Spatial distribution features of sequence types of moderate and strong earthquake in Chinese mainland

Based on 294 earthquake sequences with magnitude greater than or equal to 5.0 occurred in Chinese mainland since 1970, the spatial distribution features of sequence types have been studied. In southwestern China, it takes mainshock-aftershock sequence type （MAT） as the major in Chuan-Dian rhombic block and concerned Xianshuihe-Anninghe-Xiaojiang seismic belt, as well as in Jinshajiang-Honghe seismic belt. Multiple mainshock type （MMT） mainly distributes in western Yunnan, and Longlin and Lancang areas in Tengchong-Baoshan block in west of Nujiang-Lancangjiang fault zone. A few isolated earthquake type （IET） mainly occurred in northwestern Sichuan and there is no IET occurred in Yunnan region. In northwestern China, it takes mainshock-aftershock sequence type （MAT） as the major in west segment of South Tianshan in Xinjiang region. Some MMT also occurred in this area in the intersection of Kalpin block and the Puchang fault zone. It takes IET as the major in middle Tianshan in Xinjiang. Along the Qilianshan seismic belt, most of sequences are MAT. In Qinghai region, it takes MAT as the major, but the regional feature of the spatial distribution of sequence types is not very clear. In North China, it takes MAT as the major in Yinshan-Yanshan-Bohai seismic belt, north edge of North China, and in Hebei plain seismic belt, as well as in sub-plate of lower river area of Yangtze River. In intersection of north segment of Shanxi seismic belt and the NW-trending Yinshan-Yanshan-Bohai seismic belt, there are several moderate or strong MMT with magnitude from 5.0 to 6.0 occurred. In south of North China around the latitude line of 35°N, it takes IET as the major. The spatial distribution of sequence types is relevant to the patterns of tectonic movements. MAT is mostly produced by the ruptures of locked units or asperities or the neonatal separating segments inside the fault zones. MMT is generally relevant to the conjugate structures or intersection of many tectonic settings. Further extension of simple fault often produces IET. Spatial distribution of sequence types is also correlative to the regional and deep environment of crustal medium to some extent. MAT mainly distributes in high velocity area in upper crust or in the transition zone between high velocity area and low velocity area, MMT mostly occurred in the low velocity area in upper crust.

ISHIKAWA TYPE ITERATIVE SEQUENCES WITH ERRORS FOR LIPSCHITZIAN φ-STRONGLY ACCRETIVE OPERATOR EQUATIONS IN ARBITRARY BANACH SPACES

In this paper, we investigate the problem of approximating solutions of the equations of Lipschitzian ψ-strongly accretive operators and fixed points of Lipschitzian ψ-hemicontractive operators by lshikawa type iterative sequences with errors. Our results unify, improve and extend the results obtained previously by several authors including Li and Liu (Acta Math. Sinica 41 (4)(1998), 845-850), and Osilike (Nonlinear Anal. TMA, 36(1)(1999), 1-9), and also answer completely the open problems mentioned by Chidume (J. Math. Anal. Appl. 151 (2)(1990), 453-461).

Method discussion for quick response grey prediction of stronger aftershocks of an earthquake sequence

In this paper, we take occurrence process of early strong aftershocks of a main after shock type′s earthquake sequence as a complex grey system, and introduce predicting method for its stronger aftershocks by grey predicting theory. Through inspection prediction for 1998 Zhangbei M S=6.2 earthquake sequence, it shows that the grey predicting method maybe has active significance for the investigation of quick response prediction problems of stronger aftershocks of an earthquake sequence.

ST of Streptococcus pneumonia Circulating in Burkina Faso before the Introduction of PCV-13, 2013

