RESUMO
Whether cross-infection of respiratory pathogens between patients with non-cystic fibrosis bronchiectasis occurs is debated. Investigation with traditional microbiological culture risks simplifying the lung microbiome. We demonstrate the use of culture-independent Multilocus sequence typing to screen for Haemophilus influenzae strain types in a cohort of twenty-eight patients with non-cystic fibrosis bronchiectasis.
Assuntos
Bronquiectasia , Infecções por Haemophilus , Haemophilus influenzae , Tipagem de Sequências Multilocus , Humanos , Bronquiectasia/microbiologia , Haemophilus influenzae/genética , Haemophilus influenzae/isolamento & purificação , Haemophilus influenzae/classificação , Tipagem de Sequências Multilocus/métodos , Infecções por Haemophilus/microbiologia , Infecções por Haemophilus/diagnóstico , Masculino , Feminino , Pessoa de Meia-Idade , IdosoRESUMO
OBJECTIVE: To investigate the characteristics of Methicillin-Resistant Staphylococcus aureus (MRSA) in bone and joint infection (BJI) among children. METHODS: A total of 338 patients diagnosed with BJI from 2013 to 2022 in Children's Hospital of Fudan University were enrolled. Demographic information, microbiology culture results and laboratory findings, including white blood counts (WBC), C-reactive protein (CRP), procalcitonin (PCT), interleukin-6 (IL-6), and erythrocyte sedimentation rate (ESR) were collected and analyzed. MRSA was confirmed by antimicrobial susceptibility testing. Other MRSA-caused infections were randomly selected for comparison. Twenty-three virulence and antimicrobial resistance (AMR) genes were screened for MRSA strains. Multilocus sequence typing (MLST) and Staphylococcal protein A (spa) typing were performed using PCR amplification and sequencing. RESULTS: Of the identified pathogens in BJI, MRSA accounted for 21.0% (47/224). Patients with BJI had high levels of initial CRP, white blood cell count (WBC) and IL-6. ST59 (43.9%) and t437 (37.6%) were the main MRSA subtypes isolated from the children. The major genotypes in BJI were ST59-t437 (29.8%) and ST22-t309 (14.9%), with high carriage of hemolysins including hla (94.4-100%), hlb (66.2-93.3%), and hld (100%). Notably, Panton-Valentine leukocidin (pvl) had a high prevalence (53.3%) in ST22-t309-MRSA. Other virulence genes including tst, seg and sei were more commonly detected in ST22-t309-MRSA (40.0-46.7%) than in ST59-t437-MRSA (4.2-9.9%). High-carriage AMR genes in MRSA included aph(3')/III (66.7-80%), ermB (57.5-73.3%) and ermC (66.7-78.9%). MRSA presented high-resistance to erythromycin (52.0-100%) and clindamycin (48.0-92.5%), different genotypes displayed variation in their susceptibilities to antibiotics. CONCLUSIONS: The major MRSA genotype in BJI was ST59-t437, followed by ST22-t309, with a higher prevalence of the pvl gene. Continuous surveillance of pvl-positive ST22-t309-MRSA in pediatric BJI infections is thus required.
Assuntos
Staphylococcus aureus Resistente à Meticilina , Infecções Estafilocócicas , Criança , Humanos , Tipagem de Sequências Multilocus/métodos , Interleucina-6/genética , Infecções Estafilocócicas/microbiologia , Testes de Sensibilidade Microbiana , Antibacterianos/farmacologia , Antibacterianos/uso terapêuticoRESUMO
Hospital-acquired infections pose significant costly global challenges to patient care. Rapid and sensitive methods to identify potential outbreaks are integral to infection control measures. Whole-genome sequencing (WGS)-based bacterial strain typing provides higher discriminatory power over standard nucleotide banding pattern-based methods such as repetitive sequence-based PCR (rep-PCR). However, integration of WGS into clinical epidemiology is limited by the lack of consensus in methodology and data analysis/interpretation. In this study, WGS was performed on genomic DNA extracted from 22 multidrug-resistant Pseudomonas aeruginosa (MDR-PA) isolates using next-generation sequencing. Resulting high-quality reads were analyzed for phylogenetic relatedness using a whole-genome multilocus sequence typing (wgMLST)-based software program and single-nucleotide variant phylogenomics (SNVPhyl). WGS-based results were compared with conventional MLST and archived rep-PCR results. Rep-PCR identified three independent clonal clusters of MDR-PA. Only one clonal cluster identified by rep-PCR, an endemic strain within the pediatric cystic fibrosis population at Texas Children's Hospital, was concordantly identified using wgMLST and SNVPhyl. Results were highly consistent between the three sequence-based analyses (conventional MLST, wgMLST, and SNVPhyl), and these results remained consistent with the addition of 74 MDR-PA genomes. These WGS-based methods provided greater resolution for strain discrimination than rep-PCR or standard MLST classification, and the ease of use of wgMLST software renders it clinically viable for analysis, interpretation, and reporting of WGS-based strain typing.
