Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established ...Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established for the phylogenetic and epidemiology analysis. Methods To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods. Results After comparison of the genome, seven high discrimination gene loci （recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR） were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types （STs） were identified. Based on the Hunter-Gaston Index （HGI）, MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types （ST） came into a main cluster, showing the major clonal complexes in those 44 strains. Conclusion MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.展开更多
Objective:To explore the genetic variation and differentiation of 2 echinostomes from genus Echinostoma,i.e.Echinostoma revolutum(E.revolution) and Echinostoma malayanum(E. malayanum) from Khon Kaen Province,Thailand....Objective:To explore the genetic variation and differentiation of 2 echinostomes from genus Echinostoma,i.e.Echinostoma revolutum(E.revolution) and Echinostoma malayanum(E. malayanum) from Khon Kaen Province,Thailand.Methods:These parasites were compared at 22 enzymes encoding a presumptive 30 loci by using multilocus enzyme electrophoresis (MEE) technique.Results:Twenty-two loci can be used as diagnostic markers to differentiate these 2 species.E.revolutum and E.malayanum had fixed genetic differences at 70%of loci, whereas both species had fixed genetic differences from the liver fluke,Opisthorchis viverrini at 91%of loci.Intraspecific variation within a population of E.revolutum was observed at 5 polymorphic loci.Conclusions:MEE is a powerful technique to investigate genetic variation and differentiation of E.revolutum and E.malayanum.展开更多
Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule ba...Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17 bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three house-keeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.展开更多
Background Streptococcus pneumoniae （S.pneumoniae） is a major causative agent of severe infections,including sepsis,pneumonia,meningitis,and otitis media,and has become a major public health concern.We report the pn...Background Streptococcus pneumoniae （S.pneumoniae） is a major causative agent of severe infections,including sepsis,pneumonia,meningitis,and otitis media,and has become a major public health concern.We report the pneumococcal serotype and sequence type （ST） distribution,and antimicrobial resistance of 39 S.pneumoniae strains from seven hospitals in China.Methods Blood/cerebrospinal fluid （CSF） and sputum isolates from patients were analyzed to determine S.pneumoniae serotypes by polymerase chain reaction （PCR） and the Neufeld Quellung reaction,the multilocus sequence types （MLST） by PCR and sequencing,and susceptibility to antimicrobial agents by the VITEK Gram Positive Susceptibility Card.Results A total of 39 isolates were collected including 21 blood/CSF and 18 sputum isolates.Conventional serotyping by the Quellung reaction required 749 reactions.In contrast,PCR based typing needed only 106 PCR reactions.The most frequent serotypes from the blood/CSF isolates were 14 （38.1%）,19A （14.3%）,23F （9.5%）,and 18C （9.5%）.In the sputum isolates the most frequent serotypes were 19F （33.3%）,23F （16.7%）,19A （11.1%）,and 3 （11.1%）.The incidence of penicillin resistance in the blood/CSF and sputum isolates was 66.7% and 55.6%,respectively.Statistical analysis showed that patients ≤5 years old had a higher resistance to penicillin when they compared with the patients ≥65 years old （P=0.011）.Serotypes 14,19A and 19F were significantly associated with penicillin resistance （P 〈0.001）.ST320,ST271,and ST876 isolates showed high resistant rates to several antibiotics including penicillin （P=0.006）.All of the isolates of serotype 19A were resistant to both penicillin and erythromycin,and they were all multi-drug resistant （MDR） isolates.Conclusions The specificity and sensitivity of multiplexPCR are good,and this method represents a substantial savings of time and money,and can be widely used in the laboratory and clinical practice.Data from this research showed an extremely high prevalence of penicillin resistance and an increasing prevalence of multi-drug resistant （MDR） rate in S.pneumoniae.A distinctive emergence of serotype 19A was observed which was also associated with the increasing prevalence of antimicrobial resistance.Therefore,nationwide surveillance of pneumococcal resistance and serotypes is strongly warranted.展开更多
Background According to data from the China Hospital Invasive Fungal Surveillance Net （CHIF-NET） 2010, Candida tropica/is （C. tropica/is） is the third most common pathogen causing invasive candidiasis. Moreover, t...Background According to data from the China Hospital Invasive Fungal Surveillance Net （CHIF-NET） 2010, Candida tropica/is （C. tropica/is） is the third most common pathogen causing invasive candidiasis. Moreover, the majority of fluconazole-resistant C. tropicalis isolates were from a single hospital. Therefore, a molecular epidemiological survey is necessary to investigate the genetic relatedness of C. tropica/is isolates in China. Methods In this study, 48 C. tropicalis isolates causing invasive fungal infections from four tertiary hospitals in China were studied. All the isolates were identified by sequencing the internal transcribed spacer region. Antifungal susceptibility to triazoles, amphotericin B, and caspofungin was determined by the Clinical and Laboratory Standards Institute standard broth microdilution method. Multilocus sequence typing （MLST） was performed, and phylogenetic analysis was further performed by the eBURST and maximum parsimony （MP） methods to characterize the genetic relatedness of isolates. Results MLST discriminated 40 diploid sequence types （DSTs） among 48 isolates, including 36 novel DSTs, and the XYR1 gene showed the highest discriminatory power. The DSTs obtained from this study were compared with those of previously reported C. tropicalis isolates, and there was poor type alignment with regional strains. Nine groups and 11 singletons were identified by eBURST, whereas two groups and 10 subgroups were clustered by MP analysis. Generally, there were no obvious correlations between clonal clusters generated and the specimen source or hospital origin. Seven fiuconazole-resistant isolates were confirmed and assigned to three distinguishable branches. Conclusions The results suggested diverse origins of invasive C. tropicalis isolates in China. Although most invasive C. tropicalis strains in the mainland of China were clustered with previously characterized Asian isolates, major C. tropicalis clusters identified in this study were genetically distinct from those of other geographic regions.展开更多
Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited b...Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited by a paucity of variation within selected loci. For Bartonella henselae （B. henselae）, although the MLST scheme currently used has been proven useful in defining the overall population structure of the species, its reliability for the accurate delineation of closely-related sequence types, between which allelic variation is usually limited to, at most, one or two nucleotide polymorphisms. Exploitation of high-throughput sequencing data allows a more informed selection of MLST loci and thus, potentially, a means of enhancing the sensitivity of the schemes they comprise. Methods We carried out SOLID resequencing on 12 representative B. henselae isolates and explored these data using single nucleotide polymorphism （SNP） analysis. We determined the number and distribution of SNPs in the genes targeted by the established MLST scheme and modified the position of loci within these genes to capture as much genetic variation as possible. Results Using genome-wide SNP data, we found the distribution of SNPs within each open reading frame （ORF） of MLST loci, which were not represented by the established B. henselae MLST scheme. We then modified the position of loci in the MLST scheme to better reflect the polymorphism in the ORF as a whole. The use of amended loci in this scheme allowed previously indistinguishable ST1 strains to be differentiated. However, the diversity of B. henselae was still rare in China. Conclusions Our study demonstrates the use of SNP analysis to facilitate the selection of MLST loci to augment the currently-described scheme for B. henselae. And the diversity among B. henselae strains in China is markedly less than that observed in B. henselae populations elsewhere in the world.展开更多
Objective To investigate genetic and antibiotic resistance characteristics of Campylobacter jejuni(C. jejuni) isolated from Shenzhen. Methods Multilocs sequence typing and agar dilution methods were used to define the...Objective To investigate genetic and antibiotic resistance characteristics of Campylobacter jejuni(C. jejuni) isolated from Shenzhen. Methods Multilocs sequence typing and agar dilution methods were used to define the genotype and antibiotic resistance of C. jejuni, respectively. Results In total, 126 C. jejuni strains were isolated. The prevalence of C. jejuni was 5.3% in diarrheal patients. The prevalence in poultry meat(36.5%) was higher than that in cattle meat(1.1%). However, the prevalence in poultry cloacal swabs(27.0%) was lower than that in cattle stool(57.3%). Sixty-two sequence types were obtained, among which 27 of the STs and 10 alleles were previously unreported. The most frequently observed clonal complexes were ST-21(11.9%), ST-22(10.3%), and ST-403(7.1%). ST-21, ST-45, ST-354, ST-403, and ST-443 complexes overlapped between isolates from patients and cattle, whereas ST-45 and ST-574 complexes overlapped between isolates from patients and poultry. All C. jejuni were resistant to at least one antibiotic. The highest resistance rate was toward ciprofloxacin(89.7%), followed by tetracycline(74.6%), and nalidixic acid(69.0%). Conclusion This is the first report of the genotypes and antibiotic resistance of C. jejuni in Shenzhen. Overlapping clonal complexes were found between isolates from patients and cattle, and between patients and poultry.展开更多
Objective To characterize the meningococcal strains isolated from cases and close contacts with meningococcal disease associated with an outbreak in a jail in May 2010 by investigating the national distribution of hyp...Objective To characterize the meningococcal strains isolated from cases and close contacts with meningococcal disease associated with an outbreak in a jail in May 2010 by investigating the national distribution of hyperinvasive ST-4821 serogroup C clone associated with this outbreak. Methods The cases were described based on the clinical symptoms and laboratory results. Pharyngeal swabs were cultured for N. meningitidis from men in the jail. Meningococcal isolates were identified by serogrouping, pulsed-field gel electrophoresis （PFGE） and multilocus sequence typing （MLST）, respectively. Four hundred and sixteen serogroup C N. meningitidis strains were collected from 27 provinces between 2003 and 2010 for a nationwide survey and analyzed by PFGE and MLST. Results Three persons in a jail system were infected with invasive N. meningitidis serogroup C. All isolates tested had matching PFGE patterns and belonged to the multilocus sequence type （ST） 4821 clonal complex. All 47 N. meningitidis strains were identified from the pharyngeal swabs of 166 peoples in the jail, and 26 of them belonged to ST-4821 serogroup C clone, and 90.14% （375/416） serogroup C strains identified in the nationwide survey belonged to the ST-4821 complex. The ST-4821 serogroup C clone was spread nationwide, distributed in 24 provinces, especially in eastern provinces between 2003 and 2010. Conclusion Endemic transmission and carriage rate of ST-4821 serogroup C clone are high in this jail system. The ST-4821 serogroup C clone is spreading in China and nationwide distributed despite the existence of some effective vaccines.展开更多
Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more acc...Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion(BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability,polymorphic information content(PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.展开更多
The aquatic grass Zizania latifolia grows symbiotically with the fungus Ustilago esculenta producing swollen structures called Jiaobai,widely cultivated in China.A new disease of Z.latifolia was found in Zhejiang Prov...The aquatic grass Zizania latifolia grows symbiotically with the fungus Ustilago esculenta producing swollen structures called Jiaobai,widely cultivated in China.A new disease of Z.latifolia was found in Zhejiang Province,China.Initial lesions appeared on the leaf sheaths or sometimes on the leaves near the leaf sheaths.The lesions extended along the axis of the leaf shoots and formed long brown to dark brown streaks from the leaf sheath to the leaf,causing sheath rot and death of entire leaves on young plants.The pathogen was isolated and identified as the bacterium Pantoea ananatis,based on 16 S ribosomal RNA(r RNA)gene sequencing,multilocus sequence analysis(atp D(β-subunit of ATP synthase F1),gyr B(DNA gyrase subunit B),inf B(translation initiation factor 2),and rpo B(β-subunit of RNA polymerase)genes),and pathogenicity tests.Ultrastructural observations using scanning electron microscopy revealed that the bacterial cells colonized the vascular tissues in leaf sheaths,forming biofilms on the inner surface of vessel walls,and extended between vessel elements via the perforated plates.To achieve efficient detection and diagnosis of P.ananatis,species-specific primer pairs were designed and validated by testing closely related and unrelated species and diseased tissues of Z.latifolia.This is the first report of bacterial sheath rot disease of Z.latifolia caused by P.ananatis in China.展开更多
Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant...Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant production have not been well documented in Mollisols from long-term experiments. Aimed at maintaining and recovering the productivity of Chinese Mollisols, a long-term fertilization experiment had been carried out for 29 years under a wheat-maize-soybean rotation system, involving the application of recycled organic manure (ROM), chemical fertilizers (N, P, and/or K), or ROM plus N, P, and/or K. In the present study, the effects of different treatments were evaluated by determining soil physicochemical features, soybean production, and soybean rhizobial diversity. The results showed that application of ROM plus NPK maintained or increased soil fertility, which was accompanied by higher production and higher diversity of rhizobia, as compared with the other treatments. The negative association of Bradyrhizobium japonicum with N fertilizer, positive association of B. diazoefficiens with soil pH, and alleviation of N-inhibition on the diversity of Bradyrhizobium by the addition of ROM were recorded as new findings. Therefore, application of ROM or ROM plus NPK could be a feasible strategy for maintaining and recovering the fertility of Chinese Mollisols, whereas rhizobial diversity could be an indicator of soil fertility.展开更多
Pathway analysis,also known as gene-set enrichment analysis,is a multilocus analytic strategy that integrates a priori,biological knowledge into the statistical analysis of high-throughput genetics data.Originally dev...Pathway analysis,also known as gene-set enrichment analysis,is a multilocus analytic strategy that integrates a priori,biological knowledge into the statistical analysis of high-throughput genetics data.Originally developed for the studies of gene expression data,it has become a powerful analytic procedure for indepth mining of genome-wide genetic variation data.Astonishing discoveries were made in the past years,uncovering genes and biological mechanisms underlying common and complex disorders.However,as massive amounts of diverse functional genomics data accrue,there is a pressing need for newer generations of pathway analysis methods that can utilize multiple layers of high-throughput genomics data.In this review,we provide an intellectual foundation of this powerful analytic strategy,as well as an update of the state-of-the-art in recent method developments.The goal of this review is threefold:(1)introduce the motivation and basic steps of pathway analysis for genome-wide genetic variation data;(2)review the merits and the shortcomings of classic and newly emerging integrative pathway analysis tools;and(3)discuss remaining challenges and future directions for further method developments.展开更多
Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isol...Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isolates of B. coagulans from 22 provinces or autonomous regions in China. B. coagulans isolates were highly diverse and a total of 33(sequence typings) STs were found. These isolates had a weak clonal population structure and strong indications of intraspecies recombination. The evolution direction of B. coagulans was not correlated with geography or isolation source. Fifteen strains were selected for further analysis based on proximity relationships from the phylogenetic tree. Five isolates(B. coagulans-1, B. coagulans-10, B. coagulans-39, B. coagulans-70 and B. coagulans-71) with good spore-forming ability relative to the rest of the isolates were evaluated for constipation relief. B. coagulans-39 significantly relieved constipation symptoms in mice by regulating intestinal flora, increasing the production of short-chain fatty acids and restoring the level of gastrointestinal regulatory peptides. Comparative genomic analysis showed the beneficial effects of B. coagulans-39 might be associated with specific functional genes that are involved in the utilization of various carbohydrates as primary substrates and short-chain fatty acid production.展开更多
Introduction: Enterobacter cloacae strains have been isolated from Eastern Cape hospitalised patients. Methodology: We have molecularly characterised blaOXA-48-, blaIMP- and blaVIM-expressing E. cloacae isolates demon...Introduction: Enterobacter cloacae strains have been isolated from Eastern Cape hospitalised patients. Methodology: We have molecularly characterised blaOXA-48-, blaIMP- and blaVIM-expressing E. cloacae isolates demonstrating resistance to carbapenems from five hospitals by multilocus sequence typing. Organism identification and antimicrobial susceptibility testing was done using automated systems and the isolates were screened for carbapenemases using either conventional or real-time PCR and then typed using multilocus sequence typing. Further characterisation of IMP-type-producing E. cloacae isolates, an unusual occurrence in South Africa, was performed by pulsed-field gel electrophoresis. Results and Conclusion: Twenty-five E. cloacae isolates from 24 patients were investigated. Eighteen (72%) isolates harboured either one of the following genes: blaIMP, blaVIM or blaOXA-48. Multilocus sequence typing data and pulsed-field gel electrophoresis showed that several strains from the same geographical region and hospitals were genetically related.展开更多
Weaverbirds are a speciose group of colorful passerines inhabiting the Old World Tropics.Nevertheless,the Oriental weaverbirds(Ploceus spp.),widespread across southern Asia,are much less diverse and restricted to a fe...Weaverbirds are a speciose group of colorful passerines inhabiting the Old World Tropics.Nevertheless,the Oriental weaverbirds(Ploceus spp.),widespread across southern Asia,are much less diverse and restricted to a few ecological niches compared to their African counterpart.To investigate their phylogeography,we retrieved 101 samples of Baya Weaver(P.philippinus),Streaked Weaver(P.manyar),Black-Throated Weaver(P.benghalensis)and Asian Golden Weaver(P.hypoxanthus)along with GenBank sequences of Finn's Weaver(P.megarhynchus).We reconstructed the first molecular phylogeny based on a dataset consisting of both mitochondrial and nuclear genes,dating the most recent common ancestor of Oriental Ploceus to~11 mya.Subsequent speciation appears to have been a combination of divergence within the Indian subcontinent and dispersal across a barrier situated between the Indian subcontinent and the Indochinese region,which provided habitats with a varying degree of isolations and ultimately promoted divergences in allopatry.Two descendants of the earliest nodes,P.megarhynchus and P.hypoxanthus,are both rare and local,often found near large river systems,which perhaps reflects niche conservatism and a lack of adaptive potential.The three smaller species are all widespread,common and less habitat specific.The most recent divergence,between western and eastern P.philippinus populations,is supported by both phylogenetic and morphological evidence,pointing toward limited gene flow between them.However,a zone of intergradation may exist in Myanmar and Brahmaputra flood plains,thus preventing a recommendation for species level recognition without further study.展开更多
