Predominance of ON1 and BA9 genotypes of human respiratory syncytial virus in children with acute respiratory infection in Chiang Mai, Thailand, 2020-2021.

BACKGROUND: Human respiratory syncytial virus (hRSV) is an important cause of acute respiratory infection, especially in children. Few studies have investigated molecular epidemiology of hRSV infection in Thailand. The aims of this study were to investigate the prevalence and genotype diversity of hRSV in children with acute respiratory infection (ARI) in Thailand. METHODS: A total of 383 nasopharyngeal swabs collected from children with ARI from October 2020 to September 2021 were screened for hRSV and nucleotide sequences of the hypervariable region 2 (HVR2) of G gene of the detected hRSV were analysed. RESULTS: Of 383 nasopharyngeal swabs, 104 (27.2 %) were positive for hRSV, of which 51 (49.0 %), 43 (41.3 %), and 10 (9.6 %) were hRSV-A, hRSV-B, and untypeable strains, respectively. All hRSV-A and hRSV-B were ON1 genotype and BA9 genotype, respectively. Most of the hRSV strains were detected in the cool months, November 2020 to February 2021. Phylogenetic analysis of the HVR2 sequence of G gene revealed three clusters of hRSV-A (ON1 genotype) and two clusters of hRSV-B (BA9 genotype). The hRSV-A strains in cluster 1 and 3 were closely related to the hRSV-A reference strains reported previously from other regions of Thailand whereas those in cluster 2 were closely related to the hRSV-A reference strains reported previously from Europe and Africa. For the hRSV-B strains, both clusters 1 and 2 were closely related to the hRSV-B reference strains reported previously from Europe, Australia, and Taiwan. The predicted N- and O-linked glycosylation sites were found along the length of HVR2 of G protein, mostly in the hRSV-B strains. CONCLUSIONS: The ON1 and BA9 were the only two hRSV genotypes that were co-predominant and solely detected in this study. The findings indicated that the ON1 and BA9 are the only two hRSV genotypes currently circulating in children with ARI in northern Thailand.

Highly specific and sensitive detection of Burkholderia pseudomallei genomic DNA by CRISPR-Cas12a.

Detection of Burkholderia pseudomallei, a causative bacterium for melioidosis, remains a challenging undertaking due to long assay time, laboratory requirements, and the lack of specificity and sensitivity of many current assays. In this study, we are presenting a novel method that circumvents those issues by utilizing CRISPR-Cas12a coupled with isothermal amplification to identify B. pseudomallei DNA from clinical isolates. Through in silico search for conserved CRISPR-Cas12a target sites, we engineered the CRISPR-Cas12a to contain a highly specific spacer to B. pseudomallei, named crBP34. The crBP34-based detection assay can detect as few as 40 copies of B. pseudomallei genomic DNA while discriminating against other tested common pathogens. When coupled with a lateral flow dipstick, the assay readout can be simply performed without the loss of sensitivity and does not require expensive equipment. This crBP34-based detection assay provides high sensitivity, specificity and simple detection method for B. pseudomallei DNA. Direct use of this assay on clinical samples may require further optimization as these samples are complexed with high level of human DNA.

Characterization of Erythromycin and Tetracycline Resistance Genes of Streptococcus gallolyticus Subspecies pasteurianus Strains Isolated from Patients with Septicemia and Bacteremia in Thailand.

BACKGROUND: Streptococcus gallolyticus subspecies (subsp.) pasteurianus, previously known as Streptococcus bovis biotype II/2, has been described as a causative agent of endocarditis, neonatal sepsis, meningitis, bacteremia, and colorectal carcinoma in humans. The aim of this study was to characterize the erythromycin and tetracycline resistance genes of S. gallolyticus subsp. pasteurianus strains isolated from patients with septicemia and bacteremia in Thailand. METHODS: The clinical isolates of Streptococcus gallolyticus were identified by using conventional biochemical tests, PCR, and sodA gene sequence analysis. The erythromycin and tetracycline susceptibilities were determined by disk diffusion and agar dilution methods, while the resistance genes were identified by nucleotide sequence analysis. RESULTS: From a total of 108 blood cultures, 36 (33%) were identified as S. gallolyticus subsp. pasteurianus with the nucleotide sequence identities of partial sodA gene with the reference strains ranging from 98.1 to 100%. Of these, 25 (69.4%) contained erythromycin resistance genes and erm(B) was the most predominant gene (30.6%), followed by erm(T) (19.4%) and mef(A) (5.6%). In addition, erm(B) was also detected in combination with lnu(B) (8.3%), erm(T) and mef(A) (2.8%), and mef(A) and lnu(B) (2.8%). It was interesting to note that lnu(B) was detected for the first time in S. gallolyticus subsp. pasteurianus in this study. For tetracycline resistance genes, tet(L) and tet(M) were detected at 13.9% and 11.1%, respectively. However, tet(M) in combination with tet(L) was detected most commonly at 69.4% and with tet(L) and tet(O) at 5.6%. CONCLUSIONS: A number of erythromycin and tetracycline resistance genes were detected in S. gallolyticus subsp. pasteurianus strains circulating in Thailand.

Detection of environmental sources of Histoplasma capsulatum in Chiang Mai, Thailand, by nested PCR.

Histoplasmosis is a systemic mycosis caused by inhaling spores of Histoplasma capsulatum, a dimorphic fungus. This fungus grows in soil contaminated with bat and avian excreta. Each year, patients with disseminated histoplasmosis have been diagnosed in Chiang Mai, northern Thailand. No published information is currently available on the environmental sources of this fungus in Chiang Mai or anywhere else in Thailand. The aim of this study was to detect H. capsulatum in soil samples contaminated with bat guano and avian droppings by nested PCR. Two hundred and sixty-five samples were collected from the following three sources: soil contaminated with bat guano, 88 samples; soil contaminated with bird droppings, 86 samples; and soil contaminated with chicken droppings, 91 samples. Genomic DNA was directly extracted from each sample, and H. capsulatum was detected by nested PCR using a primer set specific to a gene encoding 100-kDa-like protein (HcI, HcII and HcIII, HcIV). Histoplasma capsulatum was detected in seven of 88 soil samples contaminated with bat guano, one of 21 soil samples contaminated with pigeon droppings and 10 of 91 soil samples contaminated with chicken droppings. The results indicate the possibility of the association of bat guano and chicken droppings with H. capsulatum in this area of Thailand.

Molecular epidemiology of Rhodococcus equi of intermediate virulence isolated from patients with and without acquired immune deficiency syndrome in Chiang Mai, Thailand.

We investigated the prevalence of virulent Rhodococcus equi in clinical isolates from 69 sporadic cases (60 men, 8 women, and 1 patient of unknown sex) in Chiang Mai, Thailand, between 1993 and 2001. Fifty were human immunodeficiency virus (HIV) positive, 3 were HIV negative, and HIV status was unknown for 16. Fifty-two (75%) of 69 isolates were strains of intermediate virulence that contained the virulence-associated 20-kDa antigen, and 17 isolates (25%) were avirulent. No virulent strains with the virulence-associated 15-17-kDa antigens were identified. R. equi was isolated from HIV-positive patients' houses and those of their neighbors: avirulent strains were widespread, but only 1 strain of intermediate virulence was isolated. R. equi strains of intermediate virulence were isolated from 4 (0.8%) of 500 submaxillary lymph nodes from apparently healthy pigs in Chiang Mai. The routes of R. equi acquisition should be investigated from the viewpoint of zoonosis and public health.