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1.
Nat Commun ; 12(1): 2619, 2021 05 11.
Artículo en Inglés | MEDLINE | ID: mdl-33976183

RESUMEN

After the Zika virus (ZIKV) epidemic in the Americas in 2016, both Zika and dengue incidence declined to record lows in many countries in 2017-2018, but in 2019 dengue resurged in Brazil, causing ~2.1 million cases. In this study we use epidemiological, climatological and genomic data to investigate dengue dynamics in recent years in Brazil. First, we estimate dengue virus force of infection (FOI) and model mosquito-borne transmission suitability since the early 2000s. Our estimates reveal that DENV transmission was low in 2017-2018, despite conditions being suitable for viral spread. Our study also shows a marked decline in dengue susceptibility between 2002 and 2019, which could explain the synchronous decline of dengue in the country, partially as a result of protective immunity from prior ZIKV and/or DENV infections. Furthermore, we performed phylogeographic analyses using 69 newly sequenced genomes of dengue virus serotype 1 and 2 from Brazil, and found that the outbreaks in 2018-2019 were caused by local DENV lineages that persisted for 5-10 years, circulating cryptically before and after the Zika epidemic. We hypothesize that DENV lineages may circulate at low transmission levels for many years, until local conditions are suitable for higher transmission, when they cause major outbreaks.


Asunto(s)
Virus del Dengue/inmunología , Dengue/epidemiología , Susceptibilidad a Enfermedades/inmunología , Epidemias/estadística & datos numéricos , Infección por el Virus Zika/inmunología , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Anticuerpos Antivirales/inmunología , Brasil/epidemiología , Niño , Preescolar , Dengue/inmunología , Dengue/transmisión , Dengue/virología , Virus del Dengue/genética , Virus del Dengue/aislamiento & purificación , Epidemias/prevención & control , Monitoreo Epidemiológico , Femenino , Genoma Viral/genética , Humanos , Inmunidad Heteróloga , Incidencia , Lactante , Recién Nacido , Masculino , Persona de Mediana Edad , Tipificación Molecular , Mosquitos Vectores/virología , Filogeografía , Serotipificación , Adulto Joven , Virus Zika/inmunología , Infección por el Virus Zika/epidemiología
2.
J Med Microbiol ; 70(5)2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33999798

RESUMEN

Introduction. New Delhi metallo-ß-lactamase (NDM)-producing Klebsiella pneumoniae has become a serious global health concern.Hypothesis/Gap Statement. Due to the high genetic diversity among NDM-positive K. pneumoniae, we need further surveillance and studies to better understand the relationships between them. In addition, the coexistence of several plasmid replicon types in NDM-positive K. pneumoniae may affect the copy number of bla NDM, the MIC level to antibiotics, as well as increasing the chance of horizontal gene transfer.Aim. The aim of this study was to determine incompatible plasmid groups and copy numbers of bla NDM, and to investigate the genetic relationship of 37 NDM-positive K. pneumoniae in Kerman, Iran.Methodology. The bla NDM-1 gene was detected and confirmed by PCR-sequencing. The plasmid replicon types were determined by PCR-based replicon typing (PBRT) and the copy number of bla NDM-1 was determined by quantitaive real time-PCR (qPCR). Random amplified polymorphic DNA (RAPD)-PCR typing was used to detect genetic relationships between the strains.Results. In this study, 10 different replicon types, including Frep [n=25 (67.5 %)], FIIAs [n=11 (29.7 %)], FIA [n=5 (13.5 %)], FIB [n=3 (8.1 %)], I1-Iγ [n=2 (5.4 %)], L/M [n=7 (18.9 %)], A/C [n=7 (18.9 %)], Y [n=3 (8.1 %)], P [n=1 (2.7 %)] and FIC [n=1 (2.7 %)] were reported. The copy numbers of the bla NDM-1 gene varied from 30.00 to 5.0×106 and no statistically significant correlation was observed between a rise of the MIC to imipenem and the copy numbers of bla NDM-1 (P>0.05). According to RAPD typing results, 35 strains were divided into five clusters, while two strains were non-typeable.Conclusion. The spread of NDM-1-producing K. pneumoniae strains that carry several plasmid replicon types increases the chance of horizontal transfer of antibiotic resistance genes in hospital settings. In this study, 10 different replicon types were identified. We could not find any relationship between the increase of MIC levels to imipenem and the copy numbers of bla NDM-1. Therefore, due to the identification of different replicon types in this study, the type and genetic characteristics of bla NDM-1-carrying plasmids, and other factors such as antibiotic selective pressure, probably affect the copy number of bla NDM-1 and change the MIC level to imipenem.