Beef is a source of human Campylobacter infections.Antimicrobial treatment is needed when patients are immuno‑compromised or have other comorbidities.Therefore,we investigated the prevalence and antimicrobial resistan...Beef is a source of human Campylobacter infections.Antimicrobial treatment is needed when patients are immuno‑compromised or have other comorbidities.Therefore,we investigated the prevalence and antimicrobial resistance of Campylobacter spp.in beef cattle in Japan.Rectal swab samples were collected from 164 beef cattle at an abattoir between March 2021 and August 2021,and Campylobacter spp.were isolated from 94(57.3%)cattle.C.jejuni and C.coli were isolated from 68 and 26 cattle,respectively.For Campylobacter jejuni,the resistant rates against ampicillin,tetracycline and ciprofoxacin were 20.6,75.0 and 64.7%,respectively.For C.coli,the resistant rates against ampicil‑lin,tetracycline and ciprofoxacin were 53.8,76.9 and 88.5%,respectively.No Campylobacter isolates were resistant to erythromycin.By multilocus sequence typing,C.jejuni and C.coli isolates were classifed into 22 and 2 sequence types(STs).The top three STs of C.jejuni were ST806(12 isolates),ST21(nine isolates),and ST459(eight isolates).The most frequent ST of C.coli was ST1068(23 isolates).The results suggest that Campylobacter spp.are prevalent in the gastrointestinal tract of beef cattle slaughtered at abattoirs.Furthermore,the administration of erythromycin is efec‑tive against human campylobacteriosis caused by beef consumption.Monitoring the prevalence and antimicrobial resistance of Campylobacter spp.in beef cattle could be useful for managing the risk of human campylobacteriosis.展开更多
Nasal carriage of <i>Staphylococcus aureus</i> has been identified as a risk factor for the development of staphylococcal infections caused by endogenous colonizing strains. Information on the genotypic di...Nasal carriage of <i>Staphylococcus aureus</i> has been identified as a risk factor for the development of staphylococcal infections caused by endogenous colonizing strains. Information on the genotypic diversity of <i>Staphylococcus aureus</i> is relevant for managing epidemiological and clinical challenges resulting from the evolutionary differences of this bacterium. The objective of this study was to determine and compare the molecular diversity of <i>Staphylococcus aureus</i> isolates from three high-risk populations in Yaounde, Cameroon. Molecular analysis confirmed that 95% of 100 tested isolates were <i>S. aureus</i>. The <i>mec</i>A and Panton Valentine-Leukocidin (PVL) genes (<i>lukS/F-PV</i>) were detected in 37% (35/95) and 43% (41/95) of isolates respectively and 18% (17/95) of the isolates harboured both the <i>mec</i>A and <i>lukS/F-PV</i> genes. A mixed distribution of both methicillin sensitive <i>S. aureus</i> (MSSA)/PVL and methicillin resistant <i>S. aureus</i> (MRSA)/PVL strains were detected within the study population. Community associated MRSA accounted for 94% (33/35) of the isolates, further classified into allotypes SCC<i>mec</i> type IV 54% (19/35) and SCC<i>mec</i> type V 40% (14/35), while two isolates were hospital associated SCC<i>mec</i> type II strains. A majority of the isolates harboured a single aggressive gene regulator allele <i>agr</i> type I. Pulsed Field Gel Electrophoresis (PFGE) generated 18 pulsotypes that grouped isolates irrespective of the study population. Multilocus Sequence Typing (MLST) of 12 selected isolates was assigned to six pandemic clonal complexes (CC): CC5 (ST5), CC8 [ST8, (n = 3)], CC15 (ST 15), CC25 (ST 25), CC72 [ST72 (n = 2)] and CC121 [ST 121 (n = 2)] and three atypical sequence types ST 508, ST 699 (CC45) and ST 1289 (CC 88). The study population represents an important reservoir for MRSA, MRSA-PVL and MSSA-PVL which could serve as focal point for further dissemination bringing about significant clinical and epidemiological implications. The predominance of SCC<i>mec</i> IV and <i>agr</i> types in this setting warrants further investigation. Isolates were genetically diverse with MLST indicating that pandemic ST8 was predominant. Detection of atypical STs has provided an insight into the necessity for constant monitoring.展开更多
Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most p...Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.展开更多
Multilocus genome-wide association study has become the state-of-the-art tool for dissecting the genetic architecture of complex and multiomic traits.However,most existing multilocus methods require relatively long co...Multilocus genome-wide association study has become the state-of-the-art tool for dissecting the genetic architecture of complex and multiomic traits.However,most existing multilocus methods require relatively long computational time when analyzing large datasets.To address this issue,in this study,we proposed a fast mrMLM method,namely,best linear unbiased prediction multilocus random-SNP-effect mixed linear model(BLUPmrMLM).First,genome-wide single-marker scanning in mrMLM was replaced by vectorized Wald tests based on the best linear unbiased prediction(BLUP)values of marker effects and their variances in BLUPmrMLM.Then,adaptive best subset selection(ABESS)was used to identify potentially associated markers on each chromosome to reduce computational time when estimating marker effects via empirical Bayes.Finally,shared memory and parallel computing schemes were used to reduce the computational time.In simulation studies,BLUPmrMLM outperformed GEMMA,EMMAX,mrMLM,and FarmCPU as well as the control method(BLUPmrMLM with ABESS removed),in terms of computational time,power,accuracy for estimating quantitative trait nucleotide positions and effects,false positive rate,false discovery rate,false negative rate,and F1 score.In the reanalysis of two large rice datasets,BLUPmrMLM significantly reduced the computational time and identified more previously reported genes,compared with the aforementioned methods.This study provides an excellent multilocus model method for the analysis of large-scale and multiomic datasets.The software mrMLM v5.1 is available at BioCode(https://ngdc.cncb.ac.cn/biocode/tool/BT007388)or GitHub(https://github.com/YuanmingZhang65/mrMLM).展开更多
基金supported by the fund of State Key Laboratory for Infectious Diseases Prevention and Control (2011SKLID208)the project "Transmission Mode of Tuberculosis"of National Key Program of Mega Infectious Diseases (2008ZX100/03-010)
文摘Objective Tuberculosis remains one of the most serious infectious diseases in the world. In this study, a scheme of Mycobacterium tuberculosis （M. tuberculosis） multilocus sequence analysis （MLSA） was established for the phylogenetic and epidemiology analysis. Methods To establish the scheme of M. tuberculosis MLSA, the genome of H37Rv, CCDC5079 and CCDC5180 were compared, and some variable genes were chosen to be the MLSA typing scheme. 44 M. tuberculosis clinical isolates were typed by MLSA, IS6110-RFLP, and soligotyping, to evaluate the MLSA methods. Results After comparison of the genome, seven high discrimination gene loci （recX, rpsL, rmlC, rpmG1, mprA, gcvH, ideR） were chosen to be the MLSA typing scheme finally. 11 variable SNP sites of those seven genes were found among the 44 M. tuberculosis isolate strains and 11 sequence types （STs） were identified. Based on the Hunter-Gaston Index （HGI）, MLSA typing was not as good for discrimination at the strain level as IS6110-RFLP, but the HGI was much better than that of spoligotyping. In addition, the MEGA analysis result of MLSA data was similar to spoligotyping/PGG lineage, showing a strong phylogenetic signal in the modern strains of M. tuberculosis. The MLSA data analysis by eBURST revealed that 4 sequence types （ST） came into a main cluster, showing the major clonal complexes in those 44 strains. Conclusion MLSA genotyping not only can be used for molecular typing, but also is an ideal method for the phylogenetic analysis for M. tuberculosis.
基金supported by the Thailand Research Fund and the Commission on Higher Education(grant no. MRG5180102 to Weerachai Saijuntha).