Assuntos
Pseudomonas aeruginosa , Sequências Repetitivas de Ácido Nucleico , Técnicas de Tipagem Bacteriana/métodos , Criança , Humanos , Tipagem de Sequências Multilocus/métodos , Filogenia , Reação em Cadeia da Polimerase/métodos , Pseudomonas aeruginosa/genética , Sequenciamento Completo do Genoma/métodosRESUMO
This study provides an update on invasive Haemophilus influenzae disease in Bellvitge University Hospital (2014-2019), reporting its evolution from a previous period (2008-2013) and analysing the non-typeable H. influenzae (NTHi) population structure using a clade-related classification. Clinical data, antimicrobial susceptibility and serotyping were studied and compared with those of the previous period. Population structure was assessed by multilocus sequence typing (MLST), SNP-based phylogenetic analysis and clade-related classification. The incidence of invasive H. influenzae disease remained constant between the two periods (average 2.07 cases per 100â000 population), while the 30 day mortality rate decreased (20.7-14.7â%, respectively). Immunosuppressive therapy (40â%) and malignancy (36â%) were the most frequent comorbidities. Ampicillin and fluoroquinolone resistance rates had increased between the two periods (10-17.6â% and 0-4.4â%, respectively). NTHi was the main cause of invasive disease in both periods (84.3 and 85.3â%), followed by serotype f (12.9 and 8.8â%). NTHi displayed high genetic diversity. However, two clusters of 13 (n=20) and 5 sequence types (STs) (n=10) associated with clade V included NTHi strains of the most prevalent STs (ST3 and ST103), many of which showed increased frequency over time. Moreover, ST103 and ST160 from clade V were associated with ß-lactam resistance. Invasive H. influenzae disease is uncommon, but can be severe, especially in the elderly with comorbidities. NTHi remains the main cause of invasive disease, with ST103 and ST160 (clade V) responsible for increasing ß-lactam resistance over time.
Assuntos
Farmacorresistência Bacteriana , Fluoroquinolonas/farmacologia , Infecções por Haemophilus/epidemiologia , Haemophilus influenzae/classificação , Tipagem de Sequências Multilocus/métodos , Polimorfismo de Nucleotídeo Único , Adulto , Idoso , Idoso de 80 Anos ou mais , Resistência a Ampicilina , Monitoramento Epidemiológico , Feminino , Infecções por Haemophilus/mortalidade , Haemophilus influenzae/genética , Humanos , Incidência , Masculino , Pessoa de Meia-Idade , Mortalidade , Filogenia , Espanha/epidemiologia , Sequenciamento Completo do Genoma , Adulto JovemRESUMO
The genotyping of pathogens within cystic fibrosis cohorts is an important process, enabling the detection of transmissible and clinically-important strains. Traditionally this has been via culture-dependent processes. However, culture-independent investigation of respiratory samples is becoming more common, with such approaches highlighting the limitations of culture-based methods. In this study we describe the culture-independent application of multilocus sequence typing (MLST) for Pseudomonas aeruginosa, performed on DNA extracted from the sputa of cystic fibrosis patients. We compare the output to conventional culture-dependent MLST applied to the same samples and demonstrate high concordance. Culture-independent MLST enabled genotyping of culture-negative samples in patients from whom P. aeruginosa was intermittently isolated, and revealed the hidden presence of transmissible strains. Culture-independent MLST is also capable of highlighting samples containing multiple strains, albeit inconsistently. We conclude that culture-independent MLST can be a useful genotyping tool for screening cohorts and identifying patients that warrant further detailed investigation.
