanding the difference between Leptospira isolates causing mild and severe leptospirosis, illumina sequencing was used to sequence genomic DNA in both serotypes. DNA of Leptospira isolated from two patients, one with mild and another with severe symptoms, were included in this study. The paired-end reads were removed adapters and trimmed with Q30 score using Trimmomatic. Trimmed reads were constructed to contigs and scaffolds using SPAdes. Cross-contamination of scaffolds was evaluated by ContEst16s. Prokka tool for bacterial annotation was used to annotate sequences from both Leptospira isolates. Predicted amino acid sequences from Prokka were searched in EggNOG and David gene ontology database to characterize gene ontology. In addition, Leptospira from mild and severe patients, that passed the criteria e-value < 10e-5 from blastP against virulence factor database, were used to analyze with Venn diagram. From this study, we found 13 and 12 genes that were unique in the isolates from mild and severe patients, respectively. The 12 genes in the severe isolate might be virulence factor genes that affect disease severity. However, these genes should be validated in further study.

An investigation of antimicrobial and wound healing potential of Allium ascalonicum Linn.

BACKGROUND: The pharmacological properties of Allium ascalonicum Linn., commonly called shallot, have been reported as including those that are antibacterial and antioxidant. OBJECTIVE: The present study aimed to evaluate the antimicrobial effect and wound-healing activity ofthe ethanolic extracts of Allium ascalonicum Linn. (AAE). MATERIAL AND METHOD: The antimicrobial activity of AAE was tested in vitro against using the disc diffusion method and a broth micro-dilution technique to determine the minimal inhibition concentrations (MIC) and the minimal microbicidal concentrations (MMC). Wound-healing activity of the extract was performed on rat test subjects. RESULTS: The AAE showed potential antimicrobial activity by inhibiting gram-positive bacteria Staphylococcus epidermidis and Bacillus subtilis ATCC 6633. MIC and MMC varied from 25-50 mg/ml and 25-200 mg/ml, respectively. After surgery 14 days, wound contractions oftreated groups and standard group were 78.61 +/- 1.20%, 78.55 +/- 1.93% and 100%, respectively; but, in the control group, wound contraction was 64.90 +/- 3.55%. Histological studies showed the complete epidermis and found the collagen fibers and fibroblasts as similar appearance as standard group in dermis. The results of histological evaluation have confirmed remarkable wound-healing activities of AAE. CONCLUSION: Taken together the present study provides evidence that AAE extract processes antimicrobial and wound-healing activities.

Antioxidant, antimicrobial and wound healing activities of Boesenbergia rotunda.

The ethanolic extract of Boesenbergia rotunda (L.) Mansf was studied for its wound-healing potential. Since wound healing is interrelated with microbial infection and reactive oxygen species (ROS), this study was conducted to evaluate the antimicrobial and antioxidant activity of B. rotunda. The antimicrobial activity of B. rotunda was studied against six bacterial and two yeast strains using disc diffusion, minimum inhibitory concentration (MIC), and minimum microbicidal concentration (MMC). The B. rotunda extract displayed potential antimicrobial and antifungal activities by inhibiting the Gram-positive bacteria Staphylococcus aureus (ATCC 25923), S. epidermidis, and Bacillus subtilis (ATCC 6633), and the yeasts Candida albicans (ATCC 10231), and Saccharomyces cerevisiae. MIC and MMC values varied from 0.04 to 25 mg/mL and from 0.16 to 25 mg/mL, respectively. The antioxidant activity of B. rotunda was evaluated by measuring the Ferric Reducing/Antioxidant Power (FRAP) and DPPH free radical scavenging activity. The FRAP and DPPH values were 22.2 microM/microg and 76.3 mg/mL, respectively. In the wound-healing studies, the topical application of the B. rotunda extract indicated a significantly increased percentage of wound contraction on day 12 compared with the control group. Histological studies showed the complete epidermis and found collagen fibers and hair follicles in the dermis. The results of the present study support the continued and expanded utilization of B. rotunda in Thai folk medicine.

Functional characterization of a masquerade-like serine proteinase homologue from the black tiger shrimp Penaeus monodon.

A cDNA encoding a masquerade-like serine proteinase homologue (PmMasSPH) from the black tiger shrimp, Penaeus monodon, has been cloned and characterized. The transcript of PmMasSPH is induced in response to Vibrio harveyi infection. To further characterize the function(s) of the protein, (i) the N-terminal region comprising the glycine-rich repeats and the clip domain, and (ii) the C-terminal SP-like domain of the PmMasSPH were separately cloned into the pET-28b(+) expression vector and transformed into Escherichia coli Rosetta (DE3). The two recombinant proteins were then assayed for various biological functions; proteinase activity, hemocyte adhesion, bacterial binding, bacterial clearance and antimicrobial activity. The C-terminal SP-like domain lacks proteolytic activity but mediates hemocyte adhesion and displays binding activity to the shrimp pathogenic bacterium, V. harveyi and specific binding to the bacterial cell wall component, lipopolysaccharide (LPS). The N-terminal region exhibited in vitro antimicrobial activity against Gram-positive bacteria. In addition, the in vivo study revealed the opsonic activity of the PmMasSPH protein as shown by a higher bacterial clearance rate of V. harveyi coated with the recombinant proteins as compared with V. harveyi only. The results suggest that the PmMasSPH protein is a multifunctional immune molecule in shrimp defense.

Molecular cloning, characterization and expression of a masquerade-like serine proteinase homologue from black tiger shrimp Penaeus monodon.

A full-length cDNA of a masquerade-like serine proteinase homologue (PmMasSPH) of Penaeus monodon was cloned and characterized by rapid amplification cDNA end (RACE) method. The complete cDNA sequence of 1958bp contains an open reading frame (ORF) of 1572bp, encoding a 523 amino acid protein including a 19 amino acid signal peptide. The calculated molecular mass of the mature protein (504 amino acids) is 51.58kDa with an estimated pI of 4.86. PmMasSPH has most of the structural characteristics of insect prophenoloxidase activating factors (PPAFs) (the N-terminal clip domain and the C-terminal serine proteinase-like domain) but in the N-terminal region there are extensive glycine-rich repeats (LGGQGGG). Sequence comparison showed that the deduced amino acid of PmMasSPH has an overall similarity of 69%, 68% and 61% to those of Apis mellifera PPAF, Callinectes sapidus PPAF and Tenebrio molitor PPAF, respectively. A neighbour-joining tree revealed a clear differentiation of each species and also indicated that PmMasSPH and C. sapidus PPAF are closely related phylogenetically. In situ hybridisation and real-time RT-PCR analyses showed that PmMasSPH transcript in haemocytes of P. monodon increased within 24h after Vibrio harveyi injection.