文摘Objective:To explore the genetic variation and differentiation of 2 echinostomes from genus Echinostoma,i.e.Echinostoma revolutum(E.revolution) and Echinostoma malayanum(E. malayanum) from Khon Kaen Province,Thailand.Methods:These parasites were compared at 22 enzymes encoding a presumptive 30 loci by using multilocus enzyme electrophoresis (MEE) technique.Results:Twenty-two loci can be used as diagnostic markers to differentiate these 2 species.E.revolutum and E.malayanum had fixed genetic differences at 70%of loci, whereas both species had fixed genetic differences from the liver fluke,Opisthorchis viverrini at 91%of loci.Intraspecific variation within a population of E.revolutum was observed at 5 polymorphic loci.Conclusions:MEE is a powerful technique to investigate genetic variation and differentiation of E.revolutum and E.malayanum.
文摘Lupinus is known to form endophytic associations with both nodulating and non-nodulating bacteria. In this study, multilocus sequence analysis (MLSA) was used to analyze phylogenetic relationships among root nodule bacteria associated with Lupinus and soybean. Out of 17 bacterial strains analyzed, 13 strains isolated from root nodules of Lupinus spp. were obtained from the National Rhizobium Germplasm Resource Collection, USDA. Additionally, two strains of root-nodule bacteria isolated each from native lupinus and domestic soybean were examined. Sequences of the 16S rRNA gene and three house-keeping genes (atpD, dnaK and glnII) were used. All the reference genes were retrieved from the existing complete genome sequences only. The clustering of 12 of the strains was consistent among single and concatenated gene trees, but not USDA strains 3044, 3048, 3504, 3715, and 3060. According to the concatenated phylogeny, we suggest that USDA 3040, 3042, 3044, 3048, 3051, 3060, 3504, 3709 and 3715 are Bradyrhizobium, USDA 3063 and 3717 are Mesorhizobium, USDA 3043 is Burkholderia and USDA 3057a is Microvirga. The two strains isolated from native lupines in this study are Burkholderia and Rhizobium, whereas the two from domestic soybean are Bradyrhizobium. This study emphasizes the robustness of MLSA, the diversity of bacterial species that are capable of nodulating lupine and the substantial capability of Burkholderia spp. to colonize lupine root nodules.
文摘Background Streptococcus pneumoniae （S.pneumoniae） is a major causative agent of severe infections,including sepsis,pneumonia,meningitis,and otitis media,and has become a major public health concern.We report the pneumococcal serotype and sequence type （ST） distribution,and antimicrobial resistance of 39 S.pneumoniae strains from seven hospitals in China.Methods Blood/cerebrospinal fluid （CSF） and sputum isolates from patients were analyzed to determine S.pneumoniae serotypes by polymerase chain reaction （PCR） and the Neufeld Quellung reaction,the multilocus sequence types （MLST） by PCR and sequencing,and susceptibility to antimicrobial agents by the VITEK Gram Positive Susceptibility Card.Results A total of 39 isolates were collected including 21 blood/CSF and 18 sputum isolates.Conventional serotyping by the Quellung reaction required 749 reactions.In contrast,PCR based typing needed only 106 PCR reactions.The most frequent serotypes from the blood/CSF isolates were 14 （38.1%）,19A （14.3%）,23F （9.5%）,and 18C （9.5%）.In the sputum isolates the most frequent serotypes were 19F （33.3%）,23F （16.7%）,19A （11.1%）,and 3 （11.1%）.The incidence of penicillin resistance in the blood/CSF and sputum isolates was 66.7% and 55.6%,respectively.Statistical analysis showed that patients ≤5 years old had a higher resistance to penicillin when they compared with the patients ≥65 years old （P=0.011）.Serotypes 14,19A and 19F were significantly associated with penicillin resistance （P 〈0.001）.ST320,ST271,and ST876 isolates showed high resistant rates to several antibiotics including penicillin （P=0.006）.All of the isolates of serotype 19A were resistant to both penicillin and erythromycin,and they were all multi-drug resistant （MDR） isolates.Conclusions The specificity and sensitivity of multiplexPCR are good,and this method represents a substantial savings of time and money,and can be widely used in the laboratory and clinical practice.Data from this research showed an extremely high prevalence of penicillin resistance and an increasing prevalence of multi-drug resistant （MDR） rate in S.pneumoniae.A distinctive emergence of serotype 19A was observed which was also associated with the increasing prevalence of antimicrobial resistance.Therefore,nationwide surveillance of pneumococcal resistance and serotypes is strongly warranted.
文摘Background According to data from the China Hospital Invasive Fungal Surveillance Net （CHIF-NET） 2010, Candida tropica/is （C. tropica/is） is the third most common pathogen causing invasive candidiasis. Moreover, the majority of fluconazole-resistant C. tropicalis isolates were from a single hospital. Therefore, a molecular epidemiological survey is necessary to investigate the genetic relatedness of C. tropica/is isolates in China. Methods In this study, 48 C. tropicalis isolates causing invasive fungal infections from four tertiary hospitals in China were studied. All the isolates were identified by sequencing the internal transcribed spacer region. Antifungal susceptibility to triazoles, amphotericin B, and caspofungin was determined by the Clinical and Laboratory Standards Institute standard broth microdilution method. Multilocus sequence typing （MLST） was performed, and phylogenetic analysis was further performed by the eBURST and maximum parsimony （MP） methods to characterize the genetic relatedness of isolates. Results MLST discriminated 40 diploid sequence types （DSTs） among 48 isolates, including 36 novel DSTs, and the XYR1 gene showed the highest discriminatory power. The DSTs obtained from this study were compared with those of previously reported C. tropicalis isolates, and there was poor type alignment with regional strains. Nine groups and 11 singletons were identified by eBURST, whereas two groups and 10 subgroups were clustered by MP analysis. Generally, there were no obvious correlations between clonal clusters generated and the specimen source or hospital origin. Seven fiuconazole-resistant isolates were confirmed and assigned to three distinguishable branches. Conclusions The results suggested diverse origins of invasive C. tropicalis isolates in China. Although most invasive C. tropicalis strains in the mainland of China were clustered with previously characterized Asian isolates, major C. tropicalis clusters identified in this study were genetically distinct from those of other geographic regions.