Asunto(s)
Antibacterianos/farmacología , Carbapenémicos/farmacología , Dosificación de Gen , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Plásmidos , beta-Lactamasas/genética , Humanos , Irán , Klebsiella pneumoniae/clasificación , Tipificación Molecular , Técnica del ADN Polimorfo Amplificado Aleatorio , Replicón , Resistencia betalactámica
3.
Medicine (Baltimore) ; 100(20): e25930, 2021 May 21.
Artículo en Inglés | MEDLINE | ID: mdl-34011066

RESUMEN

BACKGROUND: To study the epidemic features of hand-foot-mouth disease (HFMD) in mainland China through systematic review and meta-analysis so as to provide evidence for the future prevention and control of HFMD. METHODS: Articles on the epidemic features of HFMD in mainland China, written in English or Chinese and released between January 1, 2015 and January 1, 2020, were searched from English literature databases including Embase, Web of Science, PubMed, Cochrane library, Google academic, and Chinese literature databases including China national knowledge infrastructure (CNKI), Wanfang, and China Biology Medicine (CBM). Papers were selected according to the inclusion and exclusion criteria, and quality scoring was performed. Meta-analysis, sensitivity analysis, and identification of publication bias were finished through STATA version 12.0 software. RESULTS: A total of 23 articles were included in this study, the total number of cases was 377,083, of which the total number of male cases was 231,798 and the total number of female cases was 145,285, the sex ratio was about 1.6:1, and the incidence of HFMD in China was 1.61‰ (95% confidence interval [CI]: 1.21‰-1.94‰). The results of the subgroup analysis showed that the incidence of HFMD in mainland China was the highest in South China, in 2014, in 1-year-old group and in other types of enteroviruses, respectively, with the rate of 3.48‰ (95% CI: 1.22‰-5.73‰), 1.81‰ (95% CI: 1.06‰-2.57‰), 15.20‰ (95% CI: 5.00‰-25.30‰), and 1.83‰ (95% CI: 1.32‰-2.33‰), respectively. The differences among the above 4 subgroups were statistically significant (P < .05). There were no publication bias in this study, and the sensitivity analysis results suggested that the meta-analysis results were robust. CONCLUSION: There were differences in the distribution of region, time, population, and etiology of HFMD in mainland China. Health departments should adopt key strategies and measures for key populations in key areas to prevent and control the development of HFMD, and improve the ability of pathogen detection and typing in laboratories.


Asunto(s)
Enterovirus/aislamiento & purificación , Enfermedad de Boca, Mano y Pie/epidemiología , Distribución por Edad , Preescolar , China/epidemiología , Enterovirus/genética , Femenino , Geografía , Enfermedad de Boca, Mano y Pie/virología , Humanos , Incidencia , Lactante , Recién Nacido , Masculino , Epidemiología Molecular , Tipificación Molecular/estadística & datos numéricos , Distribución por Sexo
4.
Nat Commun ; 12(1): 2296, 2021 04 16.
Artículo en Inglés | MEDLINE | ID: mdl-33863880

RESUMEN

Brazil experienced a large dengue virus (DENV) epidemic in 2019, highlighting a continuous struggle with effective control and public health preparedness. Using Oxford Nanopore sequencing, we led field and classroom initiatives for the monitoring of DENV in Brazil, generating 227 novel genome sequences of DENV1-2 from 85 municipalities (2015-2019). This equated to an over 50% increase in the number of DENV genomes from Brazil available in public databases. Using both phylogenetic and epidemiological models we retrospectively reconstructed the recent transmission history of DENV1-2. Phylogenetic analysis revealed complex patterns of transmission, with both lineage co-circulation and replacement. We identified two lineages within the DENV2 BR-4 clade, for which we estimated the effective reproduction number and pattern of seasonality. Overall, the surveillance outputs and training initiative described here serve as a proof-of-concept for the utility of real-time portable sequencing for research and local capacity building in the genomic surveillance of emerging viruses.


