Accurate Prediction of Ion Mobility Collision Cross-Section Using Ion's Polarizability and Molecular Mass with Limited Data

The rotationally averaged collision cross-section (CCS) determined by ion mobility-mass spectrometry (IM-MS) facilitates the identification of various biomolecules. Although machine learning (ML) models have recently emerged as a highly accurate approach for predicting CCS values, they rely on large data sets from various instruments, calibrants, and setups, which can introduce additional errors. In this study, we identified and validated that ion's polarizability and mass-to-charge ratio (m/z) have the most significant predictive power for traveling-wave IM CCS values in relation to other physicochemical properties of ions. Constructed solely based on these two physicochemical properties, our CCS prediction approach demonstrated high accuracy (mean relative error of <3.0%) even when trained with limited data (15 CCS values). Given its ability to excel with limited data, our approach harbors immense potential for constructing a precisely predicted CCS database tailored to each distinct experimental setup. A Python script for CCS prediction using our approach is freely available at https://github.com/MSBSiriraj/SVR_CCSPrediction under the GNU General Public License (GPL) version 3.

Traveling Wave Ion Mobility-Derived Collision Cross Section Database for Plant Specialized Metabolites: An Application to Ventilago harmandiana Pierre

The combination of ion mobility mass spectrometry (IM-MS) and chromatography is a valuable tool for identifying compounds in natural products. In this study, using an ultra-performance liquid chromatography system coupled to a high-resolution quadrupole/traveling wave ion mobility spectrometry/time-of-flight MS (UPLC-TWIMS-QTOF), we have established and validated a comprehensive TWCCSN2 and MS database for 112 plant specialized metabolites. The database included 15 compounds that were isolated and purified in-house and are not commercially available. We obtained accurate m/z, retention times, fragment ions, and TWIMS-derived CCS (TWCCSN2) values for 207 adducts (ESI+ and ESI-). The database included novel 158 TWCCSN2 values from 79 specialized metabolites. In the presence of plant matrix, the CCS measurement was reproducible and robust. Finally, we demonstrated the application of the database to extend the metabolite coverage of Ventilago harmandiana Pierre. In addition to pyranonaphthoquinones, a group of known specialized metabolites in V. harmandiana, we identified flavonoids, xanthone, naphthofuran, and protocatechuic acid for the first time through targeted analysis. Interestingly, further investigation using IM-MS of unknown features suggested the presence of organonitrogen compounds and lipid and lipid-like molecules, which is also reported for the first time. Data are available on the MassIVE (https://massive.ucsd.edu, data set identifier MSV000090213).

Novel Organization of the Staphylococcal Cassette Chromosome mec Composite Island in Clinical Staphylococcus haemolyticus and Staphylococcus hominis Subspecies hominis Isolates from Dogs

Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis are common coagulase-negative staphylococcus opportunistic pathogens. In Thailand, the clinical strains S. haemolyticus 1864 and 48 and S. hominis subsp. hominis 384 and 371 have been recovered from sick dogs. These strains were methicillin resistant with the nontypeable staphylococcal cassette chromosome mec (NT-SCCmec). The SCCmec element distribution in the clinical isolates from dogs was analyzed using whole-genome sequencing, which revealed the presence of different SCCmec composite islands (CIs) and gene structure. The SCCmec-CIs of ψSCCmec1864 (13 kb) and ψSCC1864 (11 kb) with a class C1 mec complex but no ccr gene were discovered in S. haemolyticus 1864. The CIs of ψSCCmec48 with a C1 mec complex (28 kb), SCC48 with ccrA4B4 (23 kb), and ψSCC48 (2.6 kb) were discovered in S. haemolyticus 48. In SCC48, insertion sequence IS256 contained an aminoglycoside-resistant gene [aph(2″)-Ia]. Two copies of IS431 containing the tetracycline-resistant gene tet(K) were found downstream of ψSCC48. In S. hominis subsp. hominis, the SCCmec-CI in strain 384 had two separate sections: ψSCCmec384 (20 kb) and SCCars (23 kb). ψSCCmec384 lacked the ccr gene complex but carried the class A mec complex. Trimethoprim-resistant dihydrofolate reductase (dfrC) was discovered on ψSCCmec384 between two copies of IS257. In strain 371, SCCmec VIII (4A) (37 kb) lacking a direct repeat at the chromosomal end was identified. This study found SCCmec elements in clinical isolates from dogs that were structurally complex and varied in their genetic content, with novel organization. IMPORTANCE In Thailand, the staphylococcal cassette chromosome mec (SCCmec) element, which causes methicillin resistance through acquisition of the mec gene, has been studied in clinical coagulase-negative Staphylococcus isolates from various companion animals, and Staphylococcus haemolyticus and Staphylococcus hominis subsp. hominis were found to have the most nontypeable (NT)-SCCmec elements. These species are more prone to causing illness and more resistant to a variety of antimicrobials than other coagulase-negative staphylococci. However, full characterization of NT-SCCmec in clinical S. haemolyticus and S. hominis subsp. hominis isolates from such animals has been limited. Our findings support the use of full nucleotide sequencing rather than PCR designed for Staphylococcus aureus in further research of novel SCCmec elements. Moreover, several antimicrobial resistance and heavy metal resistance genes were identified on the SCCmec elements; these are important as they could limit the therapeutic options available in veterinary medicine.

Comparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand

Leptospira weilii belongs to the pathogenic Leptospira group and is a causal agent of human and animal leptospirosis in many world regions. L. weilii can produce varied clinical presentations from asymptomatic through acute to chronic infections and occupy several ecological niches. Nevertheless, the genomic feature and genetic basis behind the host adaptability of L. weilii remain elusive due to limited information. Therefore, this study aimed to examine the complete circular genomes of two new L. weilii serogroup Mini strains (CUDO6 and CUD13) recovered from the urine of asymptomatic dogs in Thailand and then compared with the 17 genomes available for L. weilii. Variant calling analysis (VCA) was also undertaken to gain potential insight into the missense mutations, focusing on the known pathogenesis-related genes. Whole genome sequences revealed that the CUDO6 and CUD13 strains each contained two chromosomes and one plasmid, with average genome size and G+C content of 4.37 Mbp and 40.7%, respectively. Both strains harbored almost all the confirmed pathogenesis-related genes in Leptospira. Two novel plasmid sequences, pDO6 and pD13, were identified in the strains CUDO6 and CUD13. Both plasmids contained genes responsible for stress response that may play important roles in bacterial adaptation during persistence in the kidneys. The core-single nucleotide polymorphisms phylogeny demonstrated that both strains had a close genetic relationship. Amongst the 19 L. weilii strains analyzed, the pan-genome analysis showed an open pan-genome structure, correlated with their high genetic diversity. VCA identified missense mutations in genes involved in endoflagella, lipopolysaccharide (LPS) structure, mammalian cell entry protein, and hemolytic activities, and may be associated with host-adaptation in the strains. Missense mutations of the endoflagella genes of CUDO6 and CUD13 were associated with loss of motility. These findings extend the knowledge about the pathogenic molecular mechanisms and genomic evolution of this important zoonotic pathogen.

High-Resolution QTOF-MRM for Highly Accurate Identification and Quantification of Trace Levels of Triterpenoids in Ganoderma lucidum Mycelium

