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1.
BMC Infect Dis ; 20(1): 444, 2020 Jun 23.
Artículo en Inglés | MEDLINE | ID: mdl-32576149

RESUMEN

BACKGROUND: The syphilis epidemic continues to cause substantial morbidity and mortality worldwide, particularly in low- and middle-income countries, despite several recent disease control initiatives. Though our understanding of the pathogenesis of this disease and the biology of the syphilis agent, Treponema pallidum subsp. pallidum has improved over the last two decades, further research is necessary to improve clinical diagnosis and disease management protocols. Additionally, such research efforts could contribute to the identification of possible targets for the development of an effective vaccine to stem syphilis spread. METHODS: This study will recruit two cohorts of participants with active syphilis infection, one with de novo infection, one with repeat infection. Whole blood specimens will be collected from each study participant at baseline, 4, 12, 24, 36, and 48 weeks, to track specific markers of their immunological response, as well as to compare humoral reactivity to Treponema pallidum antigens between the two groups. Additionally, we will use serum specimens to look for unique cytokine patterns in participants with early syphilis. Oral and blood samples, as well as samples from any syphilitic lesions present, will also be collected to sequence any Treponema pallidum DNA found. DISCUSSION: By furthering our understanding of syphilis pathogenesis and human host immune response to Treponema pallidum, we will provide important data that will help in development of new point-of-care tests that could better identify active infection, leading to improved syphilis diagnosis and management. Findings could also contribute to vaccine development efforts.


Asunto(s)
Vacunas Bacterianas/uso terapéutico , Sífilis/epidemiología , Sífilis/prevención & control , Treponema pallidum/inmunología , Vacunación , Antígenos Bacterianos/inmunología , Secuencia de Bases , Estudios de Cohortes , Citocinas/análisis , ADN Bacteriano/genética , Estudios de Seguimiento , Humanos , Tipificación Molecular , Perú/epidemiología , Sífilis/sangre , Sífilis/inmunología , Treponema pallidum/genética
2.
Indian J Med Res ; 151(5): 450-458, 2020 May.
Artículo en Inglés | MEDLINE | ID: mdl-32474553

RESUMEN

Background & objectives: SARS-CoV-2 (Severe acute respiratory syndrome coronavirus-2) is evolving with the progression of the pandemic. This study was aimed to investigate the diversity and evolution of the coronavirus SARS-CoV-2 with progression of the pandemic over time and to identify similarities and differences of viral diversity and evolution across geographical regions (countries). Methods: Publicly available data on type definitions based on whole-genome sequences of the SARS-CoV-2 sampled during December and March 2020 from 3636 infected patients spread over 55 countries were collected. Phylodynamic analyses were performed and the temporal and spatial evolution of the virus was examined. Results: It was found that (i) temporal variation in frequencies of types of the coronavirus was significant; ancestral viruses of type O were replaced by evolved viruses belonging to type A2a; (ii) spatial variation was not significant; with the spread of SARS-CoV-2, the dominant virus was the A2a type virus in every geographical region; (iii) within a geographical region, there was significant micro-level variation in the frequencies of the different viral types, and (iv) the evolved coronavirus of type A2a swept rapidly across all continents. Interpretation & conclusions: SARS-CoV-2 belonging to the A2a type possesses a non-synomymous variant (D614G) that possibly eases the entry of the virus into the lung cells of the host. This may be the reason why the A2a type has an advantage to infect and survive and as a result has rapidly swept all geographical regions. Therefore, large-scale sequencing of coronavirus genomes and, as required, of host genomes should be undertaken in India to identify regional and ethnic variation in viral composition and its interaction with host genomes. Further, careful collection of clinical and immunological data of the host can provide deep learning in relation to infection and transmission of the types of coronavirus genomes.


Asunto(s)
Betacoronavirus/genética , Infecciones por Coronavirus/epidemiología , Infecciones por Coronavirus/virología , Pandemias , Neumonía Viral/epidemiología , Neumonía Viral/virología , ARN Viral/análisis , Betacoronavirus/patogenicidad , Evolución Molecular , Humanos , India/epidemiología , Internacionalidad , Tipificación Molecular , Filogeografía , ARN Viral/genética , Análisis Espacio-Temporal
3.
New Microbiol ; 43(2): 82-88, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32310301

RESUMEN

In order to investigate molecular typing and fatty acid methyl esters (FAMEs) typing of clinical Stenotrophomonas maltophilia (S.maltophilia) isolates based on Random Amplification Polymorphic DNA (RAPD) and Gas Chromatography-Mass Spectrometer (GC-MS) methods, we collected 35 drug-resistant S. maltophilia isolates from March to December 2017 in a comprehensive hospital. The VITEK 2 Compact System was used to determine bacterial antibiotic susceptibility. The analysis of molecular typing was performed by RAPD. GC-MS was used to obtain FAMEs profiles. In total, all 35 isolates were multidrug-resistant S.maltophilia. Their resistance rates to CAZ and LEV were 21.4% and 21.1%, and to SXT up to 13.5%. S. maltophilia isolates were typed to six main clones by RAPD methods and four main clones by FAMEs fingerprint, respectively. The concordance rate of these two methods was 69.0%. Clonal typing provides evidence that multidrug-resistant isolates are prevalent among wards in the hospital. FAMEs profiles may be an easy and sensitive method for bacteria classification. The effectiveness and feasibility of different typing methods should be comprehensively considered.


