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Cheng-Hsun Chiu

Publications and source records attributed to Cheng-Hsun Chiu.

At least 19 recordsLinked to original sources
PubMed2026

Monitoring kinetic changes and restriction of influenza A virus RNA species during infection using a Flu-Stranded CRISPR platform.

UNLABELLED: Influenza A virus (IAV) generates three closely related RNA species: viral RNA (vRNA), complementary RNA (cRNA), and messenger RNA (mRNA), whose strand-specific quantification remains limited by sensitivity and quantitative dynamic range, particularly at low RNA abundance. Here, we developed Flu-Stranded CRISPR-Cas12a, a strand-specific detection platform integrating tagged reverse transcription, segment-specific PCR, and Cas12a collateral cleavage to support quantitative analysis of all three RNA species across a broad dynamic range. The assay enables reliable detection down to 102 copies per reaction, extending the lower quantitative boundary relative to both SYBR Green and TaqMan reverse transcription quantitative PCR (RT-qPCR) under matched conditions. Validated in infected cell lines, murine lung tissues, and clinical nasopharyngeal specimens, the platform enabled subtype-discriminating, strand-resolved detection, including samples near or below the quantitative range of SYBR Green RT-qPCR. Using finely resolved infection time-course analyses in NP and NA segments, we identified a reproducible early vRNA decline within the early post-infection phase. This decline was partially attenuated in RIG-I knockout A549 cells, while subsequent vRNA accumulation was enhanced, consistent with a modulatory rather than essential role for RIG-I in early viral RNA dynamics. Subcellular fractionation localized this decline to cytoplasmic incoming genomes. In contrast, importazole-mediated inhibition of nuclear import abolished vRNA recovery without affecting the early decline, indicating that nuclear entry functionally separates early genome reduction from subsequent productive replication. These findings establish Flu-Stranded CRISPR-Cas12a as a strand-resolved framework for monitoring IAV RNA dynamics and reveal an early window of genome vulnerability during cytoplasmic transit that shapes infection outcome. IMPORTANCE: The early fate of incoming influenza virus genomes remains unclear, limiting our understanding of how infection is established or aborted in host cells. We developed Flu-Stranded CRISPR-Cas12a, a strand-specific platform for sensitive and quantitative analysis of influenza viral RNA (vRNA), complementary RNA (cRNA), and messenger RNA (mRNA) across experimental and clinical samples. Using high-resolution time-course analysis, we identified a reproducible early decline in vRNA during the post-entry phase. Our data suggest that this early genome loss arises from multiple processes, with RIG-I acting as a modulatory factor rather than a primary driver. Subcellular fractionation localized this effect to cytoplasmic incoming genomes, whereas importin-β-mediated nuclear entry was required for subsequent vRNA recovery. These findings support a model of an early cytoplasmic phase of genome attrition that is distinct from replication and provide a framework for understanding early influenza RNA kinetics and for guiding strand-resolved diagnostics and antiviral evaluation.

CRISPR-Cas12a↗
PubMed2026

Long-read transcriptomics corrects Trichomonas vaginalis intron annotations and refines transcript-end features.