The accurate quantification of triterpenoids in Ganoderma lucidum mushroom in the mycelium stage is challenging due to their low concentrations, interference from other possible isomers, and the complex matrix. Here, a high-resolution quadrupole-time-of-flight mass spectrometry "multiple reaction monitoring" with target enhancement (HR-QTOF-MRM) method was developed to quantify seven target triterpenoids in G. lucidum. The performance of this method was compared against an optimized QQQ-MRM method. The HR-QTOF-MRM was shown to be capable of distinguishing target triterpenoids from interferent peaks in the presence of matrices. The HR-QTOF-MRM LOD and LLOQ values were found to be one to two times lower than those derived from the QQQ-MRM method. Intraday and interday variabilities of the HR-QTOF-MRM demonstrated better reproducibility than the QQQ-MRM. In addition, excellent recoveries of the analytes ranging from 80 to 117% were achieved. Spiking experiments were carried out to verify and compare the quantitative accuracy of the two methods. The HR-QTOF-MRM method provided better percent accuracy, ranging from 84% to 99% (<3% RSD), compared with the range of 69 to 114% (<4%RSD) given by the QQQ-MRM method. These results demonstrate that the new HR-QTOF-MRM mode is able to improve sensitivity, reproducibility, and accuracy of trace level analysis of triterpenoids in the complex biological samples. The triterpenoid concentrations were in the range of nondetect to 0.06-6.72 mg/g of dried weight in fruiting body and to 0.0009-0.01 mg/g of dried weight in mycelium.

Leptospira infection and shedding in dogs in Thailand

BACKGROUND

Leptospirosis is a widespread zoonosis and has been recognized as a re-emerging infectious disease in humans and dogs, but prevalence of Leptospira shedding in dogs in Thailand is unknown. The aim of this study was to determine urinary shedding of Leptospira in dogs in Thailand, to evaluate antibody prevalence by microscopic agglutination test (MAT) and enzyme-linked immunosorbent assay (ELISA), and to assess risk factors for Leptospira infection. In Northern, Northeastern, and Central Thailand, 273 stray (n = 119) or client-owned (n = 154) dogs from rural (n = 139) or urban (n = 134) areas were randomly included. Dogs that had received antibiotics within 4 weeks prior to sampling were excluded. No dog had received vaccination against Leptospira. Urine was evaluated by real-time polymerase chain reaction (PCR) specific for lipL32 gene of pathogenic Leptospira. Additionally, urine was cultured for 6 months in Ellinghausen-McCullough-Johnson-Harris (EMJH) medium. Antibodies were measured by ELISA and MAT against 24 serovars belonging to 15 serogroups and 1 undesignated serogroup. Risk factor analysis was performed with backwards stepwise selection based on Wald.

RESULTS

Twelve of 273 (4.4%; 95% confidence interval (CI): 2.0-6.8%) urine samples were PCR-positive. In 1/273 dogs (0.4%; 95% CI: 0.01-1.1%) Leptospira could be cultured from urine. MAT detected antibodies in 33/273 dogs (12.1%; 95% CI: 8.2-16.0%) against 19 different serovars (Anhoa, Australis, Ballum, Bataviae, Bratislava, Broomi, Canicola, Copenhageni, Coxi, Grippotyphosa, Haemolytica, Icterohaemorrhagiae, Khorat, Paidjan, Patoc, Pyrogenes, Rachmati, Saxkoebing, Sejroe). In 111/252 dogs (44.0%; 95% CI: 37.9-50.2%) immunoglobulin M (IgM) and/or immunoglobulin G (IgG) antibodies were found by ELISA. Female dogs had a significantly higher risk for Leptospira infection (p = 0.023).

CONCLUSIONS

Leptospira shedding occurs in randomly sampled dogs in Thailand, with infection rates comparable to those of Europe and the USA. Therefore, the potential zoonotic risk should not be underestimated and use of Leptospira vaccines are recommended.

Chronology of emergence of the genus Leptospira and over-representation of gene families enriched by vitamin B2, B12 biosynthesis, cell adhesion and external encapsulating structure in L. interrogans isolates from asymptomatic dogs

The spirochete species Leptospira interrogans is the most common cause of leptospirosis, producing acute to chronic infections in most mammalian species. This pathogenic bacterium has an ability to evolve in many ways to occupy various environments and hosts. In this study, we performed chronology analysis to look for insight into the emergence of Leptospira species, focusing on L. interrogans, and investigated gene gain and loss related to their adaptation in strains isolated from asymptomatic dogs. Chronology analysis revealed that the emergence of L. interrogans was around 53.7 million years ago (MYA), corresponding to the Paleogene period that coincided with an optimal climatic temperature and the evolution of suitable mammalian hosts. Gene families encoding for vitamin B2, B12 biosynthesis, cell adhesion and external encapsulating structure were found to be enriched in L. interrogans isolated from the urine of asymptomatic dogs. The activity of these gene families may have favored adaptations resulting in chronic infections.