Asunto(s)
Ácidos Grasos , Tipificación Molecular , Stenotrophomonas maltophilia , Antibacterianos/farmacología , Ácidos Grasos/análisis , Cromatografía de Gases y Espectrometría de Masas , Infecciones por Bacterias Gramnegativas/microbiología , Humanos , Pruebas de Sensibilidad Microbiana , Técnica del ADN Polimorfo Amplificado Aleatorio , Stenotrophomonas maltophilia/química , Stenotrophomonas maltophilia/clasificación , Stenotrophomonas maltophilia/efectos de los fármacos
4.
Zhonghua Liu Xing Bing Xue Za Zhi ; 41(3): 423-428, 2020 Mar 10.
Artículo en Chino | MEDLINE | ID: mdl-32294847

RESUMEN

Objective: To investigate the isolation rate, antimicrobial resistance phenotype, and molecular type characteristics of Klebsiella pneumoniae from infectious diarrhea outpatients in Tai'an. Methods: A total of 866 stool samples were collected from infectious diarrhea cases in sentinel hospitals in 6 counties of Tai'an from 2013 to 2017. The strains were isolated from stool samples of the cases and identified by biochemical test. Micro broth dilution method was used to detect the drug resistance of the strains. The molecular typing was conducted by using pulsed field gel electrophoresis (PFGE). Results: The detection rate of Klebsiella pneumoniae in the stool samples was 7.97% (69/866), with significant differences among the 6 counties (χ(2)=39.627, P=0.000). Sixty- eight out of the 69 strains were resistant to 15 antibiotics with resistance rate 98.55%(68/69). The resistance to ampicillin (AMP) was highest (84.06%) (58/69), followed by sulfamethoxazole (SOX) (72.46%)(50/69). There were 40 drug resistance profiles, and the predominant resistance profile was AMP-SOX detected (n=10). The multi-drug resistant (MDR) strains accounted for 33.33% (23/69). The 69 strains could be divided into 65 PFGE patterns, and no predominant PFGE pattern or cluster was observed. Conclusions: Klebsiella pneumoniae was detected in the stool samples of diarrhea- syndrome outpatients, indicating the risk for community-acquired infection; the strains were resistant to multiplex antibiotics, with wide drug-resistance profiles and high multi-drug resistance rates. The PFGE patterns were diverse, which showed no correlation with drug resistance profiles. Our study indicated that it necessary to strengthen the surveillance and detection of Klebsiella pneumoniae from diarrhea outpatients, which could facilitate the prevention of the emergence and spread of drug resistance strains and the protection of susceptible population.


Asunto(s)
Farmacorresistencia Bacteriana , Disentería/microbiología , Infecciones por Klebsiella/diagnóstico , Klebsiella pneumoniae , Pacientes Ambulatorios/estadística & datos numéricos , Antibacterianos/farmacología , China , Electroforesis en Gel de Campo Pulsado , Humanos , Klebsiella pneumoniae/clasificación , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/aislamiento & purificación , Tipificación Molecular
6.
MMWR Morb Mortal Wkly Rep ; 69(12): 335-338, 2020 Mar 27.
Artículo en Inglés | MEDLINE | ID: mdl-32214081

RESUMEN

Cryptosporidium is an enteric pathogen that is transmitted through animal-to-person or person-to-person contact or through ingestion of contaminated water or food. In the United States, Cryptosporidium affects an estimated 750,000 persons each year; however, only approximately 11,000 cases are reported nationally (1,2). Persons infected with Cryptosporidium typically develop symptoms within 2 to 10 days after exposure. Common symptoms include watery diarrhea, abdominal cramps, nausea, vomiting, or fever, which can last 1 to 2 weeks. Cryptosporidiosis is a nationally notifiable disease in the United States. Nebraska presents a unique setting for the evaluation of this pathogen because, compared with other states, Nebraska has a greater reliance on agriculture and a higher proportion of the population residing and working in rural communities. Cryptosporidium species and subtypes are generally indistinguishable using conventional diagnostic methods. Using molecular characterization, Nebraska evaluated the genetic diversity of Cryptosporidium and found a dichotomy in the distribution of cases of cryptosporidiosis caused by Cryptosporidium parvum and Cryptosporidium hominis among rural and urban settings. Characterizing clusters of C. hominis cases revealed that several child care facilities were affected by the same subtype, suggesting community-wide transmission and indicating a need for effective exclusion policies. Several cases of cryptosporidiosis caused by non-C. parvum or non-C. hominis species and genotypes indicated unique animal exposures that were previously unidentified. This study enhanced epidemiologic data by validating known Cryptosporidium sources, confirming outbreaks, and, through repeat interviews, providing additional information to inform cryptosporidiosis prevention and control efforts.


