Biology subjects

Thaipadungpanit, J.

Publications and source records attributed to Thaipadungpanit, J..

6 recordsLinked to original sources

bioRxiv2026

A 28-year evolution experiment on Burkholderia pseudomallei survival in nutrient-depleted sterile water

Environmental persistence allows opportunistic pathogens to survive a range of harsh conditions, increasing the likelihood of eventual infection. Burkholderia pseudomallei, the causative agent of melioidosis, can endure long-term nutrient-depletion in the environment, but its adaptive mechanisms remain poorly understood. Here, we investigated the evolutionary trajectory of a clinical B. pseudomallei strain maintained in sterile water since 1994. The strain was inoculated into nine individual tubes at nine initial concentrations (102-1010 CFU/mL) and has remained viable to date. Liquid chromatography-mass spectrometry analysis of the water identified potential carbon sources, including phthalic acid -- a plastic degradation product likely leached from inoculation tubes -- which the strain can metabolise via an intact catabolic operon. Genomic variations accumulated between 1994 and 2022 were characterised using both single-colony and plate-sweep sequencing which provided complementary insights. Across all tubes, we identified 249 single-nucleotide polymorphisms (SNPs), 73 indels, and a large-scale deletion. Cultures from each tube displayed a consistently low mutation rate (3.18 x 10- SNPs per site per year), suggesting that cells entered a dormant or slow-growth state. Of 393 genes with mutations, 193 were independently mutated in more than one tube, particularly those involved in signal transduction, cell wall and membrane biogenesis, and secondary metabolite synthesis. These patterns indicate parallel adaptation to long-term nutrient deprivation through modulation of cell-density-related functions and loss of metabolically costly pathways. Remarkably, B. pseudomallei from this experiment remain viable after nearly three decades, providing a rare natural model for understanding how environmental bacteria endure and adapt in extremely nutrient-depleted conditions.

evolutionary biology↗

bioRxiv2025

Pathogenic Leptospira species identified in dogs and cats during neutering in Thailand

Pathogenic species of Genus Leptospira cause an underdiagnosed zoonosis in humans and animals called leptospirosis. Animal reservoirs getting infections without signs can carry and shed the active spirochete into the environment through their urine, making the control of leptospirosis transmission to humans more challenging. Asymptomatic leptospirosis in human companions, such as dogs and cats, leading to unawareness of infections, has been demonstrated in a few countries. Monitoring disease prevalence and investigating molecular epidemiology is essential for controlling and preventing human and animal leptospirosis transmission. To investigate the prevalence of Leptospira infection among cats and dogs in Thailand, we collected 567 urine samples through a neutering program in seven provinces across the central, western and southern regions. The urine samples were screened for Leptospiras DNA and further speciation using the Sanger Sequencing Analysis. 34/303 (11.2%) dogs and 22/264 (8.3%) cats tested positive for Leptospira in the Pathogen clade. The partial rrs gene analysis identified L. interrogans, L. weilii, and L. borgpetersenii (4.4%). We first reported L. yasudae (1.0%) and other new species of the Pathogen subclade 2 (1.4%) infections among these dogs and cats. Three key pathogenic Leptospira species commonly causing human leptospirosis in Southeast Asia were identified in healthy owned and free-roaming dogs and cats, suggesting the risk of human leptospirosis in the areas. These animal reservoirs (probably living under the same roof as us) can transmit diseases daily to owners (caretakers), other animals and the environment. Effective public awareness campaigns on the transmission might encourage dog and cat health surveillance and vaccinations, reducing human infection risks. Author SummaryLeptospirosis, a neglected zoonotic disease caused by pathogenic species of genus Leptospira, can be transmitted to humans through contact with infected animal body fluids or contaminated environments. Free-ranging dogs and cats can shed infectious Leptospira in their urine, posing a significant risk. In Thailand, animal vaccine coverage for diseases like leptospirosis in these animals is unknown and unregulated, raising concerns about zoonotic transmission and reflecting a lack of routine veterinary support. Our study joined non-profit, volunteer-led neutering programs that travel to various provinces, offering free services for owned and unowned pets. This allowed our team to collect urine specimens directly from the urinary bladder for the detection of Leptospira. We found nearly 10% of the recruited asymptomatic dogs and cats were infected by the molecular screening assay. Three pathogenic Leptospira species, commonly infecting humans globally, were identified. Notably, we report the first detection of L. yasudae in animal urine samples, providing evidence of infectivity for a species not previously recognised for its pathogenicity and typically reported from the environment. This highlights the risk of human leptospirosis from contact with cats and dogs, emphasising the need for public awareness and annual vaccination programs for all pets.

