Gilman Kit-Hang Siu

Carbapenem-resistant Escherichia coli (CR-E. coli) is an emerging One Health threat, but recent shifts in predominant lineages and genomic links between clinical and food reservoirs in Hong Kong remain poorly defined. We analyzed 271 CR-E. coli isolates from four hospitals (2022-2026) and 585 isolates recovered from 4,917 retail food samples (2022-2025). Isolates underwent antimicrobial susceptibility testing, whole-genome sequencing, multilocus sequence typing, resistance-gene and plasmid profiling, core-genome SNP phylogenetics, and comparative genomics. Food isolates were mainly from raw pork (268/585, 45.8%) and raw chicken (231/585, 39.5%). blaNDM-5 was detected in 527/585 (90.1%) food and 241/271 (88.9%) clinical isolates. ST69 was the most frequent defined sequence type in both collections, representing 44/585 (7.5%) food and 36/271 (13.3%) clinical isolates, in contrast to the heterogeneous lineages and carbapenemases previously reported in Hong Kong. Applying a predefined ≤50-pairwise-SNP threshold for close genomic relatedness, core-genome phylogeny of 80 ST69 isolates identified two major mixed-source clusters collectively comprising 28 clinical and 27 food isolates. Clustered isolates showed similar antimicrobial resistance profiles, carried blaNDM-5 and blaTEM-1, and were associated with IncI1 MLST | ST136 plasmids. Comparative analyses showed >99.85% average nucleotide identity and broad conservation of the blaNDM-5-associated plasmid backbone across sources. These findings indicate the emergence of blaNDM-5-carrying ST69 as a prominent CR-E. coli lineage in Hong Kong and demonstrate close genomic relatedness between selected clinical and retail food isolates. Although transmission direction have not been inferred yet, the findings support integrated One Health surveillance and source-tracing across clinical, food, animal, and environmental sectors.

The MALDI-TOF MS Bruker Biotyper MBT subtyping IVD module enables the early detection of cfiA-positive Bacteroides fragilis (cfiA+ BF) during bacterial identification. However, the relationship between genetic positivity, phenotypic resistance, and clinical outcomes has not been fully elucidated. This retrospective study analyzed B. fragilis isolates from three Hong Kong hospitals between 2021 and 2025 to examine their prevalence and the clinical utility of MALDI-TOF MS in rapid cfiA detection. Antibiotic susceptibility testing, cfiA gene detection using MALDI-TOF MS, and Oxford Nanopore sequencing were performed. Medical records were reviewed, and univariate analyses and multivariate logistic regression were used to identify factors associated with cfiA positivity and 30-day all-cause mortality. Overall, B. fragilis exhibited a high rate of antibiotic resistance. Concomitant resistance to carbapenems and metronidazole was identified in three isolates. Among the 166 isolates, 40 (24.1%) were cfiA-positive. cfiA detection by MALDI-TOF MS showed 100% concordance with the gene sequencing results and correlated strongly with phenotypic carbapenem resistance (Φ = 0.82, p < 0.001 for meropenem; Φ = 0.70, p < 0.001 for ertapenem; Φ = 0.63, p < 0.001 for imipenem). Phylogenetic analysis revealed two distinct clusters corresponding to cfiA status, each exhibiting genetic diversity based on multi-locus sequence typing (MLST). The cfiA+ BF isolates demonstrated high-level phenotypic carbapenem resistance in the presence of upstream insertion sequences. The predominant sequence type (ST) among cfiA+ BF isolates was ST157, and 70% of ST157 isolates harbored IS1187 in the upstream region of cfiA. Gene sequencing also identified other emerging beta-lactamase genes bla_OXA-347 and bla_MUN. The 30-day all-cause mortality following B. fragilis infection was 13.3%, with independent predictors including a high Charlson Comorbidity Index (OR = 1.30; p = 0.02) and the absence of early source control (OR = 4.84; p = 0.03). This study highlights the widespread occurrence of cfiA+ BF in Hong Kong and the clinical significance of rapid cfiA detection. Continuous surveillance is essential to monitor the ongoing threat of antibiotic resistance in B. fragilis.