Asunto(s)
Virus del Dengue/genética , Dengue/epidemiología , Epidemias/prevención & control , Monitoreo Epidemiológico , Brasil/epidemiología , Dengue/prevención & control , Dengue/transmisión , Dengue/virología , Virus del Dengue/aislamiento & purificación , Estudios de Factibilidad , Variación Genética , Genoma Viral/genética , Humanos , Unidades Móviles de Salud , Epidemiología Molecular , Tipificación Molecular , Filogenia , Prueba de Estudio Conceptual , ARN Viral/genética , ARN Viral/aislamiento & purificación , Reacción en Cadena en Tiempo Real de la Polimerasa , Estudios Retrospectivos , Secuenciación Completa del Genoma
5.
Gene ; 787: 145639, 2021 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-33848576

RESUMEN

Anomopoda is the widespread planktonic microcrustacean, which plays a crucial role in aquatic ecosystem. There are few studies about the evolutionary relationships among various Anomopoda basing on molecular data. In the present study, phylogenetic analysis of eight Anomopoda was carried out. Firstly, the culture system was developed to breed cladocerans. By using this system, eight species (Daphnia magna, D. pulex, D. sinensis, Ceriodaphnia reticulata, Moina micrura, Scapholeberis kingi, Simocephalus vetulus and Eurycercus lamellatus) were purified and cultured stably in the laboratory. Then, transcriptomic sequences and partial mitochondrial DNA sequences were both used to reconstruct the phylogenetic tree among 8 species. Transcriptomic sequences were sequenced on Illumina Hiseq 2500 platform. After assembly and annotation, transcriptomic sequences were spliced together and aligned for phylogenetic analysis. Basing on the orthologous genes derived from transcriptomic sequences, the phylogenetic analysis showed that 4 genera of Daphniidae were clustered into one group, and among the 4 genera, Ceriodaphnia was closer to Daphnia than Simocephalus, while Scapholeberis was farthest from other species. In addition, Eurycercidae was closer to Daphniidae than Moinidae. The phylogenetic trees based on both 12S rRNA and 16S rRNA sequences were similar with that based on transcriptomic sequences. Meanwhile, the phylogenetic tree based on 16S rRNA sequences was more suitable than that based on 12S rRNA sequences. These results suggested that the phylogenetic analysis basing on the transcriptomic sequences was available in cladocerans, which will help us to effectively understand the phylogenetic relationships among various cladocerans.


Asunto(s)
Cladóceros/clasificación , Cladóceros/genética , ADN Mitocondrial , Animales , Anotación de Secuencia Molecular , Tipificación Molecular , Filogenia , Análisis de Secuencia de ADN , Especificidad de la Especie , Transcriptoma
6.
Mol Biol Rep ; 48(4): 3629-3635, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33893925

RESUMEN

PCR Single-Strand Conformation Polymorphism is a method used to identify and detect mutations and is now well known for its many applications on living beings. This paper will discuss the experimental details, limitations and sensitivity of the PCR Single-Strand Conformation Polymorphism method in relation to all existing literature available to us until today. Genomic DNA extraction, PCR amplification and Single-Strand Conformation Polymorphism conditions (concentration of polyacrylamide slab gel electrophoresis, dissociation treatment of double- stranded DNA) and comparison with PCR Restriction Fragment Length Polymorphism are presented. Since its discovery in 1989, there have been many variations, innovations, and modifications of the method, which makes it very easy, safe, fast and for this reason widely applied in clinical diagnostic, forensic medicine, biochemical, veterinary, microbiological, food and environmental laboratories. One of the possible applications of the method is the diagnosis and identification of mutations in new strains of coronaviruses, because science needs more tools to tackle the problem of this pandemic. The PCR Single-Strand Conformation Polymorphism method can be applied in many cases provided that control samples are available and the required conditions of the method are achieved.


Asunto(s)
Reacción en Cadena de la Polimerasa/métodos , Polimorfismo Conformacional Retorcido-Simple , Animales , Coronavirus/clasificación , Coronavirus/genética , Coronavirus/aislamiento & purificación , Humanos , Tipificación Molecular/métodos , Patología Molecular/métodos , Polimorfismo de Longitud del Fragmento de Restricción , Análisis de Secuencia/métodos
7.
Int J Food Microbiol ; 347: 109188, 2021 Jun 02.
Artículo en Inglés | MEDLINE | ID: mdl-33839439