Introduction: Burkina Faso experiences regular cases of Streptococcus pneumoniae meningitis. As part of the strategy to reduce cases of meningitis, the 13-valent pneumococcal conjugate vaccine (PCV-13) has been introduced in the Expanded Programme on Immunisation (EPI). Despite these efforts, there are some cases of pneumococcal meningitis including both vaccine and non-vaccine serotypes. The objective of this study was to describe the pneumococcal sequence types (ST) circulating in Burkina Faso before the introduction of the 13-valent pneumococcal conjugate vaccine (PCV-13). Methods: It was a descriptive cross-sectional study that took place from 27th October 2013 to 7th January 2014. S. pneumoniae strains were collected in Burkina Faso and Multi Locus Sequence Typing (MLST) was performed at the Pneumococcal Laboratory at the Centers for Disease Control and Prevention (CDC) in the USA (United States of America). MLST consists of 4 steps: amplification, purification, sequencing and interpretative reading of the results. The amplification used 7 primers consisting of sequences of aroe, gdh, gki, recP, spi, xpt, ddl genes. Results: Of 37 strains tested, 10 serotypes were identified. Serotype 1 was prevalent in 48.7% (18/37) followed by serotype 25F in 10.8% (4/37). Serotypes 5 and 12F/12A/12B/44/46 were 8.1% (3/37) each. Serotype 1 contained 5 STs including ST303 24.3% (9/37), ST217 8.1% (3/37) and ST618 8.1% (3/37);followed by serotype 25F with ST105 10.8% (4/37), serotype 5 with ST289 8.1% (3/37) and serogroup 12F/12A/12B/44/46 with ST 989 8.1% (3/37). Conclusion: Pneumococci are characterised by their great variability both in number of serotypes and in ST within the same serotype. Thus, 10 serotypes have been identified. Also, within serotype 1, 5 different STs have been described. These data indicate the complexity of the pneumococcus which is strongly involved in purulent bacterial meningitis at national level. This requires continuous surveillance of pneumococcal meningitis through laboratory capacity building.

Disease burden,antimicrobial resistance and molecular characterization of invasive group B Streptococcus among non-pregnant adults in Malaysia:A protocol study

and pili genes are also investigated.Methods:This multicentre,prospective,observational study is conducted in seven major tertiary hospitals in Malaysia among non-pregnant adults.Simultaneously,a retrospective study is conducted in the selected hospitals with similar approaches.GBS isolates are subjected to phenotyping,serotyping by multiplex PCR,antimicrobial susceptibility testing and PCR-detection of GBS virulence and pilus genes.Seven housekeeping genes are amplified and sequenced for multi-locus sequence typing.Discussion:Findings from the study may contribute to the management of clinical practice to diagnose and prevent GBS related diseases in a timely manner.Prudent use of antibiotics is encouraged by monitoring antimicrobial resistance.

Characteristics of colistin-resistant Escherichia coli from pig farms in Central China

The emergence and dissemination of colistin resistance in Enterobacterioceae mediated by plasmid-borne mcr genes in recent years now pose a threat to public health.In this study,we isolated and characterized colistin-resistant and for mcr-positive£coli from pig farms in Central China.Between 2018 and 2019,594 samples were collected and recovered 445 E.coli isolates.Among them,33 with colistin resistance phenotypes and 37 that were positive for mcr genes were identified,including 34 positive for mcr-1,one positive for mcr-3,and two positive for both mcr-1 and mcr-3.An insertion of nine bases("CTGGATACG")into mcr-7 in four mcr-positive isolates led to gene dysfunction,and therefore did not confer the colistin resistance phenotype.Antimicrobial susceptibility testing revealed that 37 mcr-positive isolates showed severe drug resistance profiles,as 50% of them were resistant to 20 types of antibiotics.Multilocus sequence typing revealed a heterogeneous group of sequence types in mcr-positive isolates,among which ST10(5/37),ST156(5/37),and 5T617(4/37)were the predominant types.Plasmid conjugation assays showed that mcr-carrying plasmids of 25 mcr-positive isolates were conjugated with£coli recipient,with conjugation frequencies ranging from 1.7 × 10^(-6) to 4.1 × 10^(-3) per recipient.Conjugation of these mcr genes conferred a colistin resistance phenotype upon the recipient bacterium.PCR typing of plasmids harbored in the 25 transconjugants determined six types of plasmid replicons,including lncX4(14/25),FrepB(4/25),Incl2(3/25),lncHI2(2/25),FIB(1/25),and Inch(1/25).This study contributes to the current understanding of antibiotic resistance and molecular characteristics of colistin-resistant£coli in pig farms.

Molecular Characteristics of Neisseria meningitidis Isolated during an Outbreak in a Jail: Association with the Spread and Distribution of ST-4821 Complex Serogroup C Clone in China

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.