文摘Background Multi-locus sequence typing （MLST） is widely used to explore the population structure of numerous bacterial pathogens. However, for genotypically-restricted pathogens, the sensitivity of MLST is limited by a paucity of variation within selected loci. For Bartonella henselae （B. henselae）, although the MLST scheme currently used has been proven useful in defining the overall population structure of the species, its reliability for the accurate delineation of closely-related sequence types, between which allelic variation is usually limited to, at most, one or two nucleotide polymorphisms. Exploitation of high-throughput sequencing data allows a more informed selection of MLST loci and thus, potentially, a means of enhancing the sensitivity of the schemes they comprise. Methods We carried out SOLID resequencing on 12 representative B. henselae isolates and explored these data using single nucleotide polymorphism （SNP） analysis. We determined the number and distribution of SNPs in the genes targeted by the established MLST scheme and modified the position of loci within these genes to capture as much genetic variation as possible. Results Using genome-wide SNP data, we found the distribution of SNPs within each open reading frame （ORF） of MLST loci, which were not represented by the established B. henselae MLST scheme. We then modified the position of loci in the MLST scheme to better reflect the polymorphism in the ORF as a whole. The use of amended loci in this scheme allowed previously indistinguishable ST1 strains to be differentiated. However, the diversity of B. henselae was still rare in China. Conclusions Our study demonstrates the use of SNP analysis to facilitate the selection of MLST loci to augment the currently-described scheme for B. henselae. And the diversity among B. henselae strains in China is markedly less than that observed in B. henselae populations elsewhere in the world.
基金supported by Sanming Project of Medicine in Shenzhen[SZSM201803081]Shenzhen Technology and Innovation Plan,China[JCYJ 20140416095154399]Nanshan District Technology and Innovation Plan,Shenzhen,China[2016064]
文摘Objective To investigate genetic and antibiotic resistance characteristics of Campylobacter jejuni(C. jejuni) isolated from Shenzhen. Methods Multilocs sequence typing and agar dilution methods were used to define the genotype and antibiotic resistance of C. jejuni, respectively. Results In total, 126 C. jejuni strains were isolated. The prevalence of C. jejuni was 5.3% in diarrheal patients. The prevalence in poultry meat(36.5%) was higher than that in cattle meat(1.1%). However, the prevalence in poultry cloacal swabs(27.0%) was lower than that in cattle stool(57.3%). Sixty-two sequence types were obtained, among which 27 of the STs and 10 alleles were previously unreported. The most frequently observed clonal complexes were ST-21(11.9%), ST-22(10.3%), and ST-403(7.1%). ST-21, ST-45, ST-354, ST-403, and ST-443 complexes overlapped between isolates from patients and cattle, whereas ST-45 and ST-574 complexes overlapped between isolates from patients and poultry. All C. jejuni were resistant to at least one antibiotic. The highest resistance rate was toward ciprofloxacin(89.7%), followed by tetracycline(74.6%), and nalidixic acid(69.0%). Conclusion This is the first report of the genotypes and antibiotic resistance of C. jejuni in Shenzhen. Overlapping clonal complexes were found between isolates from patients and cattle, and between patients and poultry.
基金supported by Research Fund from Ministry of Health and Ministry of Science and Technology of the People’s Republic of China,2013ZX10004221,2012ZX10004215,and 2011CB504900
文摘Objective To characterize the meningococcal strains isolated from cases and close contacts with meningococcal disease associated with an outbreak in a jail in May 2010 by investigating the national distribution of hyperinvasive ST-4821 serogroup C clone associated with this outbreak. Methods The cases were described based on the clinical symptoms and laboratory results. Pharyngeal swabs were cultured for N. meningitidis from men in the jail. Meningococcal isolates were identified by serogrouping, pulsed-field gel electrophoresis （PFGE） and multilocus sequence typing （MLST）, respectively. Four hundred and sixteen serogroup C N. meningitidis strains were collected from 27 provinces between 2003 and 2010 for a nationwide survey and analyzed by PFGE and MLST. Results Three persons in a jail system were infected with invasive N. meningitidis serogroup C. All isolates tested had matching PFGE patterns and belonged to the multilocus sequence type （ST） 4821 clonal complex. All 47 N. meningitidis strains were identified from the pharyngeal swabs of 166 peoples in the jail, and 26 of them belonged to ST-4821 serogroup C clone, and 90.14% （375/416） serogroup C strains identified in the nationwide survey belonged to the ST-4821 complex. The ST-4821 serogroup C clone was spread nationwide, distributed in 24 provinces, especially in eastern provinces between 2003 and 2010. Conclusion Endemic transmission and carriage rate of ST-4821 serogroup C clone are high in this jail system. The ST-4821 serogroup C clone is spreading in China and nationwide distributed despite the existence of some effective vaccines.
基金supported by grants from the National Program on the Development of Basic Research (2011CB100100)the Priority Academic Program Development of Jiangsu Higher Education Institutions, the National Natural Science Foundations (31391632, 31200943, 31171187, and 91535103)+3 种基金the National High-tech R&D Program (863 Program) (2014AA10A601-5)the Natural Science Foundations of Jiangsu Province (BK20150010)the Natural Science Foundation of the Jiangsu Higher Education Institutions (14KJA210005)the Innovative Research Team of Universities in Jiangsu Province (KYLX_1352)
文摘Many complex traits are highly correlated rather than independent. By taking the correlation structure of multiple traits into account, joint association analyses can achieve both higher statistical power and more accurate estimation. To develop a statistical approach to joint association analysis that includes allele detection and genetic effect estimation, we combined multivariate partial least squares regression with variable selection strategies and selected the optimal model using the Bayesian Information Criterion(BIC). We then performed extensive simulations under varying heritabilities and sample sizes to compare the performance achieved using our method with those obtained by single-trait multilocus methods. Joint association analysis has measurable advantages over single-trait methods, as it exhibits superior gene detection power, especially for pleiotropic genes. Sample size, heritability,polymorphic information content(PIC), and magnitude of gene effects influence the statistical power, accuracy and precision of effect estimation by the joint association analysis.