Public washrooms (toilets) are potential hubs for pathogen transmission, yet the risk of microbial re-contamination via post-handwashing surfaces remains understudied. We characterized the prevalence and distribution of multidrug-resistant organisms (MDROs) and antimicrobial resistance genes (ARGs) in post-handwashing areas by sampling four high-contact sites, including faucets, paper dispensers, hand dryers, and exit door handles, in public washrooms across healthcare, commercial, and recreational facilities. From the 232 post-handwashing surface samples collected, we isolated 17 MDROs (7.33% prevalence) from cultures, including extended-spectrum beta-lactamase (ESBL)-producing Enterobacterales (ESBL-E, n = 10), carbapenem-resistant Pseudomonas aeruginosa (CRPA, n = 5), and methicillin-resistant Staphylococcus aureus (MRSA, n = 2). Additionally, we novelly employed targeted probe capture metagenomics (TCM), which utilizes oligonucleotide probes to enrich and detect low-abundance microbial species and ARG sequences. TCM revealed the detection of human pathogenic taxa in 65.2% of samples, including P. aeruginosa (78.4%), Acinetobacter baumannii (77.9%), and S. aureus (71.1%). Clinically critical ARGs, such as blaCTX-M (2.0%), blaNDM (2.9%), blaSHV (3.4%), and mecA (62.3%), were detected in 63.7% of samples, indicating a potential transmission within the post-handwashing area. Our findings highlight the role of post-handwashing areas as underrecognized reservoirs for MDROs, particularly MRSA. Furthermore, this study demonstrates the utility of TCM in public health surveillance by enabling a sensitive detection of rare but high-risk microbial species and drug resistance determinants in low-biomass environmental samples. This study offers a comprehensive and nuanced view of the microbial and resistome landscape of washroom environments, offering a revolutionary approach for future environmental surveillance.

The global rise of multidrug-resistant Extended Spectrum β-Lactamase Producing-Enterobacterales (ESBL-PE) poses a critical threat to public health, driving the urgent need for alternative therapeutic approaches. This study evaluates the antimicrobial properties of 20 Chinese medicinal herbs against 14 ESBL-PE strains from seven bacterial species, utilizing three extraction methods: traditional water decoction, 80% ethanol maceration, and 50% ethanol with ultrasound-assisted extraction (UAE). Among the herbs tested, Coptis chinensis Franch. demonstrated the most potent anti-ESBL-PE activity, effectively inhibiting multiple strains, including Escherichia coli, Klebsiella pneumoniae, Hafnia alvei, Citrobacter freundii and Proteus hauseri. C. chinensis extracts obtained via UAE exhibited superior antibacterial activity to the other two extraction methods, attributed to enhanced extraction efficiency and improved bioactive compound yields. Specifically, UAE increased the extraction yield of alkaloids in C. chinensis by 80.9%, compared to the ethanol maceration method, and the increase in berberine, the key antimicrobial compound, was 75.4%. Berberine demonstrated significant antibacterial effects against ESBL-PE strains, while other phytochemicals in C. chinensis extracts have an additional effect with berberine, further amplifying the overall antimicrobial activity. These findings highlight that the UAE is a promising method for enhancing the therapeutic potential of C. chinensis and other Chinese medicinal herbs against multidrug-resistant bacteria.

In October 2024, twelve primates from 4 species died of sepsis at the Hong Kong Zoological and Botanical Gardens. Postmortem examinations and microbiological analyses confirmed Burkholderia pseudomallei infection. Phylogenetic analysis revealed a clonal sequence type 46 strain with minimal variation, signifying a single source. This outbreak highlights melioidosis risk in zoo settings.

Zika virus (ZIKV) is an emerging flavivirus primarily transmitted by Aedes mosquitoes. It has gained significant attention due to its potential teratogenic effects during pregnancy, particularly the increased risk of severe congenital outcomes such as microcephaly and fetal mortality. ZIKV's ability to breach the fetal-maternal interface and compromise placental function distinguishes it from other arboviruses. This mini-review explores how ZIKV targets key placental cells, including cytotrophoblasts, extravillous trophoblasts, syncytiotrophoblasts, and Hofbauer cells, to establish infection in the placenta. We first explore the molecular mechanisms of ZIKV replication, focusing on viral entry, replication strategies, and evasion of host immunity in trophoblasts. We then discuss how ZIKV infection triggers cellular stress responses, such as oxidative stress, endoplasmic reticulum stress, and inflammatory pathways, along with metabolic reprogramming. These processes ultimately lead to placental insufficiency and adverse pregnancy outcomes. Drawing on recent findings from trophoblast organoids and in vivo models, we highlight novel therapeutic opportunities, including vasoactive intestinal peptide, endoplasmic reticulum stress modulators, and immunomodulatory interventions that may protect pregnancy. Finally, we propose future directions for mitigating ZIKV's impact on maternal-fetal health, emphasizing the need for comprehensive research into viral pathogenesis, advanced model systems, and vector control programs to prevent this devastating infection.