Assuntos
Técnicas de Tipagem Bacteriana/métodos , Infecção Hospitalar , Tipagem de Sequências Multilocus/métodos , Infecções por Pseudomonas , Pseudomonas aeruginosa/genética , Estudos de Coortes , Infecção Hospitalar/diagnóstico , Infecção Hospitalar/microbiologia , Fibrose Cística/complicações , Humanos , Infecções por Pseudomonas/complicações , Infecções por Pseudomonas/diagnóstico , Infecções por Pseudomonas/microbiologia , Escarro/microbiologiaRESUMO
BACKGROUND: American cutaneous leishmaniasis (ACL) is caused by different Leishmania parasites, which stimulate and direct the immune response against the infection. OBJECTIVE: To evaluate the TaqMan probe technology applicability to diagnose and identifying of Leishmania spp. related to the ACL etiology. METHODOLOGY: Through the MEGA 6.0 software, performed an in silico analysis using multiple alignments of Leishmania spp. which were available on GenBank for different genomic targets. The efficiency (e), specificity and detection limit (DL) were calculated for each system, these were associated to compose a duplex-qPCR (DqPCR). The samples of blood, lesion biopsy and lesion imprint on filter paper from patients residing in states of Amazonas (AM) and Pernambuco (PE)-Brazil, (cases and controls) were used to perform the DqPCR technique. The capacity to identify the Leishmania species was determined by comparison with isoenzymes method and sequencing analysis. RESULTS: Internal Transcribed Spacer 1 (rDNA) was the target selected. Two sets of primers and probes were designed and combined: SVS for subgenus Viannia and LaS for L. (L.) amazonensis. The results were: SVSe = 93.24%, SVS DL = 50 fg/µL; LaSe = 89.3%, LaSLD = 5 fg/µL presented 100% of specificity. In total, 236 individuals participated of the present study, wherein were 101 blood samples, 33 biopsies and 147 lesion imprints. The imprint was the most sensitive sample, showing 83.06% of sensitivity, 86.96% of specificity and substantial agreement between the techniques analysis (k = 0.531; p < 0,001). Regarding the species identification, DqPCR and sequencing/isoenzymes have agreed at 100%, since the infection is caused by a single Leishmania species. CONCLUSION: The DqPCR technique was applicable in diagnosis and identification of Leishmania spp. (subgenus Viannia and L. amazonensis). Furthermore, the lesion imprint is less invasive, allowing a fewer discomfort and greater acceptance by the patients, in addition of being low cost and easy handling.
Assuntos
Leishmania/classificação , Leishmania/isolamento & purificação , Leishmaniose Cutânea/diagnóstico , Reação em Cadeia da Polimerase Multiplex/métodos , Estudos de Casos e Controles , DNA de Protozoário/isolamento & purificação , DNA Espaçador Ribossômico , Éxons , Filtração/instrumentação , Proteínas de Choque Térmico HSP70/química , Humanos , Leishmaniose Cutânea/parasitologia , Tipagem de Sequências Multilocus/métodos , Valor Preditivo dos Testes , Sensibilidade e Especificidade , Trypanosoma cruzi/classificação , Trypanosoma cruzi/isolamento & purificaçãoRESUMO
Plant-rhizobacteria interaction and co-evolution developed adaptive strategies which may help the plant survive in nature. Plant rhizosphere soil isolates were analyzed to investigated the effects of rhizobacteria for promoting plant growth and suppress plant disease. Bacterial strains which isolated from plant rhizosphere soil were screened for elicitation of induced systemic resistance (ISR) on tobacco. Strain S2-3-2 results in significant reduction of disease severity on tobacco, it was identified as Bacillus pumilus by multilocus sequence analysis (MLSA). Strain S2-3-2 was deeper studied for pepper plant growth promotion and biological control activity against pepper bacterial spot disease. It was found that the pepper disease severity was decreased when the roots were drenched with strain S2-3-2, and the pepper plants had a higher weight and chlorophyll content, as compared with the mock-treated plants. Transcriptional expression of pathogenesis-related (PR) protein genes in pepper was analyzed by real-time PCR, gene expressions of CaPR1, CaPR4, and CaPR10 were increased when the plants were treated with strain S2-3-2. Moreover, strain S2-3-2 was tested for the production of indole-3-acetic acid (IAA), and it was determined to emit volatiles that enhance the growth of the tobacco plants. Interesting, heat-killed S2-3-2 enhance the pepper root growth, increase the gene expressions of CaPR4 and CaPR10 after pathogen challenge for 6 h, but limited to suppress the pepper bacterial spot disease as compare to the mock-treated plants. Strain S2-3-2 can be a potential biological control agent on the plant root for plant growth promoting and disease suppression.