Genetic Diversity, Antimicrobial Resistance, and Virulence Genes of Aeromonas Isolates from Clinical Patients, Tap Water Systems, and Food

Objective This study aimed to evaluate the genetic diversity,virulence,and antimicrobial resistance of Aeromonas isolates from clinical patients,tap water systems,and food.Methods Ninety Aeromonas isolates were obtained from Ma’anshan,Anhui province,China,and subjected to multi-locus sequence typing(MLST)with six housekeeping genes.Their taxonomy was investigated using concatenated gyr B-cpn60 sequences,while their resistance to 12 antibiotics was evaluated.Ten putative virulence factors and several resistance genes were identified by PCR and sequencing.Results The 90 Aeromonas isolates were divided into 84 sequence types,80 of which were novel,indicating high genetic diversity.The Aeromonas isolates were classified into eight different species.PCR assays identified virulence genes in the isolates,with the enterotoxin and hemolysin genes act,aer A,alt,and ast found in 47(52.2%),13(14.4%),22(24.4%),and 12(13.3%)of the isolates,respectively.The majority of the isolates(≥90%)were susceptible to aztreonam,imipenem,cefepime,chloramphenicol,gentamicin,tetracycline,and ciprofloxacin.However,several resistance genes were detected in the isolates,as well as a new mcr-3 variant.Conclusions Sequence type,virulence properties,and antibiotic resistance vary in Aeromonas isolates from clinical patients,tap water systems,and food.

Genetic and Antibiotic Resistance Characteristics ofCampylobacterjejuni Isolated from Diarrheal Patients,Poultry and Cattle in Shenzhen

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.

Statistical features of aftershock distribution size for moderate and large earthquakes in Chinese mainland

Based on data of earthquake sequences with Ms≥5.0 in Chinese mainland from 1970 to 2004, for different sequence types and different rupture modes of the main shock, the relationship between aftershock distribution size R and the magnitude of the main shock Mo has been studied statistically. Considering the rupture mode of the main shock, we give the quantitative statistical relationships between R and Mo under 95% confidence level for different sequence typos. Qualitatively, lgR, the logarithm of the aftershock distribution size, is positively correlative to the M0, but the data distribution is dispersed. Viewing from different sequence typos, the correlation between R and M0 is very weak for isolated earthquake type （lET） sequence, R distributes in the range from 5 to 60 km; For mainshock-aftershock type （MAT）, lgR is positively correlative to M0; For multiple main shock type （MMT）, the corelation between lgR and M0 is not very obvious when M0≤6.2 and R distributes in the range from 5 to 70 km, while it shows a linear correlation when M0≥6.3. The statistical results also show that the occupational ratios of different sequence types for strike-slip and oblique slip are almost the same. But for dip-slip （mostly are thrust mechanisms）, the ratio of MAT is higher than that of IET and MMT. Comparing with previous results, it indicates that, when M0 is large enough, R is mainly determined by M0 and there is almost no relationship with the rupture mode of the main shock.

MLST analysis of genetic diversity of Bacillus coagulans strains to evaluate effects on constipation model

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.

Prevalence and fuoroquinolone resistance of Campylobacter spp.isolated from beef cattle in Japan

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.

ITERATIVE PROCESS TO -HEMICONTRACTIVE OPERATOR AND-STRONGLY ACCRETIVE OPERATOR EQUATIONS

Let E be an arbitrary real Banach space and K be a nonempty closed convex subsets of E. Let T:K→K be a uniformly continuous _hemicontractive operator with bounded range and a n,b n,c n,a ′ n,b ′ n,c ′ n be sequences in [0,1] satisfying:ⅰ) a n+b n+c n=a ′ n+b ′ n+c ′ n=1. n≥0; ⅱ) lim b n= lim b ′ n= lim c ′ n= 0; ⅲ)∑∞n=0b n=∞; ⅳ) c n=o(b n). For any given x 0,u 0,v 0∈K, define the Ishikawa type iterative sequence x n as follows: x n+1 =a nx n+b nTy n+c nu n, y n=a ′ nx n+b ′ nTx n+c ′ nv n (n≥0), where u n and v n are bounded sequences in K. Then x n converges strongly to the unique fixed point of T. Related result deals with the convergence of Ishikawa type iterative sequence to the solution of _strongly accretive operator equations.

Family Competition Pheromone Genetic Algorithm for Comparative Genome Assembly

Genome assembly is a prerequisite step for analyzing next generation sequencing data and also far from being solved. Many assembly tools have been proposed and used extensively. Majority of them aim to assemble sequencing reads into contigs; however, we focus on the assembly of contigs into scaffolds in this paper. This is called scaffolding, which estimates the relative order of the contigs as well as the size of the gaps between these contigs. Pheromone trail-based genetic algorithm （PGA） was previously proposed and had decent performance according to their paper. From our previous study, we found that family competition mechanism in genetic algorithm is able to further improve the results. Therefore, we propose family competition pheromone genetic algorithm （FCPGA） and demonstrate the improvement over PGA.