During the COVID-19 pandemic, stringent public health measures led to historically low influenza activity in Hong Kong. However, after these interventions were relaxed in 2023, Influenza A viruses (IAV), including A(H1N1)pdm09 and A(H3N2), rapidly resurfaced. In this study, 1,046 clinical cases collected throughout 2023 underwent comprehensive genomic analysis using Oxford Nanopore Technologies (ONT). Phylogenetic analyses of the assembled genome segments were conducted alongside several global public sequences for comparison. The dataset is comprised of 593 A(H1N1)pdm09 sequences, predominantly of hemagglutinin (HA) subclade 5a.2a and neuraminidase (NA) subclade C.5.3, and 453 A(H3N2) sequences classified mainly as HA subclade 2a.3a.1 and NA subclade B.4.3. Phylogenetic comparisons revealed close genetic relationships between the studied viruses and 30 A(H1N1)pdm09 and 27 A(H3N2) sequences published in other regions during the same time. Additionally, identified amino acid substitutions may affect antigenicity and viral fitness. These findings underscore Hong Kong's high post-COVID-19 influenza diversity and the need for ongoing molecular surveillance to monitor emerging viral variants.

Rapid and accurate pathogen identification is critical for managing acute invasive infections. Conventional culture methods are time-consuming, delaying effective treatment. Nanopore sequencing offers real-time, long-read capabilities suitable for clinical diagnostics, yet standardized workflows remain lacking. This study developed and evaluated two optimized nanopore sequencing workflows: Nanopore Targeted Sequencing (NTS) and Nanopore Metagenomic Sequencing (NMgS), for pathogen and antimicrobial resistance (AMR) detection in 177 normally sterile body fluid samples. NTS used multiplex PCR to amplify 16S rRNA, ITS, and 21 AMR genes, while NMgS applied host DNA depletion followed by unbiased sequencing. Both workflows were benchmarked against culture-based diagnostics. Among the 304 species cultured from 177 body fluid samples, NTS identified 78.95%, with 77.30% meeting the threshold of relative abundance (T _RA ) of 0.058 and 71.38% having at least 10 classified reads. In comparison, NMgS identified 39.47% of cultured species at the species level and 9.54% at the genus level. Of the 28 samples containing AMR ESKAPE pathogens, NTS detected associated AMR genes in 24 samples (85.71%), while NMgS identified AMR genes linked to 9 of the 32 ESKAPE pathogens (28.13%). The turnaround times for NTS and NMgS workflows were 10.75 and 12.82 hours, respectively. In conclusion, this study demonstrated the clinical utility of Nanopore sequencing for rapid diagnosis in clinical microbiology. The heightened sensitivity of Nanopore targeted sequencing renders it ideal for routine clinical microbiology diagnoses, whereas unbiased Nanopore metagenomic sequencing is advantageous in identifying infections of unknown etiology.

Talaromyces marneffei is a dimorphic fungus that transitions from a filamentous form at 25 °C to a pathogenic yeast form at 37 °C, demonstrating pathogenicity mostly in immunocompromised individuals, such as those with human immunodeficiency virus/AIDS. Though it is one of the most severe infectious fungi in Southeast Asia, the lack of comprehensive genomic analysis has hindered advancement in strain differentiation, diagnosis and treatment. In this study, we assembled a high-quality genome of T. marneffei ATCC 18224, resulting in a 28.9 Mb genome distributed across 11 contigs, using third-generation Oxford Nanopore Technologies sequencing reads. Notably, we identified a strain-specific 740-kb segmental duplication in strain ATCC 18224, potentially mediated by inserting a Ty1/ Copia long terminal repeat (LTR) retrotransposon. This segmental duplication includes various functional genes, with 75 differentially expressed during its dimorphic transition. Comparative genomic analysis revealed large-scale rearrangements in strains PM1 and 11CN-20-091, which were inconsistent with the phylogenomic trees of six T. marneffei strains and required further investigation. Additionally, we observed substantial genetic structural variations in LTR retrotransposons, particularly within the Ty1/ Copia family, including two significant recent expansions in strain ATCC 18224. In summary, the identification and characterization of these extensive genomic structural variations in T. marneffei contribute to a deep understanding of its genetic diversity and will facilitate improvements in genotyping, classification and genomic surveillance.