Assuntos
Bacillus pumilus/isolamento & purificação , Raízes de Plantas/crescimento & desenvolvimento , Rizosfera , Microbiologia do Solo , Bacillus pumilus/genética , Bacillus pumilus/fisiologia , Capsicum/genética , Capsicum/crescimento & desenvolvimento , Capsicum/microbiologia , Resistência à Doença/genética , Regulação da Expressão Gênica de Plantas , Tipagem de Sequências Multilocus/métodos , Doenças das Plantas/genética , Doenças das Plantas/microbiologia , Proteínas de Plantas/genética , Proteínas de Plantas/metabolismo , Raízes de Plantas/genética , Raízes de Plantas/microbiologia , Nicotiana/genética , Nicotiana/crescimento & desenvolvimento , Nicotiana/microbiologiaRESUMO
BACKGROUND: Giardia duodenalis is one of the most prevalent and highly diverse human parasites, encompassing a complex of eight genetically distinct assemblages, each further divided into sub-assemblages. While in recent years, G. duodenalis genotype distribution patterns in humans have been intensely studied, there is still very little information available on the diversity of Giardia genotypes and sub-assemblages infecting people in Romania. In the present study, we investigated the genetic diversity of Giardia duodenalis in asymptomatic patients from Romania. METHODS: Over an 11-month period, human feces from 7805 healthy adults were screened by microscopic analysis for G. duodenalis cysts during their obligatory periodic check-ups. DNA extraction was performed from microscopic-positive fecal samples, followed by multilocus sequence typing of four genetic loci of the ITS region, gdh, tpi and bg genes, followed by DNA sequencing and phylogenetic analysis. Statistical analysis was performed using EpiInfo 2000 software. RESULTS: The prevalence of giardiasis in the present study was 0.42% (33/7805). Twenty-three samples (76.67%) were successfully genotyped at each locus. The bg and tpi genes had the highest typing success rate (100%). The identified assemblages were assemblage A in 27 cases (subtypes A2 and A3), and B in 3 cases. CONCLUSIONS: To our knowledge, the present study is the first report of multilocus sequence typing of G. duodenalis isolated from humans in Romania. The present results may shed light on G. duodenalis infection in humans at a regional and national level, thus increasing awareness against this parasitic infection.
Assuntos
Giardia lamblia , Giardíase/parasitologia , Tipagem de Sequências Multilocus/métodos , Proteínas do Citoesqueleto/genética , DNA Espaçador Ribossômico/genética , Genes de Protozoários , Variação Genética , Giardia lamblia/genética , Giardia lamblia/isolamento & purificação , Giardíase/epidemiologia , Glutamato Desidrogenase/genética , Humanos , Filogenia , Prevalência , Proteínas de Protozoários/genética , Romênia/epidemiologia , Triose-Fosfato Isomerase/genéticaRESUMO
OBJECTIVE: To describe the clinical features, outcomes, and molecular epidemiology of an outbreak of multidrug resistant (MDR) A. baumannii. METHODS: We performed a retrospective analysis of all MDR A. baumannii isolates recovered during an outbreak from 2011 to 2015 in a tertiary care cancer hospital. Cases were classified as colonized or infected. We determined sequence types following the Bartual scheme and plasmid profiles. RESULTS: There were 106 strains of A. baumannii isolated during the study period. Sixty-six (62.3%) were considered as infection and 40 (37.7%) as colonization. The index case, identified by molecular epidemiology, was a patient with a drain transferred from a hospital outside Mexico City. Ninety-eight additional cases had the same MultiLocus Sequence Typing (MLST) 758, of which 94 also had the same plasmid profile, two had an extra plasmid, and two had a different plasmid. The remaining seven isolates belonged to different MLSTs. Fifty-three patients (50%) died within 30 days of A. baumanniii isolation: 28 (20%) in colonized and 45 (68.2%) in those classified as infection (p<0.001). In multivariate regression analysis, clinical infection and patients with hematologic neoplasm, predicted 30-day mortality. The molecular epidemiology of this outbreak showed the threat posed by the introduction of MDR strains from other institutions in a hospital of immunosuppressed patients and highlights the importance of adhering to preventive measures, including contact isolation, when admitting patients with draining wounds who have been hospitalized in other institutions.
Assuntos
Infecções por Acinetobacter/tratamento farmacológico , Infecções por Acinetobacter/mortalidade , Infecção Hospitalar/epidemiologia , Acinetobacter baumannii/genética , Acinetobacter baumannii/isolamento & purificação , Acinetobacter baumannii/patogenicidade , Adulto , Idoso , Estudos de Casos e Controles , Surtos de Doenças , Resistência a Múltiplos Medicamentos/fisiologia , Farmacorresistência Bacteriana Múltipla/efeitos dos fármacos , Farmacorresistência Bacteriana Múltipla/genética , Feminino , Hospitais Gerais , Humanos , Masculino , México , Testes de Sensibilidade Microbiana , Pessoa de Meia-Idade , Epidemiologia Molecular/métodos , Tipagem de Sequências Multilocus/métodos , Plasmídeos/efeitos dos fármacos , Plasmídeos/genética , Estudos Retrospectivos , Análise de Sequência de DNA/métodos , beta-Lactamases/genéticaRESUMO
Whole genome sequence (WGS) data could transform our ability to attribute individuals to source populations. However, methods that efficiently mine these data are yet to be developed. We present a minimal multilocus distance (MMD) method which rapidly deals with these large data sets as well as methods for optimally selecting loci. This was applied on WGS data to determine the source of human campylobacteriosis, the geographical origin of diverse biological species including humans and proteomic data to classify breast cancer tumours. The MMD method provides a highly accurate attribution which is computationally efficient for extended genotypes. These methods are generic, easy to implement for WGS and proteomic data and have wide application.