BACKGROUND: Trichomonas vaginalis causes the most prevalent non-viral sexually transmitted infection worldwide. Despite its large genome (181.5 Mb; 36,310 predicted protein-coding genes in NYU_TvagG3_2), intron annotations remain limited and inconsistently validated. A recent short-read RNA-seq study reported 63 putative active introns, but short reads can misassign splice boundaries and cannot resolve complete transcript structures. METHODS: We integrated Oxford Nanopore direct RNA sequencing (DRS), ONT cDNA long-read sequencing, and Illumina RNA-seq to refine intron annotations, transcript-end features, and UTR boundaries in T. vaginalis. Candidate introns were validated by targeted PCR and Sanger sequencing, and representative splicing events were further assessed using public SRA datasets. RESULTS: Starting from 31 historically annotated introns, motif-guided long-read screening and orthogonal validation identified 17 additional validated introns, increasing the curated set to 48 confirmed introns. Among these 17 events, three were previously unrecognized in the current NYU_TvagG3_2 reference annotation. We also corrected five reported loci, including two false-positive introns, two splice-coordinate misannotations, and one gene-sequence error. DRS further supported transcript termination site mapping, UAAA polyadenylation-signal profiling relative to poly(A) addition sites, and single-molecule poly(A)-tail estimation. StringTie mixed-mode assemblies provided updated UTR boundaries for intron-bearing transcripts and transcripts without curated introns. CONCLUSIONS: This study provides a rigorously validated, long-read-refined resource of intron annotations, UTR boundaries, and UAAA-guided transcript-end features for T. vaginalis, together with a reproducible workflow for non-model protists. These refinements improve the current reference annotation and support future studies of functional genomics, parasite biology, pathogenesis, and diagnostic development.

Trichomonas vaginalis↗
PubMed2025

Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing Streptococcus anginosus.

Streptococcus anginosus is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by S. anginosus are similar to those caused by Streptococcus pyogenes, S. anginosus lacks most of the well-characterized virulence factors of S. pyogenes. To investigate the pathogenicity of S. anginosus, we analysed the genome of a newly identified S. anginosus strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 S. anginosus strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H2O2 production was upregulated, which could optimize the competitiveness of S. anginosus in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that S. anginosus can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.

Streptococcus anginosus↗
PubMed2007

Draft genome sequence of the sexually transmitted pathogen Trichomonas vaginalis.

We describe the genome sequence of the protist Trichomonas vaginalis, a sexually transmitted human pathogen. Repeats and transposable elements comprise about two-thirds of the approximately 160-megabase genome, reflecting a recent massive expansion of genetic material. This expansion, in conjunction with the shaping of metabolic pathways that likely transpired through lateral gene transfer from bacteria, and amplification of specific gene families implicated in pathogenesis and phagocytosis of host proteins may exemplify adaptations of the parasite during its transition to a urogenital environment. The genome sequence predicts previously unknown functions for the hydrogenosome, which support a common evolutionary origin of this unusual organelle with mitochondria.

Animals↗
PubMed2007

Seroprevalence of human papillomavirus types 16 and 18 in the general population in Taiwan: implication for optimal age of human papillomavirus vaccination.

BACKGROUND: The optimal age for administration of recently approved prophylactic human papillomavirus (HPV) vaccines remains undetermined. OBJECTIVES: The aim of the study was to explore the age-specific seroprevalence of HPV 16 and 18 in the general population to design an HPV vaccination campaign for Taiwan. STUDY DESIGN: HPV seroprevalence was assessed by virus-like particle (VLP)-based ELISA in 1702 plasma samples collected in 1999. RESULTS: The sample population consisted of 1000 (58.8%) females and 702 (41.2%) males; age ranged from 17 days to 86 years. The age-specific distributions reveal a significant rise in HPV 16 seropositivity commencing at 19-25 years of age and peaking at >60 years. The trend of seropositivity increase with age was also highly significant for HPV 18 (P(Trend)<0.0001). Males had lower overall seroprevalence in gender comparison (7.6% versus 3.85% for HPV 16, 3.9% versus 2.71% for HPV 18), were older at seroconversion (19-25 years versus 26-30 years) with a more obvious seropositivity nadir in middle age. CONCLUSION: The age-specific seroprevalence of HPV 16 and 18 increases in young adults after the age of 18 years, with gender distribution varying. We conclude that the optimal age for universal HPV vaccination in Taiwan is 15 years or below.

Adolescent↗
PubMed2006

Salmonella enterica serotype Choleraesuis infections in pediatric patients.