Asunto(s)
Criptosporidiosis/epidemiología , Criptosporidiosis/transmisión , Cryptosporidium/clasificación , Cryptosporidium/genética , Adolescente , Adulto , Anciano , Niño , Preescolar , Femenino , Genotipo , Humanos , Lactante , Masculino , Persona de Mediana Edad , Tipificación Molecular , Nebraska/epidemiología , Factores de Riesgo , Adulto Joven
7.
Parasitol Res ; 119(5): 1547-1551, 2020 May.
Artículo en Inglés | MEDLINE | ID: mdl-32198626

RESUMEN

Eimeria spp. and Blastocystis are the common parasites that parasitize the intestinal tract of rabbits, which can seriously threaten the health of rabbits and lead to economic losses to the rabbit industry. However, information about the prevalence and transmission of these two parasites in rabbits is limited in China. The objective of this study was to survey the prevalence of Eimeria spp. and Blastocystis in rabbits in Shandong Province. A total of 616 rabbit fecal samples were collected from two cities (Rizhao and Weihai) in Shandong Province, eastern China, and Eimeria spp. and Blastocystis were identified by polymerase chain reaction based on species-specific markers. The prevalence of Eimeria spp. was 20% (123/616) and the Blastocystis prevalence was 0.97% (6/616). Five different Eimeria species (Eimeria intestinalis, E. perforans, E. magna, E. media, and E. irresidua) and the ST4 subtype of Blastocystis were identified in rabbits by sequence analysis. This is the first report of Blastocystis prevalence and subtype ST4 in rabbits in Shandong Province. The findings provide baseline data for the prevention and control of Eimeria spp. and Blastocystis in rabbits in Shandong Province, China.


Asunto(s)
Blastocystis/aislamiento & purificación , Eimeria/aislamiento & purificación , Infecciones Protozoarias en Animales/parasitología , Conejos/parasitología , Animales , Blastocystis/clasificación , Blastocystis/genética , China/epidemiología , ADN Protozoario/genética , Eimeria/clasificación , Eimeria/genética , Heces/parasitología , Intestinos/parasitología , Tipificación Molecular , Prevalencia , Infecciones Protozoarias en Animales/epidemiología
8.
Parasitol Res ; 119(4): 1221-1236, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32179988

RESUMEN

Members of the myxozoan genus Kudoa (Myxosporea: Multivalvulida: Kudoidae) are characterized as having four or more shell valves in a myxospore, with a corresponding number of polar capsules. Certain Kudoa spp. are critical pathogens in fish, causing postmortem myoliquefaction, unmarketable fish musculature due to unsightly macroscopic cysts, and reduced aquaculture production due to the outbreaks of neurological symptoms or cardiac diseases. Molecular genetic techniques have enabled the differentiation of Kudoa spp. with morphologically similar myxospores. In the present study, we employed integrated taxonomic approaches on five Kudoa spp. forming cysts between the trunk muscle myofibers (K. bora from Osteomugil perusii and K. lutjanus from Acanthopagrus latus), or cysts in the gallbladder wall (K. petala from Sillago sihama), and pseudocysts in the trunk muscle myofibers (K. uncinata from Nuchequula nuchalis and K. fujitai n. sp. from O. perusii). These four host fishes, which originated in the South China Sea, were purchased in the wet markets in Zhanjiang City, Guangdong Province, China, between August 2016 and April 2018. We have redescribed the four Kudoa spp. (K. bora, K. lutjanus, K. petala, and K. uncinata) on which little data are available after their original descriptions. Particularly, genetic characterization of K. bora and K. lutjanus, which are known to have myxospores morphologically similar to those of K. iwatai, was performed based on the nuclear ribosomal RNA gene and partial mitochondrial DNA genes such as cytochrome c oxidase subunit I and small and large ribosomal genes, demonstrating the validity and independence of these three kudoid species. We also provide description of a new species-K. fujitai n. sp.-in the present study. Application of integrated taxonomic approaches to known species characterized solely based on morphological criteria, as well as unknown species (e.g., K. fujitai n. sp. in the present study), contributes to better understanding of the biodiversity of Kudoa and multivalvulid myxosporeans.