Molecular Diversity of <i>Staphylococcus aureus</i>from the Nares of Hospital Personnel, HIV-Positive and Diabetes Mellitus Patients in Yaounde Cameroon

Nasal carriage of Staphylococcus aureus has been identified as a risk factor for the development of staphylococcal infections caused by endogenous colonizing strains. Information on the genotypic diversity of Staphylococcus aureus 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 Staphylococcus aureus isolates from three high-risk populations in Yaounde, Cameroon. Molecular analysis confirmed that 95% of 100 tested isolates were S. aureus. The mecA and Panton Valentine-Leukocidin (PVL) genes (lukS/F-PV) were detected in 37% (35/95) and 43% (41/95) of isolates respectively and 18% (17/95) of the isolates harboured both the mecA and lukS/F-PV genes. A mixed distribution of both methicillin sensitive S. aureus (MSSA)/PVL and methicillin resistant S. aureus (MRSA)/PVL strains were detected within the study population. Community associated MRSA accounted for 94% (33/35) of the isolates, further classified into allotypes SCCmec type IV 54% (19/35) and SCCmec type V 40% (14/35), while two isolates were hospital associated SCCmec type II strains. A majority of the isolates harboured a single aggressive gene regulator allele agr 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 SCCmec IV and agr 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.

Minimum Core Genome Sequence Typing of Brucella From China

The Gram-negative bacterial genus Brucella includes six classic species based on host specificity,pathogenicity and phenotypic differences.Four more Brucella species were identified in 2007.Although many Brucella genomes have been sequenced,genome sequences and analysis of Brucella strains isolated in China are still scarce.An efficient genome-based Brucella typing method is also needed.In this study,we used the minimum core genome(MCG)typing method to identify and type Brucella strains.Twenty Brucella isolates fromChinawere newly sequenced.The genome sequences of 55 representative Brucella strainswere downloaded.Among the 75 genomes,1089 genes and 52,030 single nucleotide polymorphisms(SNPs)shared by all isolates were considered as the MCG genes and MCG SNPs.Using these 52,030 MCG SNPs,Brucella was divided into six MCG groups.In addition,average nucleotide identity(ANI)values and the distributions of 184 virulence genes were all computed.The proportions of virulence genes were 90.96%,93.56%,95.89%,86.04%,85.78%and 91.87%for MCG groups 1 to 6,respectively.The intragroup ANI values were higher than the intergroup values,further confirming the validity of the MCG taxonomy classification.Brucella melitensis and Brucella abortus,the two main Brucella species pathogenic to humans,were well separated from other species.With the development and cost reduction of next-generation sequencing,theMCG typing method can be used for rapid identification of Brucella,which can contribute to the rapid diagnosis of brucellosis and ensure timely and effective treatment.

Serological and molecular capsular typing, antibiotic susceptibility and multilocus sequence typing of Streptococcuspneumoniae isolates from invasive and non-invasive infections

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.

The unbearable lightness of sequenced-based identification

Using the basic GenBank local alignment search tool program(BLAST)to identify fungi collected in a recently protected beech forest at Montricher(Switzerland),the number of ITS sequences associated to the wrong taxon name appears to be around 30%,even higher than previously estimated.Such results rely on the in-depth re-examination of BLAST results for the most interesting species that were collected,viz.first records for Switzerland,rare or patrimonial species and problematic species(when BLAST top scores were equally high for different species),all belonging to Agaricomycotina.This paper dissects for the first time a number of sequence-based identifications,thereby showing in every detail—particularly to the user community of taxonomic information—why sequence-based identification in the context of a fungal inventory can easily go wrong.Our first conclusion is that in-depth examination of BLAST results is too time consuming to be considered as a routine approach for future inventories:we spent two months on verification of approx.20 identifications.Apart from the fact that poor taxon coverage in public depositories remains the principal impediment for successful species identification,it can be deplored that even very recent fungal sequence deposits in GenBank involve an uncomfortably high number of misidentifications or errors with associated metadata.While checking the original publications associated with top score sequences for the few examples that were here re-examined,a positive consequence is that we uncovered over 80 type sequences that were not annotated as types in GenBank.Advantages and pitfalls of sequence-based identification are discussed,particularly in the light of undertaking fungal inventories.Recommendations are made to avoid or reduce some of the major problems with sequence-based identification.Nevertheless,the prospects for a more reliable sequence-based identification of fungi remain quite dim,unless authors are ready to check and update the metadata associated with previously deposited sequences in their publications.

Multilocus sequence typing indicates diverse origins of invasive Candida tropicalis isolates in China

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.