zoology↗

bioRxiv2025

Complete genomes of Rickettsia typhi reveal a clonal population

Murine typhus, caused by infection with Rickettsia typhi, is a neglected disease contributing to infectious disease burden in south- and southeast Asia. Despite its importance, we have minimal knowledge of the genomics of R. typhi, with only four complete genomes being sequenced prior to this work. We sequenced a further 25 genomes including historical strains collected before 1976 from both human and rat hosts, and recent genomes isolated from patients at a single hospital in Laos. Whole genome SNP analysis reveals extremely low levels of genetic diversity across the 29 genomes, with overall nucleotide diversity ({pi}) of 1.27e-05 and evidence of purifying selection, and a minimal pan-genome. Phylogenetic analysis shows clustering of the genome by historic or modern origin, with the exception of one modern strain which is most closely related to historic strains from Thailand, and no clustering by host origin. The highly conserved genome of R. typhi suggests strong constraints on genome evolution in this obligate intracellular parasite, and has implications for the design of future murine typhus diagnostic tools and vaccines. Impact StatementRickettsia typhi is the causative agent of murine typhus, an infectious disease that causes morbidity and mortality in humans. This study has expanded the genomic dataset from a small number of genomes to a comprehensive collection of 29 complete genomes. The genome comparison includes historic and modern strains and reveals a clonal population structure with minimal genetic diversity across time. This shows the evolutionary stability of R. typhi, which is most likely due to strong purifying selection and an intracellular lifestyle. This extremely low genomic variation has significant impacts for the development of murine typhus vaccines and robust diagnostic assays.

microbiology↗

bioRxiv2024

The major pathogen Haemophilus influenzae experiences pervasive recombination and purifying selection at local and global scales

Haemophilus influenzae is a major opportunistic human pathogen which causes both non-invasive and invasive disease. The H. influenzae type b (Hib) vaccine has led to a significant reduction of invasive Hib disease, but offers no protection against colonisation or disease by unencapsulated non-typeables (NT) or non-b serotypes, and H. influenzae remains a public health burden worldwide, with increasing reports of multi-drug resistance (MDR). Despite this, there is no comprehensive understanding of the species global population structure. To advance understanding about the evolution and epidemiology of the species, we whole-genome sequenced 4,475 isolates of H. influenzae from an unvaccinated paediatric carriage and pneumonia cohort from northwestern Thailand. Despite no Hib immunisation, serotype b was uncommonly found (5.7%), while 91.7% of isolates were NT. We identified a large number of nearly pan-resistant lineages that were mostly NT, and discovered that no lineages were enriched among disease samples, suggesting the ability to cause invasive disease is not restricted to any subpopulation of the species. Extensive population genetic analyses of our data combined with a worldwide collection of 5,976 published genomes revealed a highly admixed population structure, low core genome nucleotide diversity, and evidence of pervasive negative selection. The combined data confirm that MDR lineages are not confined to our cohort, and their establishment globally is an urgent concern.

microbiology↗

bioRxiv2023

Genetic diversity, determinants, and dissemination of Burkholderia pseudomallei lineages implicated in melioidosis in northeast Thailand

Melioidosis is an often-fatal neglected tropical disease caused by an environmental bacterium Burkholderia pseudomallei. However, our understanding of the disease-causing bacterial lineages, their dissemination, and adaptive mechanisms remains limited. To address this, we conducted a comprehensive genomic analysis of 1,391 B. pseudomallei isolates collected from nine hospitals in northeast Thailand between 2015 and 2018, and contemporaneous isolates from neighbouring countries, representing the most densely sampled collection to date. Our study identified three dominant lineages with unique gene sets enhancing bacterial fitness, indicating lineage-specific adaptation strategies. Crucially, recombination was found to drive lineage-specific gene flow. Transcriptome analyses of representative clinical isolates from each dominant lineage revealed heightened expression of lineage-specific genes in environmental versus infection conditions, notably under nutrient depletion, highlighting environmental persistence as a key factor in the success of dominant lineages. The study also revealed the role of environmental factors - slope of terrain, altitude, direction of rivers, and the northeast monsoons - in shaping B. pseudomallei geographical dispersal. Collectively, our findings highlight persistence in the environment as a pivotal element facilitating B. pseudomallei spread, and as a prelude to exposure and infection, thereby providing useful insights for informing melioidosis prevention and control strategies.

microbiology↗

bioRxiv2019

The spread of chloramphenicol-resistant Neisseria meningitidis in Southeast Asia

Invasive disease caused by Neisseria meningitidis is a significant health concern globally, but our knowledge of the prevailing serogroups, antimicrobial susceptibility patterns, and genetics of N. meningitidis in Southeast Asia is limited. Chloramphenicol resistance in N. meningitidis has rarely been reported, but was first described in isolates from Vietnam in 1998. Using whole-genome sequencing of meningococcal isolates from 18 patients collected between 2007 and 2018 from diagnostic microbiology laboratories in Cambodia, Thailand and the Lao Peoples Democratic Republic (Laos), of which eight were non-susceptible to chloramphenicol, we report the spread of this chloramphenicol-resistant lineage of N. meningitidis across Southeast Asia. Strains resistant to penicillin, tetracycline, and ciprofloxacin were also observed, including a chloramphenicol-resistant strain from the previously-described lineage which has acquired penicillin and ciprofloxacin resistance, and most isolates were of serogroup B. This study suggests that chloramphenicol-resistant N. meningitidis is more widespread than previously thought.

microbiology↗