Asunto(s)
Enfermedades de los Peces/microbiología , Myxozoa/clasificación , Animales , Acuicultura , Biodiversidad , China , ADN Ribosómico , Tipificación Molecular , Myxozoa/aislamiento & purificación , Filogenia , ARN Ribosómico 18S/genética , Análisis de Secuencia de ADN
9.
Parasitol Res ; 119(4): 1209-1220, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32189056

RESUMEN

This paper provides morphological and phylogenetic analyses of two new myxobolid species found infecting Piaractus brachypomus from the Amazon basin. The fish were caught in the Tapajós River, in the municipality of Santarém, in the state of Pará, Brazil. The plasmodial development of Henneguya brachypomus n. sp. occurred in the gill lamellae while Myxobolus pirapitingae n. sp. developed in the pyloric cecum. Morphological analyses did not identify inflammatory infiltrate for either species, but H. brachypomus n. sp. induced stretching of the epithelium, compression of the adjacent tissues, and displacement and deformation of the neighboring lamellae. The mature myxospores of H. brachypomus n. sp. were ellipsoid, with a length of 11.7-13.8 µm, a width of 4.0-4.6 µm, and a thickness of 3.5-4.3 µm. The polar capsules were elongated, with a length of 5.6-7.3 µm and a width of 1.3-2.0 µm, and each contained a polar filament with 8-9 coils. The caudal process was 40.5-48.1 µm long and the total length of the myxospore was 52.4-61.6 µm. Myxobolus pirapitingae n. sp. exhibited rounded mature myxospores measuring 10.0-11.1 µm in length, 7.0-7.6 µm in width, and 5.4-6.3 µm in thickness. The polar capsules were of equal size and occupied less than half the myxospore, measuring 3.5-4.0 µm in length and 2.0-2.6 µm in width, with each containing a polar filament with 6-7 coils. Phylogenetic analysis based on partial small subunit ribosomal DNA (ssrDNA) sequences showed that H. brachypomus n. sp. clustered as a sister species of Henneguya piaractus, while M. pirapitingae n. sp. was grouped in a sub-clade together with Myxobolus matosi and Myxobolus colossomatis.


Asunto(s)
Enfermedades de los Peces/parasitología , Myxobolus , Myxozoa , Enfermedades Parasitarias en Animales/parasitología , Animales , Brasil , Characiformes , Femenino , Branquias , Masculino , Tipificación Molecular , Myxobolus/clasificación , Myxobolus/aislamiento & purificación , Myxozoa/clasificación , Myxozoa/aislamiento & purificación , Filogenia , Subunidades Ribosómicas Pequeñas , Ríos
10.
PLoS Negl Trop Dis ; 14(3): e0008040, 2020 03.
Artículo en Inglés | MEDLINE | ID: mdl-32155148

RESUMEN

Salmonella Typhi (S. Typhi) is the causative agent of typhoid fever; a systemic disease affecting ~20 million people per year globally. There are little data regarding the contemporary epidemiology of typhoid in Latin America. Consequently, we aimed to describe some recent epidemiological aspects of typhoid in Colombia using cases reported to the National Public Health Surveillance System (Sivigila) between 2012 and 2015. Over the four-year reporting period there were 836 culture confirmed cases of typhoid in Colombia, with the majority (676/836; 80.1%) of reported cases originated from only seven departments. We further characterized 402 S. Typhi isolates with available corresponding data recovered from various departments of Colombia through antimicrobial susceptibility testing and molecular subtyping. The majority (235/402; 58.5%) of these typhoid cases occurred in males and were most commonly reported in those aged between 10 and 29 years (218/402; 54.2%); there were three (0.74%) reported fatalities. The overwhelming preponderance (339/402; 84.3%) of S. Typhi were susceptible to all tested antimicrobials. The most common antimicrobial to which the organisms exhibited non-susceptibility was ampicillin (30/402;7.5%), followed by nalidixic acid (23/402, 5.7%). Molecular subtyping identified substantial genetic diversity, which was well distributed across the country. Despite the diffuse pattern of S. Typhi genotypes, we identified various geographical hotspots of disease associated with local dominant genotypes. Notably, we found limited overlap of Colombian genotypes with organisms reported in other Latin American countries. Our work highlights a substantial burden of typhoid in Colombia, characterized by sustained transmission in some regions and limited epidemics in other departments. The disease is widely distributed across the country and associated with multiple antimicrobial susceptible genotypes that appear to be restricted to Colombia. This study provides a current perspective for typhoid in Latin America and highlights the importance of pathogen-specific surveillance to add insight into the limited epidemiology of typhoid in this region.