基金supported by the Key Project of National Natural Science Foundation of China(NSFC)Regional Innovation and Development Joint Foundation(No.U20A2043)the NSFC(No.31501342)。
文摘The aquatic grass Zizania latifolia grows symbiotically with the fungus Ustilago esculenta producing swollen structures called Jiaobai,widely cultivated in China.A new disease of Z.latifolia was found in Zhejiang Province,China.Initial lesions appeared on the leaf sheaths or sometimes on the leaves near the leaf sheaths.The lesions extended along the axis of the leaf shoots and formed long brown to dark brown streaks from the leaf sheath to the leaf,causing sheath rot and death of entire leaves on young plants.The pathogen was isolated and identified as the bacterium Pantoea ananatis,based on 16 S ribosomal RNA(r RNA)gene sequencing,multilocus sequence analysis(atp D(β-subunit of ATP synthase F1),gyr B(DNA gyrase subunit B),inf B(translation initiation factor 2),and rpo B(β-subunit of RNA polymerase)genes),and pathogenicity tests.Ultrastructural observations using scanning electron microscopy revealed that the bacterial cells colonized the vascular tissues in leaf sheaths,forming biofilms on the inner surface of vessel walls,and extended between vessel elements via the perforated plates.To achieve efficient detection and diagnosis of P.ananatis,species-specific primer pairs were designed and validated by testing closely related and unrelated species and diseased tissues of Z.latifolia.This is the first report of bacterial sheath rot disease of Z.latifolia caused by P.ananatis in China.
基金financially supported by the National Key Research and Development Program of China(No.2018YFD1000905)the Applied Technology Research and Development Program of Heilongjiang Province,China(Nos.GA19B101,GA19B105,and GY-2017ZB006)
文摘Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant production have not been well documented in Mollisols from long-term experiments. Aimed at maintaining and recovering the productivity of Chinese Mollisols, a long-term fertilization experiment had been carried out for 29 years under a wheat-maize-soybean rotation system, involving the application of recycled organic manure (ROM), chemical fertilizers (N, P, and/or K), or ROM plus N, P, and/or K. In the present study, the effects of different treatments were evaluated by determining soil physicochemical features, soybean production, and soybean rhizobial diversity. The results showed that application of ROM plus NPK maintained or increased soil fertility, which was accompanied by higher production and higher diversity of rhizobia, as compared with the other treatments. The negative association of Bradyrhizobium japonicum with N fertilizer, positive association of B. diazoefficiens with soil pH, and alleviation of N-inhibition on the diversity of Bradyrhizobium by the addition of ROM were recorded as new findings. Therefore, application of ROM or ROM plus NPK could be a feasible strategy for maintaining and recovering the fertility of Chinese Mollisols, whereas rhizobial diversity could be an indicator of soil fertility.
基金supported by National Institutes of Health R00 MH101367 and R01 MH119243(to P.H.Lee)。
文摘Pathway analysis,also known as gene-set enrichment analysis,is a multilocus analytic strategy that integrates a priori,biological knowledge into the statistical analysis of high-throughput genetics data.Originally developed for the studies of gene expression data,it has become a powerful analytic procedure for indepth mining of genome-wide genetic variation data.Astonishing discoveries were made in the past years,uncovering genes and biological mechanisms underlying common and complex disorders.However,as massive amounts of diverse functional genomics data accrue,there is a pressing need for newer generations of pathway analysis methods that can utilize multiple layers of high-throughput genomics data.In this review,we provide an intellectual foundation of this powerful analytic strategy,as well as an update of the state-of-the-art in recent method developments.The goal of this review is threefold:(1)introduce the motivation and basic steps of pathway analysis for genome-wide genetic variation data;(2)review the merits and the shortcomings of classic and newly emerging integrative pathway analysis tools;and(3)discuss remaining challenges and future directions for further method developments.
基金supported by the National Natural Science Foundation of China Program[No.31871773 and No.31820103010]Projects of Innovation and Development Pillar Program for Key Industries in Southern Xinjiang of Xinjiang Production and Construction Corps[2018DB002]+2 种基金National First-Class Discipline Program of Food Science and Technology[JUFSTR20180102]the BBSRC Newton Fund Joint Centre AwardCollaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isolates of B. coagulans from 22 provinces or autonomous regions in China. B. coagulans isolates were highly diverse and a total of 33(sequence typings) STs were found. These isolates had a weak clonal population structure and strong indications of intraspecies recombination. The evolution direction of B. coagulans was not correlated with geography or isolation source. Fifteen strains were selected for further analysis based on proximity relationships from the phylogenetic tree. Five isolates(B. coagulans-1, B. coagulans-10, B. coagulans-39, B. coagulans-70 and B. coagulans-71) with good spore-forming ability relative to the rest of the isolates were evaluated for constipation relief. B. coagulans-39 significantly relieved constipation symptoms in mice by regulating intestinal flora, increasing the production of short-chain fatty acids and restoring the level of gastrointestinal regulatory peptides. Comparative genomic analysis showed the beneficial effects of B. coagulans-39 might be associated with specific functional genes that are involved in the utilization of various carbohydrates as primary substrates and short-chain fatty acid production.
文摘Introduction: Enterobacter cloacae strains have been isolated from Eastern Cape hospitalised patients. Methodology: We have molecularly characterised blaOXA-48-, blaIMP- and blaVIM-expressing E. cloacae isolates demonstrating resistance to carbapenems from five hospitals by multilocus sequence typing. Organism identification and antimicrobial susceptibility testing was done using automated systems and the isolates were screened for carbapenemases using either conventional or real-time PCR and then typed using multilocus sequence typing. Further characterisation of IMP-type-producing E. cloacae isolates, an unusual occurrence in South Africa, was performed by pulsed-field gel electrophoresis. Results and Conclusion: Twenty-five E. cloacae isolates from 24 patients were investigated. Eighteen (72%) isolates harboured either one of the following genes: blaIMP, blaVIM or blaOXA-48. Multilocus sequence typing data and pulsed-field gel electrophoresis showed that several strains from the same geographical region and hospitals were genetically related.
基金supported by fellowships of the Ministry of Universities of the Spanish Government(María Zambrano/Next Generation EU)the Portuguese Foundation for Science and Technology(FCT,PTDC/BAA-AGR/28866/2017)to GF.