Assuntos
Bases de Dados Genéticas , Tipagem de Sequências Multilocus/métodos , Sequenciamento Completo do Genoma , Animais , Campylobacter/genética , Campylobacter/isolamento & purificação , Infecções por Campylobacter/genética , Infecções por Campylobacter/patologia , Reservatórios de Doenças/microbiologia , Genoma Bacteriano , Genótipo , Humanos , Polimorfismo de Nucleotídeo ÚnicoRESUMO
BACKGROUND: Footrot and interdigital dermatitis are endemic infectious diseases in all sheep farming regions, impairing welfare and production. The development of efficacious vaccines against the primary causative pathogen has been hampered by the extensive antigenic diversity of Dichelobacter nodosus. Understanding the heterogeneity of the pathogen within and between flocks is essential if the feasibility of bespoke vaccine production is to be assessed for use in the U.K. RESULTS: In this study 56 ewe and lamb isolates from 9 flocks were compared by D. nodosus serogroup and Multi Locus Sequence Type which provides significantly enhanced discriminatory power for molecular epidemiology. Serogroup heterogeneity between flocks ranged from two to five unique serogroups per flock. Three flocks contained isolates of two serogroups, two flocks contained isolates of three serogroups and one flock included isolates of five serogroups. Analysis of 25 isolates from one flock with high prevalence of lameness, identified that serogroup and sequence type was significantly correlated with age. Significantly higher proportion of lambs were infected with serogroup B (principally ST85) as opposed to serogroup H (principally ST86), which predominated amongst adult sheep. CONCLUSIONS: Genomic heterogeneity of the pathogen was significantly lower within flock compared to heterogenicity observed between flocks. Furthermore, this study indicates that within a flock, the host-pathogen dynamics and susceptibility to particular D. nodosus strains may be age dependent.
Assuntos
Dichelobacter nodosus/classificação , Heterogeneidade Genética , Infecções por Bactérias Gram-Negativas/veterinária , Tipagem de Sequências Multilocus/métodos , Doenças dos Ovinos/microbiologia , Animais , Técnicas de Tipagem Bacteriana , Dichelobacter nodosus/genética , Dichelobacter nodosus/isolamento & purificação , Dermatite Digital/microbiologia , Feminino , Pododermatite Necrótica dos Ovinos/microbiologia , Infecções por Bactérias Gram-Negativas/microbiologia , Filogenia , Sorogrupo , Ovinos , Reino UnidoRESUMO
The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 2013-2014, including 40 vanA-type and 2 vanB-type vancomycin-resistant Enterococcus faecium isolates and 1 vanC1-type Enterococcus gallinarum. Of the 42 E. faecium, 19 isolates were subjected to whole genome sequencing. Core genome multilocus sequence typing (cgMLST) analysis revealed three sequence clusters (SCs) of clonally related isolates, which were linked to different hospital wards. The first two VRE isolates, isolated early 2013 from patients in the medical intensive care unit, were grouped in SC1 (MLST [ST] 78, vanB) and differed in only 3 of 1423 cgMLST alleles. The SC2 (n = 16, special care baby unit, neonatal intensive care unit, pediatric surgery ward, and oncology ward) and SC3 (n = 1, antenatal ward) were all ST80 vanA-VRE, but the single SC3 isolate differed in 233 alleles compared with SC2. Within SC2, isolates differed in 1-23 alleles. Comparison with a larger database of E. faecium strains indicated that all isolates clustered within the previously defined hospital clade A1. A combination of Resfinder and mlplasmid analysis identified the presence of resistance genes on different plasmid predicted genetic elements among different SCs. In conclusion, this study documents the first isolates causing outbreaks with VRE in the Libyan health care system. Further surveillance efforts using molecular typing methods to monitor spread of multidrug-resistant bacteria in the Libyan health care system are urgently needed.
Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Enterococcus faecium/genética , Enterococcus faecium/isolamento & purificação , Enterococos Resistentes à Vancomicina/genética , Enterococos Resistentes à Vancomicina/isolamento & purificação , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Carbono-Oxigênio Ligases/genética , Infecção Hospitalar/tratamento farmacológico , Infecção Hospitalar/microbiologia , Surtos de Doenças , Enterococcus/efeitos dos fármacos , Enterococcus/genética , Enterococcus/isolamento & purificação , Infecções por Bactérias Gram-Positivas/tratamento farmacológico , Infecções por Bactérias Gram-Positivas/microbiologia , Hospitais , Humanos , Líbia , Tipagem de Sequências Multilocus/métodos , Vancomicina/farmacologia , Enterococos Resistentes à Vancomicina/efeitos dos fármacos , Sequenciamento Completo do Genoma/métodosRESUMO
BACKGROUND: Crocidura, the most speciose mammalian genus, occurs across much of Asia, Europe and Africa. The taxonomy of Chinese representatives has been studied primarily based on cursory morphological comparisons and their molecular phylogenetic analyses remain unexplored. In order to understand the phylogeny of this group in China, we estimated the first multilocus phylogeny and conducted species delimitation, including taxon sampling throughout their distribution range. RESULTS: We obtained one mitochondrial gene (cytb) (~ 1, 134 bp) and three nuclear genes (ApoB, BRCA1, RAG1) (~ 2, 170 bp) for 132 samples from 57 localities. Molecular analyses identified at least 14 putative species that occur within two major well-supported groups in China. Polyphyletic C. wuchihensis appears to be composed of two putative species. Two subspecies, C. rapax rapax and C. rapax kurodai should be elevated to full species status. A phylogenetic tree based on mitochondrial gene from Asian Crocidura species showed that the C. rapax rapax is embedded within C. attenuata, making the latter a paraphyletic group. Three strongly supported undescribed species (C. sp.1, C. sp.2 and C. sp.3) are revealed from Zada County of Tibet (Western China), Hongjiang County of Hunan Province (Central China) and Dongyang County of Zhejiang Province (Eastern China), Motuo County of Tibet, respectively. The divergence time estimation suggested that China's Crocidura species began to diversify during the late Pliocene (3.66 Ma) and the Early Pleistocene (2.29 Ma), followed by a series of diversifications through the Pleistocene. CONCLUSIONS: The cryptic diversity found in this study indicated that the number of species is strongly underestimated under the current taxonomy. We propose that the three undescribed species should be evaluated using extensive taxon sampling and comprehensive morphological and morphometric approaches. Climate change since the late Pliocene and the uplift of the Qinghai-Tibet Plateau may result in the diversification and speciation of China's Crocidura species. In short, the underestimated diversity underlines the need for a taxonomic revision of Chinese Crocidura species.
Assuntos
Variação Genética , Musaranhos/classificação , Musaranhos/genética , África , Animais , Ásia , China , DNA Mitocondrial/genética , Europa (Continente) , Genes Mitocondriais , Tipagem de Sequências Multilocus/métodos , Tipagem de Sequências Multilocus/veterinária , Filogenia , Filogeografia , TibetRESUMO
Bacteria and archaea make up most of natural diversity, but the mechanisms that underlie the origin and maintenance of prokaryotic species are poorly understood. We investigated the speciation history of the genus Salmonella, an ecologically diverse bacterial lineage, within which S. enterica subsp. enterica is responsible for important human food-borne infections. We performed a survey of diversity across a large reference collection using multilocus sequence typing, followed by genome sequencing of distinct lineages. We identified 11 distinct phylogroups, 3 of which were previously undescribed. Strains assigned to S. enterica subsp. salamae are polyphyletic, with two distinct lineages that we designate Salamae A and B. Strains of the subspecies houtenae are subdivided into two groups, Houtenae A and B, and are both related to Selander's group VII. A phylogroup we designate VIII was previously unknown. A simple binary fission model of speciation cannot explain observed patterns of sequence diversity. In the recent past, there have been large-scale hybridization events involving an unsampled ancestral lineage and three distantly related lineages of the genus that have given rise to Houtenae A, Houtenae B and VII. We found no evidence for ongoing hybridization in the other eight lineages, but detected subtler signals of ancient recombination events. We are unable to fully resolve the speciation history of the genus, which might have involved additional speciation-by-hybridization or multi-way speciation events. Our results imply that traditional models of speciation by binary fission and divergence are not sufficient to account for Salmonella evolution.