Asunto(s)
Salmonella typhi/aislamiento & purificación , Fiebre Tifoidea/epidemiología , Adolescente , Adulto , Distribución por Edad , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Colombia/epidemiología , Farmacorresistencia Bacteriana , Monitoreo Epidemiológico , Femenino , Variación Genética , Genotipo , Humanos , Lactante , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Tipificación Molecular , Estudios Retrospectivos , Salmonella typhi/clasificación , Salmonella typhi/efectos de los fármacos , Salmonella typhi/genética , Distribución por Sexo , Adulto Joven
11.
Parasitol Res ; 119(4): 1271-1279, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32072327

RESUMEN

To date, more than 50 Eimeria spp. have been isolated from marsupials of the family Macropodidae. Although 18 species of Eimeria have been previously detected from multiple animal species belonging to the genus Macropus of the family, limited genetic analyses of the parasites are available, and their pathogenicity remains unclear. Here, we report the isolation of Eimeria spp. from a zoo specimen of red-necked wallaby (Macropodidae; Macropus rufogriseus). Specifically, two distinct types of Eimeria oocysts were recovered, one from the feces before treatment with an anthelmintic and the second from the intestinal contents after death of the animal. The oocysts obtained from the two sources were morphologically identified as E. hestermani and E. prionotemni, respectively. We successfully determined partial gene sequences from the two isolates, including segments of the 18S rRNA genes, and for the first time have used phylogenetic analyses of these sequences to assign the species to distinct clades. In combination with further genetic data, these results are expected to help elucidate the pathogenicity and host ranges of Eimeria spp. within the respective family and genus.


Asunto(s)
Eimeria/aislamiento & purificación , Macropodidae/parasitología , Animales , Eimeria/clasificación , Heces/parasitología , Japón , Tipificación Molecular , Oocistos/clasificación , Filogenia , ARN Ribosómico 18S
12.
Epidemiol Infect ; 148: e13, 2020 01 31.
Artículo en Inglés | MEDLINE | ID: mdl-32000879

RESUMEN

In December 2016, Public Health England investigated an outbreak of campylobacteriosis in North West England, with 69 cases in total. Epidemiological, microbiological and environmental investigations associated the illness with the consumption of unpasteurised cows' milk from Farm X, where milk was predominantly sold from a vending machine. Campylobacter was detected in milk samples which, when sequenced, were identical in sequence type as pathogens isolated from cases (Clonal Complex ST-403, Sequence Type 7432). The farm was served with a Hygiene Emergency Prohibition Order to prevent further cases. To our knowledge, this is the first outbreak of campylobacter associated with unpasteurised milk in England since 1996. Our findings highlighted several important lessons, including that the current testing regime in England for unpasteurised milk is not fit for purpose and that the required warning label should include additional wording, underscoring the risk to vulnerable groups. There has been a substantial increase in both the volume of unpasteurised milk consumed in England and the use of vending machines to sell unpasteurised milk over the last 10 years, making unpasteurised milk more readily accessible to a wider population. The evidence generated from outbreaks like this is therefore critical and should be used to influence policy development.


Asunto(s)
Infecciones por Campylobacter/epidemiología , Campylobacter/aislamiento & purificación , Brotes de Enfermedades , Contaminación de Alimentos , Enfermedades Transmitidas por los Alimentos/epidemiología , Leche/microbiología , Adolescente , Adulto , Anciano , Animales , Campylobacter/clasificación , Campylobacter/genética , Bovinos , Niño , Preescolar , Inglaterra/epidemiología , Femenino , Humanos , Lactante , Masculino , Técnicas Microbiológicas , Persona de Mediana Edad , Tipificación Molecular , Estudios Retrospectivos , Análisis de Secuencia de ADN , Adulto Joven
13.
Epidemiol Infect ; 148: e15, 2020 02 04.
Artículo en Inglés | MEDLINE | ID: mdl-32014080

RESUMEN

Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005-2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.


Asunto(s)
Trazado de Contacto/métodos , Epidemiología Molecular/métodos , Tipificación Molecular/métodos , Mycobacterium/clasificación , Mycobacterium/genética , Tuberculosis/epidemiología , Secuenciación Completa del Genoma/métodos , Transmisión de Enfermedad Infecciosa , Genotipo , Humanos , Mycobacterium/aislamiento & purificación , Tuberculosis/transmisión , El Yukón/epidemiología
14.
Mikrobiyol Bul ; 54(1): 1-10, 2020 Jan.
Artículo en Turco | MEDLINE | ID: mdl-32050874