OBJECTIVE: Among >2500 nontyphoid Salmonella serotypes, Salmonella enterica serotype Choleraesuis shows a high predilection to cause systemic infections in humans. The objective of this study was to delineate the clinical and microbiologic features of pediatric patients with Salmonella Choleraesuis infections. METHODS: Between May 1999 and February 2003, a total of 33 patients who were <18 years of age had culture-confirmed S Choleraesuis infections. Clinical features, laboratory values, treatment, outcome, and antimicrobial susceptibility patterns of the bacterial isolates were analyzed. RESULTS: There were 24 males and 9 females with a mean age of 3 years. Fever (rectal temperature > or =38 degrees C; 94%) was the most common clinical presentation. Sixteen (52%) had fever lasting >5 days before admission. Only 18 (54%) patients had diarrhea. The most common mode of infection is occult bacteremia without focal infection. Compared with data obtained from adult patients, the gastrointestinal manifestations appeared more frequently seen in pediatric patients. However, among the 18 who presented with diarrhea, 14 had concomitant bloodstream infection. Only 1 patient, who was a case of acute leukemia, died of S Choleraesuis sepsis. Resistance to ceftriaxone, ciprofloxacin, ampicillin, trimethoprim-sulfamethoxazole, and chloramphenicol was found in 6%, 28%, 88%, 76%, and 83% of the isolates, respectively. CONCLUSION: Children with S Choleraesuis infections usually presented with occult bacteremia with mild gastrointestinal involvement. The mortality of S Choleraesuis infections in previously healthy children is low. Ciprofloxacin resistance among S Choleraesuis isolates from pediatric patients was lower than that of isolates from adult patients. In view of the high rate of multidrug resistance, third-generation cephalosporins seem to be the drug of choice for treatment of invasive S Choleraesuis infections.

Adolescent↗
PubMed2006

Protection of neonatal mice from lethal enterovirus 71 infection by maternal immunization with attenuated Salmonella enterica serovar Typhimurium expressing VP1 of enterovirus 71.

This study describes the potential use of attenuated Salmonella enterica serovar Typhimurium strains to express and deliver VP1 of enterovirus 71 (EV71) as a vaccination strategy to prevent EV71 infection in mice. When orally administered to BALB/c mice, both attenuated carrier strains, CNP101 and SL7207, were able to efficiently invade livers and spleens, while only the virulence plasmid-carrying strain SL7207 persisted for more than 30 days in these organs. A recombinant in vivo-regulated promoter expression plasmid expressing VP1 antigen of EV71 was constructed. The expression of the VP1, directed by the pagC promoter, in attenuated Salmonella was confirmed by Western blot hybridization. Both humoral and cellular immune responses were elicited in mice by oral immunization with such Salmonella-based VP1 vaccines. We evaluated the protective efficacy of the vaccines in mice using a maternal immunization protocol. With a lethal challenge, ICR newborn mice born to dams immunized with Salmonella-based VP1 vaccine showed a 50-60% survival; in contrast, none of the mice in the control group survived the challenge. Our data indicated that Salmonella-based VP1 subunit vaccines are a promising vaccine strategy in the prevention of EV71 infection.

Animals↗
PubMed2006

Evolution of the virulence plasmids of non-typhoid Salmonella and its association with antimicrobial resistance.