Genomic analysis of Leptospira interrogans serovar Paidjan and Dadas isolates from carrier dogs and comparative genomic analysis to detect genes under positive selection

BACKGROUND

Leptospirosis is an emerging infectious disease worldwide that can cause high morbidity and mortality rates in humans and animals. The causative spirochetes have reservoirs in mammalian hosts, but there has been limited analysis of the genomes of isolates recovered from animals. The aims of this study were to characterize genomic features of two Leptospira interrogans strains recently isolated from asymptomatic dogs in Thailand (strains CUDO5 and CDUO8), and to perform comparative genome analyses with other strains. Molecular adaptive evolution in L. interrogans as signaled by positive selection also was analyzed.

RESULTS

Whole genome sequence analysis revealed that strains CUDO5 and CUDO8 had genome sizes of approximately 4.9 Mbp with 35.1% GC contents. Using monoclonal antibodies, strains CUDO5 and CUDO8 were identified as serovars Paidjan and Dadas, respectively. These strains harbored genes known to be associated with acute and chronic infections. Using Single Nucleotide Polymorphisms phylogeny (SNPs) with 97 L. interrogans strains, CUDO5 and CUDO8 had closest genetic relatedness with each other. Nevertheless, the serovar determinant region (rfb locus) showed variations in the genes encoding sugar biosynthesis. Amongst 13 representative L. interrogans strains examined for molecular adaptive evolution through positive selection under the site-model of Phylogenetic Analysis of Maximum Likelihood, genes responsible for iron acquisition (tlyA and hbpA), motility (fliN2, flgK, and flhB) and thermal adaptation (lpxD1) were under increased selective pressure.

CONCLUSIONS

L. interrogans serovar Paidjan strain CUDO5 and serovar Dadas strain CUDO8 had close genetic relatedness as analyzed by SNPs phylogeny. They contained genes with established roles in acute and chronic leptospirosis. The rfb locus in both serovars showed gene variation associated with sugar biosynthesis. Positive selection analysis indicated that genes encoding factors involved in motility, temperature adaptation, and iron acquisition were under strong positive selection in L. interrogans. These may be associated with adaptation in the early stages of infection.

Molecular detection and isolation of pathogenic Leptospira from asymptomatic humans, domestic animals and water sources in Nan province, a rural area of Thailand

Leptospirosis is an important zoonotic disease that is often associated with animal carriers and contamination of the environment via infected urine. This study aimed to assess pathogenic leptospiral carriage in Nan province, a rural area of Thailand where leptospirosis is endemic. Samples from 20 villages were obtained during the period 2013 to 2016, comprising urine samples collected from asymptomatic people (n=37) and domestic animals (n=342), and environmental water samples (n=14). Leptospira were cultured in Ellinghauson McCullough Johnson and Harris (EMJH) media. An rrs nested PCR identified 9.92% (95% confidence interval (CI) 6.96-12.88) of the urine and water samples as being positive for Leptospira spp., and phylogenetic analysis was conducted on the 443bp amplicons. Leptospira weilii, which has not previously been identified in Thailand, was recovered from 13 cattle, 9 pigs, 2 dogs, 2 water samples and 1 goat. L. interrogans was found in 4 dogs, 3 pigs, 3 cattle, 1 human and 1 water sample. Four leptospiral strains were isolated and multilocus sequence typing (MLST) analysis was performed on these. Three novel sequence types were identified, including two singletons of L. interrogans in ST26 and ST33, and one of L. weilii in ST94, with this having a close relationship to previous isolates from cases of human leptospirosis in Laos and China. Our results revealed that pathogenic Leptospira occur commonly in asymptomatic domestic animals, humans and environmental water samples in Nan Province, and emphasize the high potential for zoonotic transmission in the province.