Assuntos
Salmonella enterica/genética , Salmonella/classificação , Salmonella/genética , Técnicas de Tipagem Bacteriana/métodos , Evolução Biológica , Classificação/métodos , Evolução Molecular , Especiação Genética , Tipagem de Sequências Multilocus/métodos , Hibridização de Ácido Nucleico/métodos , Filogenia , Salmonella enterica/metabolismoRESUMO
We previously reported the distribution of Achromobacter spp. (species and Sequence Types (ST)) in our French Cystic Fibrosis (CF) centre. In the present study we collected 109 Achromobacter isolates (1/patient) from 9 other French CF Centres for species identification, antimicrobial susceptibility testings and Multilocus-Sequence-Typing (MLST) analysis. Ten species were detected, A. xylosoxidans being the most predominant one (73.4% of the isolates). Piperacillin-tazobactam, ceftazidime, imipenem, meropenem and ciprofloxacin were respectively active against 88, 70, 79, 72 and 23% of the isolates. Among the 79 A. xylosoxidans isolates, 46 STs were detected. Interestingly, ST 137, recovered in 4 centres (5 patients), was previously detected in our centre (2 patients). The strains from the 7 patients belonged to the same pulsotype (pulsed-field-gel-electrophoresis analysis) and harboured acquired resistance to meropenem, ceftazidime, ciprofloxacin, and except for 2 isolates, to imipenem and piperacillin-tazobactam. This is the first description in France of a circulating multiresistant A. xylosoxidans strain.
Assuntos
Achromobacter denitrificans , Antibacterianos , Fibrose Cística , Infecções por Bactérias Gram-Negativas , Achromobacter denitrificans/efeitos dos fármacos , Achromobacter denitrificans/isolamento & purificação , Antibacterianos/classificação , Antibacterianos/farmacologia , Fibrose Cística/tratamento farmacológico , Fibrose Cística/epidemiologia , Fibrose Cística/microbiologia , DNA Bacteriano/isolamento & purificação , Farmacorresistência Bacteriana Múltipla , Eletroforese em Gel de Campo Pulsado/métodos , França/epidemiologia , Infecções por Bactérias Gram-Negativas/epidemiologia , Infecções por Bactérias Gram-Negativas/microbiologia , Humanos , Testes de Sensibilidade Microbiana/métodos , Testes de Sensibilidade Microbiana/estatística & dados numéricos , Tipagem de Sequências Multilocus/métodosRESUMO
The correct identification of different genera and bacterial species is essential, especially when these bacteria cause infections and appropriate therapies need to be chosen. Bacteria belonging to the Burkholderia cepacia complex are considered important opportunistic pathogens, causing different types of infections in immunocompromised, principally in patients with cystic fibrosis. Twenty-one isolates were obtained from different soil samples and identified by sequencing of 16S rRNA, 23S rRNA, recA gene, MLST and by VITEK 2 and MALDI-TOF MS systems. Then, statistical analyses were performed. VITEK 2 and MALDI-TOF MS systems showed different bacterial genera. Sequencing of the 16S rRNA, 23S rRNA gene and amplification of recA gene showed that all the isolates belong to the B. cepacia complex. Sequencing of the recA gene showed a predominance of B. cenocepacia. The PCR of the recA gene showed a high specificity when it is necessary to identify the bacteria belonging to the B. cepacia complex in comparison with 16S and 23S rRNA genes sequencing. MLST analyzes showed a diversity of STs, which have not yet been correlated to the species. Phenotypic identification was not suitable for the identification of these pathogens since in many cases different genera have been reported, including identification by using MALDI-TOF MS.
Assuntos
Técnicas de Tipagem Bacteriana/métodos , Complexo Burkholderia cepacia/classificação , Complexo Burkholderia cepacia/genética , Complexo Burkholderia cepacia/isolamento & purificação , Filogenia , Microbiologia do Solo , Proteínas de Bactérias/genética , Infecções por Burkholderia/microbiologia , Fibrose Cística/microbiologia , DNA Bacteriano/genética , Tipagem de Sequências Multilocus/métodos , Infecções Oportunistas/microbiologia , Fenótipo , Reação em Cadeia da Polimerase/métodos , RNA Ribossômico 16S/genética , RNA Ribossômico 23S/genética , Recombinases Rec A/genética , Análise de Sequência de DNA , Especificidade da Espécie , Espectrometria de Massas por Ionização e Dessorção a Laser Assistida por Matriz/métodosRESUMO
Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.
Assuntos
Helicobacter pylori/genética , Helicobacter pylori/metabolismo , Triptofano/metabolismo , DNA Bacteriano/genética , Etilenocloroidrina/análogos & derivados , Genoma Bacteriano/genética , Genótipo , Infecções por Helicobacter/genética , Humanos , Tipagem de Sequências Multilocus/métodos , Técnica de Amplificação ao Acaso de DNA Polimórfico/métodos , Reprodutibilidade dos Testes , Análise de Sequência de DNA/métodos , Neoplasias Gástricas/genéticaRESUMO
The emergence of a Japan-intrinsic community associated methicillin-resistant Staphylococcus aureus strain (CA-MRSA/J) has been reported. A 70-year-old man with recurrent colon cancer and a history of mitral valve replacement was admitted to the hospital in a state of shock. He was diagnosed with prosthetic valve endocarditis (PVE) caused by MRSA and underwent cardiac surgery. The MRSA isolates belonged to multilocus sequence type 8 and carried staphylococcal cassette chromosome mec IVl and the genes of toxic shock syndrome toxin-1, enterotoxin C, and enterotoxin L. These characteristics indicated a CA-MRSA/J clone. This is the first reported case of PVE caused by CA-MRSA/J.