文摘Weaverbirds are a speciose group of colorful passerines inhabiting the Old World Tropics.Nevertheless,the Oriental weaverbirds(Ploceus spp.),widespread across southern Asia,are much less diverse and restricted to a few ecological niches compared to their African counterpart.To investigate their phylogeography,we retrieved 101 samples of Baya Weaver(P.philippinus),Streaked Weaver(P.manyar),Black-Throated Weaver(P.benghalensis)and Asian Golden Weaver(P.hypoxanthus)along with GenBank sequences of Finn's Weaver(P.megarhynchus).We reconstructed the first molecular phylogeny based on a dataset consisting of both mitochondrial and nuclear genes,dating the most recent common ancestor of Oriental Ploceus to~11 mya.Subsequent speciation appears to have been a combination of divergence within the Indian subcontinent and dispersal across a barrier situated between the Indian subcontinent and the Indochinese region,which provided habitats with a varying degree of isolations and ultimately promoted divergences in allopatry.Two descendants of the earliest nodes,P.megarhynchus and P.hypoxanthus,are both rare and local,often found near large river systems,which perhaps reflects niche conservatism and a lack of adaptive potential.The three smaller species are all widespread,common and less habitat specific.The most recent divergence,between western and eastern P.philippinus populations,is supported by both phylogenetic and morphological evidence,pointing toward limited gene flow between them.However,a zone of intergradation may exist in Myanmar and Brahmaputra flood plains,thus preventing a recommendation for species level recognition without further study.
基金supported by grants from the Ministry of Health,Labor,and Welfare of Japan(21KA1004).
文摘Beef is a source of human Campylobacter infections.Antimicrobial treatment is needed when patients are immuno‑compromised or have other comorbidities.Therefore,we investigated the prevalence and antimicrobial resistance of Campylobacter spp.in beef cattle in Japan.Rectal swab samples were collected from 164 beef cattle at an abattoir between March 2021 and August 2021,and Campylobacter spp.were isolated from 94(57.3%)cattle.C.jejuni and C.coli were isolated from 68 and 26 cattle,respectively.For Campylobacter jejuni,the resistant rates against ampicillin,tetracycline and ciprofoxacin were 20.6,75.0 and 64.7%,respectively.For C.coli,the resistant rates against ampicil‑lin,tetracycline and ciprofoxacin were 53.8,76.9 and 88.5%,respectively.No Campylobacter isolates were resistant to erythromycin.By multilocus sequence typing,C.jejuni and C.coli isolates were classifed into 22 and 2 sequence types(STs).The top three STs of C.jejuni were ST806(12 isolates),ST21(nine isolates),and ST459(eight isolates).The most frequent ST of C.coli was ST1068(23 isolates).The results suggest that Campylobacter spp.are prevalent in the gastrointestinal tract of beef cattle slaughtered at abattoirs.Furthermore,the administration of erythromycin is efec‑tive against human campylobacteriosis caused by beef consumption.Monitoring the prevalence and antimicrobial resistance of Campylobacter spp.in beef cattle could be useful for managing the risk of human campylobacteriosis.
文摘Nasal carriage of <i>Staphylococcus aureus</i> has been identified as a risk factor for the development of staphylococcal infections caused by endogenous colonizing strains. Information on the genotypic diversity of <i>Staphylococcus aureus</i> is relevant for managing epidemiological and clinical challenges resulting from the evolutionary differences of this bacterium. The objective of this study was to determine and compare the molecular diversity of <i>Staphylococcus aureus</i> isolates from three high-risk populations in Yaounde, Cameroon. Molecular analysis confirmed that 95% of 100 tested isolates were <i>S. aureus</i>. The <i>mec</i>A and Panton Valentine-Leukocidin (PVL) genes (<i>lukS/F-PV</i>) were detected in 37% (35/95) and 43% (41/95) of isolates respectively and 18% (17/95) of the isolates harboured both the <i>mec</i>A and <i>lukS/F-PV</i> genes. A mixed distribution of both methicillin sensitive <i>S. aureus</i> (MSSA)/PVL and methicillin resistant <i>S. aureus</i> (MRSA)/PVL strains were detected within the study population. Community associated MRSA accounted for 94% (33/35) of the isolates, further classified into allotypes SCC<i>mec</i> type IV 54% (19/35) and SCC<i>mec</i> type V 40% (14/35), while two isolates were hospital associated SCC<i>mec</i> type II strains. A majority of the isolates harboured a single aggressive gene regulator allele <i>agr</i> type I. Pulsed Field Gel Electrophoresis (PFGE) generated 18 pulsotypes that grouped isolates irrespective of the study population. Multilocus Sequence Typing (MLST) of 12 selected isolates was assigned to six pandemic clonal complexes (CC): CC5 (ST5), CC8 [ST8, (n = 3)], CC15 (ST 15), CC25 (ST 25), CC72 [ST72 (n = 2)] and CC121 [ST 121 (n = 2)] and three atypical sequence types ST 508, ST 699 (CC45) and ST 1289 (CC 88). The study population represents an important reservoir for MRSA, MRSA-PVL and MSSA-PVL which could serve as focal point for further dissemination bringing about significant clinical and epidemiological implications. The predominance of SCC<i>mec</i> IV and <i>agr</i> types in this setting warrants further investigation. Isolates were genetically diverse with MLST indicating that pandemic ST8 was predominant. Detection of atypical STs has provided an insight into the necessity for constant monitoring.
文摘Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.
基金supported by the National Natural Science Foundation of China(Grant Nos.32070557 and 32270673)the Huazhong Agricultural University Scientific&Technological Self-innovation Foundation,China(Grant No.2014RC020).
文摘Multilocus genome-wide association study has become the state-of-the-art tool for dissecting the genetic architecture of complex and multiomic traits.However,most existing multilocus methods require relatively long computational time when analyzing large datasets.To address this issue,in this study,we proposed a fast mrMLM method,namely,best linear unbiased prediction multilocus random-SNP-effect mixed linear model(BLUPmrMLM).First,genome-wide single-marker scanning in mrMLM was replaced by vectorized Wald tests based on the best linear unbiased prediction(BLUP)values of marker effects and their variances in BLUPmrMLM.Then,adaptive best subset selection(ABESS)was used to identify potentially associated markers on each chromosome to reduce computational time when estimating marker effects via empirical Bayes.Finally,shared memory and parallel computing schemes were used to reduce the computational time.In simulation studies,BLUPmrMLM outperformed GEMMA,EMMAX,mrMLM,and FarmCPU as well as the control method(BLUPmrMLM with ABESS removed),in terms of computational time,power,accuracy for estimating quantitative trait nucleotide positions and effects,false positive rate,false discovery rate,false negative rate,and F1 score.In the reanalysis of two large rice datasets,BLUPmrMLM significantly reduced the computational time and identified more previously reported genes,compared with the aforementioned methods.This study provides an excellent multilocus model method for the analysis of large-scale and multiomic datasets.The software mrMLM v5.1 is available at BioCode(https://ngdc.cncb.ac.cn/biocode/tool/BT007388)or GitHub(https://github.com/YuanmingZhang65/mrMLM).