Among more than 2,500 serovars, eight contain a virulence plasmid, including medically important Salmonella enterica serovars Choleraesuis, Dublin, Enteritidis, and Typhimurium. These serovar-specific virulence plasmids vary in size, but all contain the spv operon, which plays a role in the expression of the virulence. Genetically, these virulence plasmids are likely derived from a common ancestral plasmid possessing virulence-related genes and loci. Based on the analysis of the available DNA sequences of the plasmids, the phylogenetic path may be split into two: pSPV (virulence plasmid of S. Gallinarum-Pullorum) acquires an incompatibility-related locus that differs from that of the others. At some point, pSCV (virulence plasmid of S. Choleraesuis) and pSDV (virulence plasmid of S. Dublin) lose oriT by recombination or simply by deletion, making the two unable to be mobilized. On the other hand, pSEV (virulence plasmid of S. Enteritidis) also loses some DNA by deletion but not as extensively as pSCV, and therefore pSEV is closest to pSTV (virulence plasmid of S. Typhimurium) both genetically and biologically. The pSTV shows the least alternation during the evolution. There are two types of pSDV. pSDVu recombines with non-virulence 36.6-kb plasmid to acquire additional incompatibility trait to form pSDVr. Recent reports indicated that S. Choleraesuis and S. Typhimurium could generate different types of hybrid plasmids, which consisted of the serovar-specific virulence plasmid and an array of resistance gene cassettes. The recombination gives Salmonella a survival advantage in an unfavorable drug environment. The integration of resistance genes and additional replicons into a Salmonella virulence plasmid constitutes a new and interesting example of plasmid evolution and poses a serious threat to public health.

Animals↗
PubMed2006

Hemolytic uremic syndrome associated with pneumococcal pneumonia in Taiwan.

Streptococcus pneumoniae ( S. pneumoniae ) has been associated with hemolytic uremic syndrome (HUS), which is an unusual but serious disease in childhood. We conducted a retrospective review of children aged less than 18 years with S. pneumoniae -associated HUS in northern Taiwan from January 2000 to June 2005. The demographic characters, clinical courses, and outcomes were analyzed. Seven children (three girls, four boys) with S. pneumoniae -associated HUS were studied. The median age at onset of HUS was 40 months (range: 25-60 months). The median duration of hospital stay was 36 days (range: 15-50 days). The interval between the onset of illness attributable to S. pneumoniae and the development of HUS was around 1-2 weeks. The onset of oliguria developed within 2 weeks after illness. Six patients required dialysis with median duration of 16 days. Three patients had leukopenia as the initial presentation. All seven patients had pneumococcal pneumonia complicating with empyema, and two of them received decortication via video-assisted thoracoscopic surgery. Between patients who needed dialysis or not, there was no significant difference in age, sex, duration of thrombocytopenia, incidence of extra-renal complications, such as hepatitis, pancreatitis, and hypertension, and length of hospital stay. The seven patients survived with normal renal function. HUS is a potentially fatal complication of S. pneumoniae infection. Clinicians managing patients with pneumococcal pneumonia with empyema accompanied by leukopenia should beware of the development of HUS. The long-term prognosis for recovery of renal function appears to be good in these patients in northern Taiwan.

Anti-Bacterial Agents↗
PubMed2006

Distribution of a transposon-like element carrying bla(CMY-2) among Salmonella and other Enterobacteriaceae.

OBJECTIVES: The dissemination of cephamycin resistance in Enterobacteriaceae and its correlation with a transposon-like DNA element consisting of a specific tnpA-bla(CMY-2)-blc-sugE structure were investigated. METHODS: A total of 140 enterobacterial isolates belonging to 17 species (10 genera) of Enterobacteriaceae phenotypically characterized as putative AmpC-producers were evaluated. The isolates were examined by PCR analysis, DNA-DNA hybridization and nucleotide sequencing. RESULTS: The bla(CMY-2)-carrying element was detected in 34 isolates from 10 species (9 genera), including all 14 Salmonella and 4 Shigella isolates as well as 7 of the 10 Escherichia coli isolates tested. The remaining 9 isolates were from 112 isolates of the other 14 species tested. The genetic structure of the bla(CMY-2)-carrying element was identical in 29 isolates, while in 3 E. coli and 2 Citrobacter isolates an additional insertion sequence IS1 was found inserted at various nucleotide positions close to the 3' end, either within or downstream, of tnpA. In 12 of the 14 representative isolates examined, the bla(CMY-2)-carrying element was found inserted in the finQ gene of various-sized plasmids with highly conserved 8 bp direct repeats flanking the junction regions. Among the other 106 non-CMY-2-producing isolates, plasmid-mediated ampC genes were found only in one isolate of Enterobacter aerogenes which carried a bla(DHA-1)-like gene. CONCLUSIONS: bla(CMY-2) is the most prevalent plasmid-mediated ampC gene among Enterobacteriaceae. All the bla(CMY-2) genes identified in the present study were associated with a specific transposon-like element that may be responsible for the spread of bla(CMY-2) among Enterobacteriaceae.