RESUMEN

Francisella tularensis is a gram-negative, coccobasillus, facultative intracellular bacteria and causes a zoonotic disease, tularemia in humans. F.tularensis has four subspecies, which have different virulences for humans as F.tularensis subsp. tularensis, F.tularensis subsp. holarctica, F.tularensis subsp. mediasiatica and F.tularensis subsp. novicida. F.tularensis subsp. tularensis is the most virulent subspecies and mortality rate is high in human cases. F.tularensis subsp. holarctica, which has been reported in our country to date, has lower virulence than that of subsp. tularensis, and causes rare lethality among untreated patients. According to the erythromycin resistance and the properties of glucose-glycerol fermentation, F.tularensis subsp. holarctica has three biovar as biovar I, biovar II and biovar japonica. F.tularensis subsp. mediasiatica has been reported only in a few central asian countries and its virulence is similar to the F.tularensis subsp. holarctica F.tularensis subsp. novicida is avirulent for immunocompetent individuals but has been observed to cause infection in immunocompromised individuals. The aim of this study was to determine the F.tularensis subspecies in 259 F.tularensis strains isolated from clinical specimens, drinking water and a rodent sample and 517 F.tularensis PCR-positive DNA isolated from clinical specimens between years 2009 and 2014. Conventional PCR was performed using primers specific for the RD1 (Region Difference) region of F.tularensis. Subspecies were differentiated depending on the difference in PCR amplification product size. In our study, F.tularensis subsp. holarctica was detected in 764 samples yielding 922 base pair (bp) amplification product. The DNA samples obtained from one water and 11 lymph aspirates were determined as F.tularensis subsp. holarctica biovar japonica. The DNA sequence analysis of the amplification product of the RD1 region of the isolate from water sample was determined. The 1136 bp nucleotide sequence obtained from the DNA sequence analysis was 100% similar to F.tularensis subsp. holarctica biovar japonica (FCS075 strain-accesion number AF469618) when compared with GenBank data. The whole genome sequence of this isolate was also determined and recorded to GenBank with accesion number CP007148. None of the samples used in our study belonged to other sub-species. F.tularensis subsp. holarctica biovar japonica positive 11 lymph aspirate samples were sent to our center from Ankara (n= 1), Kayseri (n= 1) and Afyon (n= 9) provinces. The results of the current study revealed that F.tularensis subsp. holarctica biovar japonica caused a tularemia outbreak in a village in Afyon province at first time and it was observed sporadically in two other different provinces.


Asunto(s)
Francisella tularensis , Tipificación Molecular , Tularemia , Animales , ADN Bacteriano/genética , Francisella tularensis/clasificación , Francisella tularensis/genética , Francisella tularensis/patogenicidad , Humanos , Tularemia/microbiología , Turquia , Virulencia , Zoonosis/microbiología
15.
Epidemiol Infect ; 148: e51, 2020 02 13.
Artículo en Inglés | MEDLINE | ID: mdl-32052718

RESUMEN

In June 2017, an outbreak of Salmonella Kottbus infection was suspected in Germany. We investigated the outbreak with whole-genome sequencing (WGS) and a case-control study. Forty-six isolates from 69 cases were subtyped. Three WGS clusters were identified: cluster 1 (n = 36), cluster 2 (n = 5) and cluster 3 (n = 3). Compared to controls, cluster 1 cases more frequently consumed raw smoked ham (odds ratio (OR) 10, 95% confidence interval (CI) 1.2-88) bought at supermarket chain X (OR 36, 95% CI 4-356; 9/10 consumed ham Y). All four cluster 2 cases interviewed had consumed quail eggs. Timely WGS was invaluable in distinguishing concurrent outbreaks of a rare Salmonella serotype.


Asunto(s)
Brotes de Enfermedades , Enfermedades Transmitidas por los Alimentos/epidemiología , Epidemiología Molecular/métodos , Tipificación Molecular/métodos , Infecciones por Salmonella/epidemiología , Salmonella enterica/clasificación , Secuenciación Completa del Genoma/métodos , Adulto , Anciano , Anciano de 80 o más Años , Estudios de Casos y Controles , Análisis por Conglomerados , Conducta Alimentaria , Femenino , Enfermedades Transmitidas por los Alimentos/microbiología , Alemania/epidemiología , Humanos , Masculino , Persona de Mediana Edad , Infecciones por Salmonella/microbiología , Salmonella enterica/genética , Salmonella enterica/aislamiento & purificación
16.
BMC Infect Dis ; 20(1): 143, 2020 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-32059706

RESUMEN

BACKGROUND: Chagas disease is caused by the haemoflagellate protozoan Trypanosoma cruzi. Currently, T. cruzi recognizes seven discrete typing units (DTUs): TcI to TcVI and Tcbat. The genetic diversity of T. cruzi is suspected to influence the clinical outcome. Acute clinical manifestations, which include myocarditis and meningoencephalitis, are sometimes fatal; occur most frequently in children and in immunocompromised individuals. Acute disease is often overlooked, leading to a poor prognosis. CASE PRESENTATION: A 38-year-old man from a subtropical area of the Andes mountains of Ecuador was hospitalized after 3 weeks of evolution with high fever, chills, an enlarged liver, spleen, and lymph nodes, as well as facial edema. ECG changes were also observed. T. cruzi was identified in blood smears, culture and amplification of DNA by PCR. Tests for anti-T. cruzi IgG and IgM and HIV were negative. Molecular typing by restriction fragment length polymorphism (PCR-RFLP) determined the parasite to DTU TcI. In the absence of a timely anti-T. cruzi medication, the patient died. CONCLUSIONS: This is a case of severe pathogenicity and the virulence of a DTU TcI strain in an adult patient. The severe acute Chagas disease was probably overlooked due to limited awareness and its low incidence. Our findings suggest that T. cruzi DTU TcI strains circulating in Ecuador are capable of causing fatal acute disease. Early diagnosis and prompt treatment is of paramount importance to avoid fatalities in acute infections.