Assuntos
Endocardite Bacteriana/microbiologia , Próteses Valvulares Cardíacas/efeitos adversos , Staphylococcus aureus Resistente à Meticilina/genética , Infecções Relacionadas à Prótese/microbiologia , Infecções Estafilocócicas/microbiologia , Idoso , Infecções Comunitárias Adquiridas/microbiologia , Humanos , Masculino , Staphylococcus aureus Resistente à Meticilina/classificação , Staphylococcus aureus Resistente à Meticilina/isolamento & purificação , Estenose da Valva Mitral/cirurgia , Tipagem de Sequências Multilocus/métodos , Choque Séptico/microbiologiaRESUMO
Cystic fibrosis (CF) is an inherited recessive disease that affects mucocillary clearance in the lung, allowing it to be colonised with bacteria such as Staphylococcus aureus. To survive in the CF lung S. aureus adapts both phenotypically and genotypically, through various mechanisms. In this study, multiple specimens were collected from the participants and were processed routinely and were additionally cultured in chromogenic media. Multiplex PCR assays were employed to detect methicillin resistance and selected virulence and quaternary ammonium compound (qac) genes. Genetic relatedness of the S. aureus was determined using agr, SCCmec and spa typing as well as pulsed field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Thirty-three S. aureus isolates were isolated, of which 51% (17/33) were methicillin resistant S. aureus (MRSA). The virulence and qac genes were more prevalent in MRSA than the methicillin sensitive S. aureus (MSSA) isolates. The PFGE analysis showed nine distinct pulsotypes while MLST showed eight sequence types. All the STs detected in this study, except for ST508 have been previously isolated from CF patients according to the literature. This study showed a genetically diverse S. aureus population with a high prevalence of virulence genes among the MRSA isolates from the CF clinic.
Assuntos
Fibrose Cística/microbiologia , Staphylococcus aureus/genética , Staphylococcus aureus/patogenicidade , Adolescente , Adulto , Toxinas Bacterianas/genética , Criança , Pré-Escolar , Eletroforese em Gel de Campo Pulsado/métodos , Exotoxinas/genética , Feminino , Genótipo , Humanos , Lactente , Masculino , Resistência a Meticilina/efeitos dos fármacos , Staphylococcus aureus Resistente à Meticilina/genética , Testes de Sensibilidade Microbiana , Epidemiologia Molecular , Tipagem de Sequências Multilocus/métodos , África do Sul , Infecções Estafilocócicas/microbiologia , Centros de Atenção Terciária , Fatores de Virulência/genéticaRESUMO
The genus Anthroherpon Reitter, 1889 exhibits the most pronounced troglomorphic characters among Coleoptera, and represents one of the most spectacular radiations of subterranean beetles. However, radiation, diversification, and biogeography of this genus have never been studied in a phylogenetic context. This study provides a comprehensive evolutionary analysis of the Anthroherpon radiation, using a dated molecular phylogeny as a framework for understanding Anthroherpon diversification, reconstructing the ancestral range, and exploring troglomorphic diversity. Based on 16 species and 22 subspecies, i.e. the majority of Anthroherpon diversity, we reconstructed the phylogeny using Bayesian analysis of six loci, both mitochondrial and nuclear, comprising a total of 4143 nucleotides. In parallel, a morphometric analysis was carried out with 79 landmarks on the body that were subjected to geometric morphometrics. We optimized morphometric features to phylogeny, in order to recognize the way troglomorphy was expressed in different clades of the tree, and did character evolution analyses. Finally, we reconstructed the ancestral range of the genus using BioGeoBEARS. Besides further elucidating the suprageneric classification of the East-Mediterranean Leptodirini, our main findings also show that Anthroherpon dates back to the Early Miocene (ca. 22 MYA) and that the genus diversified entirely underground. Biogeographic reconstruction of the ancestral range shows the origin of the genus in the area comprising three high mountains in western Montenegro, which is in the accordance with the available data on the paleogeography of the Balkan Peninsula. Character evolution analysis indicates that troglomorphic morphometric traits in Anthroherpon mostly evolve neutrally but may diverge adaptively under syntopic competition.