Cephalosporin Resistance↗
PubMed2006

The role of Helicobacter pylori infection in children with acute immune thrombocytopenic purpura.

The outcome of immune thrombocytopenic purpura (ITP) is classified as acute or chronic depending on whether platelet count returns to normal. The prevalence of Helicobacter pylori infection increases with age and is independent of gender. We investigated the prevalence of H. pylori infection in Chinese children from Northern Taiwan and analyzed the association between H. pylori infection and acute ITP. Our prospective cohort studies found no statistically significant relation between H. pylori infection and acute ITP. There is therefore no indication to screen children with presumed acute ITP for H. pylori infection.

Acute Disease↗
PubMed2006

Clinical responses of patients with Kawasaki disease to different brands of intravenous immunoglobulin.

OBJECTIVE: To determine whether different brands of intravenous immunoglobulin (IVIG) administered to children with Kawasaki disease (KD) result in different outcomes. STUDY DESIGN: We analyzed children with KD and divided them into 4 groups according to the brand of IVIG. A coronary artery abnormality (CAA) was defined as having a lumen diameter (inner border to inner border) of > or =3 mm in KD cases <5 years old and > or =4 mm in cases > or =5 years old, and giant aneurysm was defined as a lumen diameter > or =8 mm. Patients were considered nonresponsive to IVIG therapy if fever persisted longer than 2 days after completion of treatment and needed retreatment with IVIG. RESULTS: We collected 437 cases, 29 (6.6%) were nonresponsive, 17 (3.9%) had CAA at convalescence, and 3 (0.7%) had giant aneurysm, 2 of whom had development of myocardial infarcts. Patients receiving Brand C IVIG, prepared with beta-propiolactone, had higher rates (10%, 9/93, P = .01) of CAA at convalescence and nonresponsiveness (13%, 12/93, P = .001); giant aneurysm occurred in 3/93 (3%) receiving Brand C IVIG and in 0/344 who received the other 3 brands (P = .008). CONCLUSIONS: IVIG, prepared with beta-propiolactone, was most significantly associated with nonresponsiveness, CAA at convalescence, and giant aneurysm. Physicians should be cautious when using IVIG prepared with beta-propiolactone or enzyme digestion to treat KD.

Child↗
PubMed2006

Dissemination of extended-spectrum beta-lactamase-producing Enterobacteriaceae in intensive care units of a medical center in Taiwan.

The prevalence of extended-spectrum beta-lactamase (ESBL)-producing Enterobacteriaceae in a tertiary hospital in Taiwan was assessed over a 16-month period. A total of 125 nonrepetitive ESBL-producing isolates of Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae were available for investigation using molecular methods. Four predominant intensive care units (ICUs) were identified, and SHV-12 (59%), CTX-M- 3 (36%), and CTX-M-14 (14%) were the three most frequent ESBLs. SHV-12 was predominant among E. cloacae in the burn unit and K. pneumoniae in the other three chest medicine-related ICUs. CTX-M-3 was predominant among E. coli and K. pneumoniae in three other ICUs. The dissemination of ESBL-producing Enterobacteriaceae in four ICUs of a medical center in Taiwan is a consequence of the clonal dissemination of a few epidemic strains along with the horizontal transmission of resistance genes-carrying plasmids among bacterial organisms.

Enterobacteriaceae↗
PubMed2006

Neurologic manifestations in children with influenza B virus infection.