Asunto(s)
Enfermedad de Chagas/etiología , Trypanosoma cruzi/genética , Trypanosoma cruzi/patogenicidad , Adulto , Enfermedad de Chagas/parasitología , Ecuador , Variación Genética , Humanos , Masculino , Tipificación Molecular , Reacción en Cadena de la Polimerasa , Polimorfismo de Longitud del Fragmento de Restricción , Trypanosoma cruzi/clasificación
17.
BMC Infect Dis ; 20(1): 140, 2020 Feb 14.
Artículo en Inglés | MEDLINE | ID: mdl-32059712

RESUMEN

BACKGROUND: Anthrax is an endemic disease that persists in the rural regions of China. The global genetic population structure of B.anthracis has also been defined by the canonical single-nucleotide polymorphisms (canSNP) and multiple-locus variable-number tandem repeat analysis (MLVA). Five canSNP lineages were found in China, and the A.Br.Ames lineage has been the second predominant group in recent years in China. The objective of this study was to reveal genetic diversity of the Ames lineage strains by MLVA. METHODS: Two molecular typing methods, canSNP and MLVA with 15markers were used to study the genetic relationship among the Ames lineage strains. The outbreak information associated with these strains was also collected and investigated. RESULTS: From 2007 to 2018, a total of 21 human anthrax infection outbreaks (68 patients) associated with B. anthracis Ames lineage strains were reported in China. Ames lineage strain-associated human anthrax is mainly distributed in the northern part of China, including the provinces of Inner Mongolia, Liaoning, Gansu, and Xinjiang. In the study, a total of 30 Ames lineage strains were included and 10 MLVA15 genotypes were identified. These strains were mainly found in northeast China, Inner Mongolia and Liaoning. In recent years, the Ames lineage strains were isolated in the two provinces every year. The 18 Ames lineage strains isolated from Inner Mongolia were divided into eight MLVA15 genotypes. From 2010 to 2015, there were continuous reports of outbreaks in Keyouzhongqi County, Inner Mongolia, and the strains that were isolated annually in succession belonged to the MLVA15-30 genotype. CONCLUSIONS: The Ames lineage strains are widely distributed in northern China. Their genetic diversity can be illustrated by the results of the MLVA. The genetic characteristics of the Ames lineage strains from outbreaks in different provinces varied. In some areas, human anthrax outbreaks occurred annually in succession, and these related strains grouped together. These observations indicate that the local environment was persistently contaminated with B. anthracis spores, vaccination of livestock should become the fundamental control measure in the areas.


Asunto(s)
Carbunco/microbiología , Bacillus anthracis/genética , Variación Genética , Animales , Carbunco/epidemiología , Bacillus anthracis/aislamiento & purificación , China/epidemiología , Brotes de Enfermedades , Genética de Población , Genotipo , Humanos , Ganado/microbiología , Repeticiones de Minisatélite , Tipificación Molecular , Polimorfismo de Nucleótido Simple
18.
DNA Cell Biol ; 39(4): 579-598, 2020 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-32069124

RESUMEN

The genus Schizothorax is one of the most diverse groups of schizothoracine fish. Many species within this genus possess highly similar morphological characters and are very difficult to be identified accurately only based on morphology. The present study aims to test the effectiveness of mitochondrial cytochrome c oxidase subunit I (COI) gene and cytochrome b (Cytb) gene for discriminating the Schizothorax fish. A total of 185 individuals of 11 species for COI gene and 264 individuals of 23 species for Cytb gene were used for analyzing, respectively. According to the genetic distances, only one species based on COI gene and five species based on Cytb gene had "barcoding gaps," respectively. The tree-based analysis displayed that four species based on COI gene and six species based on Cytb gene clustered monophyletic group with strong support, respectively. The optimal threshold value of Schizothorax is 0.005 based on COI gene and 0.008 based on Cytb gene. The results of genetic similarity tests performed through online BLAST showed that 108 of 185 similarity searches succeeded in identifying conspecific sequences based on COI gene and 199 of 264 succeeded in identifying conspecific sequences based on Cytb gene. Considering greater interspecific genetic distance in Kimura 2-parameter (K2P) analysis and many clades with higher supporting values in tree-based analysis, we suggest that Cytb gene has better resolution in discrimination of Schizothorax species than COI gene. However, there are still many confused clustering relationships based on molecular data currently available. Incomplete lineage sorting, the existence of possible cryptic species and problematic morphological identification, etc. might have greatly weakened the resolution of Cytb gene in discrimination of Schizothorax species.