During a 29-month period, 11 (12%) of 92 hospitalized patients with influenza B virus infection presented neurologic manifestations, which included febrile seizure in 4 cases and encephalopathy/encephalitis in 7 cases. Without appropriate antiviral therapy, recovery was uneventful in all but 1 patient, who had neurologic sequelae of quadriplegia and developmental delay.

Child↗
PubMed2006

Detection of multidrug-resistant Salmonella enterica serovar typhimurium phage types DT102, DT104, and U302 by multiplex PCR.

Salmonella enterica serovar Typhimurium is a common cause of nontyphoidal salmonellosis in humans and animals. Multidrug-resistant serovar Typhimurium phage type DT104, which emerged in the 1990s, has become widely distributed in many countries. A total of 104 clinical isolates of Salmonella serogroup B were collected from three major hospitals in Taiwan during 1997 to 2003 and were examined by a multiplex PCR targeting the resistance genes and the spv gene of the virulence plasmid. A total of 51 isolates (49%) were resistant to all drugs (ACSSuT [resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide, and tetracycline]), and all contained a 1.25-kb PCR fragment of integron that is part of the 43-kb Salmonella genomic island 1 (SGI1). The second group was resistant to SSu (28%), and the third was susceptible to all five drugs (13%). Fifty-nine isolates were serotyped to be serovar Typhimurium by the tube agglutination method using H antisera. The virulence plasmid was found in 54 (91.5%) of the 59 serovar Typhimurium isolates. A majority (94.1%) of the Salmonella serogroup B isolates with the ACSSuT resistance pattern harbored a virulence plasmid. Phage typing identified three major phage types: DT104, DT120, and U302. Analysis of the isolates by pulsed-field gel electrophoresis showed six genotypes. We found two genotypes in DT104 strains, two in DT120, and the other two in U302. The presence of a monophasic serovar (4,5,12:i:-) has added difficulty in the determination of the serovars of multidrug-resistant Salmonella serogroup B isolates. Nevertheless, the multiplex PCR devised in the present study appears to be efficient and useful in the rapid identification of ACSSuT-type serovar Typhimurium with SGI1, irrespective of their phage types.

Bacterial Proteins↗
PubMed2006

Clinical observation of meningitis caused by penicillin-susceptible and -non-susceptible Streptococcus pneumoniae in Taiwanese children.

AIM: To compare differences between clinical features and outcome in bacterial meningitis caused by penicillin-susceptible Streptococcus pneumoniae (PSSP) with that caused by penicillin-non-susceptible Streptococcus pneumoniae (PNSP). METHODS: All patients <18 yrs hospitalised with pneumococcal meningitis between January 1984 and December 2002 at Chang Gung Children's Hospital, Taipei were reviewed retrospectively. RESULTS: There were 28 PNSP (63.6%) and 16 PSSP cases of meningitis eligible for the study. The incidence of PNSP meningitis increased significantly over the 8-yr period (p = 0.007). Age <4 yrs (78.6% vs 50%), a lower initial white blood count (mean 11.7 vs 19.9 x10(9)/L), admission to the intensive care unit (70.4% vs 50%) and mortality (28.6% vs 6.3%) were more common in the PNSP group. However, the only significant finding was a lower proportion of polymorphic neutrophils in the CSF of the PNSP meningitis group (p = 0.04). CONCLUSIONS: There was an increase in PNSP isolates from patients with meningitis over the 8-yr study period. No major differences were observed in clinical or laboratory features or outcome between the PSSP and PNSP groups.

Adolescent↗
PubMed2006

Fulminant septicaemia caused by multi-drug-resistant Streptococcus mitis following unrelated cord blood transplantation.

Streptococcus mitis (a common and usually harmless bacterium found in the nose, mouth and throat) can have an unusually high level of resistance to beta-lactam antibiotics. We report a patient who developed fatal Streptococcus mitis septicaemia following unrelated cord blood transplantation. Administration of vancomycin to patients with recurrent fever during allogeneic stem cell transplantation might be indicated.

Child↗