Asunto(s)
Cyprinidae/clasificación , Citocromos b/genética , ADN Mitocondrial/genética , Complejo IV de Transporte de Electrones/genética , Animales , Secuencia de Bases , Cyprinidae/genética , Variación Genética/genética , Mitocondrias/enzimología , Mitocondrias/genética , Tipificación Molecular/métodos , Análisis de Secuencia de ADN , Tibet
19.
Int J Infect Dis ; 92: 123-126, 2020 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-31935536

RESUMEN

BACKGROUND: Candida haemulonii is an emergent, multi-resistant opportunistic pathogenic yeast that like Candida auris, can be misidentified when conventional diagnostic methods are used. Timely molecular identification using DNA sequence analysis variation in the internal transcriber spacer region, ITS1-ITS4 and the 28S ribosomal DNA gene (28S rDNA), and in vitro antifungal susceptibility assessment can lead to rapid therapeutic success. CASE REPORT: A case of Candida haemulonii candidiasis suffered by a male paediatric patient attended at Federico Gómez Children's Hospital of México City in September 2016 is reported. The isolate was yielded from peripheral blood and central catheter blood specimens. From in vitro antifungal susceptibility data, caspofungin was administered to the patient, who showed clear improvements at the end of antimicrobial administration, and the removal of the central venous catheter. Using a molecular phylogenetic approach, we identified the clinical isolate as C. haemulonii. The clinical isolate has been named as Candida haemulonii ENCB-87 from now on. C. haemulonii ENCB-87 grew well between the temperatures, 28 °C and 35 °C but not at 37 °C in YPD culture medium. The clinical isolate was susceptible to caspofungin, which resulted in therapeutic success for the patient. CONCLUSIONS: C. haemulonii is an emergent, opportunistic pathogen, closely related to C. auris, therefore, the timely and accurate identification and antifungal susceptibility assessments are paramount in generating a robust epidemiology of this emerging Candida species.


Asunto(s)
Candida/aislamiento & purificación , Candidiasis/etiología , Infecciones Relacionadas con Catéteres/microbiología , Hospitales Pediátricos , Antifúngicos/uso terapéutico , Candida/clasificación , Candidiasis/tratamiento farmacológico , Caspofungina/uso terapéutico , ADN de Hongos , ADN Ribosómico , Humanos , Lactante , Masculino , México , Pruebas de Sensibilidad Microbiana , Tipificación Molecular , Filogenia , Análisis de Secuencia de ADN
20.
Gene ; 734: 144382, 2020 Apr 15.
Artículo en Inglés | MEDLINE | ID: mdl-31978513

RESUMEN

Japanese macaque (Macaca fuscata) is an indigenous Old World monkey (OWM) species that inhabits the Japanese archipelago. There are two subspecies of Japanese macaque: Yakushima macaque (M. f. yakui) which inhabits Yakushima Island exclusively, and Hondo macaque (M. f. fuscata) which inhabits the mainland of Japan. Yakushima macaque is considered to be branched off from a certain parental macaque group that had inhabited the mainland of Japan. However, the process of sub-speciation of the Yakushima macaque is still unclear at present. In this study, to gain new insight into the process of sub-speciation of Japanese macaque, we utilized the simian foamy virus (SFV) as a marker. SFVs are found in virtually all primates except humans and undergo species-specific cospeciation with the hosts. The phylogenetic analysis of conserved regions of the env gene in SFVs remarkably resembled that of the OWMs with high statistical confidence. The phylogenetic analyses also indicated that there are four (1-4) genotypes among Asian OWMs investigated. SFVs derived from Asian OWMs except Yakushima macaque were classified as genotypes 1-3, whereas SFVs isolated from all Yakushima macaques and one Hondo macaque were classified as genotype 4. Interestingly, genotype 4 was firstly branched off from the rest of the genotypes, which might indicate that the macaques infected with genotype 4 SFV were derived from the "older" population of Japanese macaques. The high prevalence of genotype 4 SFVs among Yakushima macaque might reflect the possibility that they are a descendant of the population settled earlier, which has been geographically isolated in Yakushima Island.


Asunto(s)
Macaca fuscata/virología , Virus Espumoso de los Simios/clasificación , Animales , Células Cultivadas , Genes Virales , Genes env , Integrasas/genética , Tipificación Molecular , Filogenia , Virus Espumoso de los Simios/genética , Virus Espumoso de los Simios/aislamiento & purificación , Especificidad de la Especie
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