RESUMEN

Vibrio parahaemolyticus, which is commonly found in marine and estuarine environments worldwide and isolated from aquatic products, is one of the most important food-borne pathogens. Among the various typing methods, serotyping is widely accepted and utilized by infectious disease specialists and infection control agencies for the detection and epidemiological investigation of this pathogen. Thus far, 13 O serotypes and 71 K serotypes have been defined; however, untypeable strains are frequently isolated during routine detection, and some new O and/or K antigens have been identified and characterized. During a serotyping survey in Shandong province, China from 2016 to 2018, we collected 411 clinical V. parahaemolyticus strains and found that nine of them are untypeable K antigen strains. In this study, we identified three K serotypes of V. parahaemolyticus through in-depth genetic analysis of the K antigen gene cluster, serological tests, and the production of antisera. Among the nine strains, seven possess K untypeable 2 (KUT2) antigens, which have been reported recently by another group. However, two new O and K combinations (O3:KUT2 and O11:KUT2) were first characterized by us, with the remaining two each representing a novel K serotype. Moreover, through comparative genomic analysis, we showed that the Shandong KUT2 strains exhibit different virulence profiles compared to their identical K serotype partners from Zhejiang province, another Chinese coastal province; however, strains from these two regions are clustered into the same linage and may have evolved from a recent common ancestor. Additionally, one isolate, SD2016062, was phylogenetically similar to the strains associated with several local gastroenteritis outbreaks, with similar toxin patterns, suggesting its potential to cause sporadic occurrences of disease or even local pandemics. Finally, we developed a sero-specific PCR assay targeting the three novel K serotypes, which can monitor the V. parahaemolyticus spectrum for clinical and epidemiological purposes. Thus, we identified and characterized novel strains of V. parahaemolyticus and proposed a new technique for tracking the diversity of strains, which can help manage this food-borne pathogen.


Asunto(s)
Antígenos Bacterianos/genética , Antígenos de Superficie/genética , Vibriosis/epidemiología , Vibriosis/microbiología , Vibrio parahaemolyticus/genética , China/epidemiología , Gastroenteritis/epidemiología , Gastroenteritis/microbiología , Humanos , Tipificación Molecular , Antígenos O/genética , Filogenia , Reacción en Cadena de la Polimerasa , Serogrupo , Vibrio parahaemolyticus/clasificación , Vibrio parahaemolyticus/patogenicidad , Virulencia/genética
8.
Parasitol Res ; 120(5): 1755-1770, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33687566

RESUMEN

Cercarial emission of schistosomes is a determinant in the transmission to the definitive host and constitutes a good marker to identify which definitive host is responsible for transmission, mainly in introgressive hybridization situations. Our goal was to test the hypothesis that micro-mammals play a role in Schistosoma haematobium, S. bovis, and/or S. haematobium x S. bovis transmission. Small mammal sampling was conducted in seven semi-lacustrine villages of southern Benin. Among the 62 animals trapped, 50 individuals were investigated for Schistosoma adults and eggs: 37 Rattus rattus, 3 Rattus norvegicus, 9 Mastomys natalensis, and 1 Crocidura olivieri. Schistosoma adults were found in four R. rattus and two M. natalensis, with a local prevalence reaching 80% and 50%, respectively. Two cercarial chronotypes were found from Bulinus globosus experimentally infected with miracidia extracted from naturally infected M. natalensis: a late diurnal and nocturnal chronotype, and an early diurnal, late diurnal, and nocturnal chronotype. The cytochrome C oxidase subunit I mtDNA gene of the collected schistosomes (adults, miracidia, and cercariae) belonged to the S. bovis clade. Eleven internal transcribed spacer rDNA profiles were found; four belonged to S. bovis and seven to S. haematobium x S. bovis. These molecular results together with the observed multi-peak chronotypes add M. natalensis as a new host implicated in S. haematobium x S. bovis transmission. We discuss the origin of the new chronotypes which have become more complex with the appearance of several peaks in a 24-h day. We also discuss how the new populations of offspring may optimize intra-host ecological niche, host spectrum, and transmission time period.


Asunto(s)
Introgresión Genética , Murinae/parasitología , Schistosoma haematobium/fisiología , Schistosoma/fisiología , Esquistosomiasis/parasitología , Esquistosomiasis/transmisión , Animales , Benin , Bulinus/parasitología , Cercarias/genética , ADN Mitocondrial , ADN Ribosómico , Ecosistema , Femenino , Interacciones Huésped-Parásitos , Masculino , Tipificación Molecular , Prevalencia , Ratas , Schistosoma/genética , Schistosoma haematobium/genética , Esquistosomiasis Urinaria/parasitología , Esquistosomiasis Urinaria/transmisión , Musarañas/parasitología
9.
Acta Trop ; 218: 105905, 2021 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-33775628

RESUMEN

Haemoproteus species (Haemosporida, Haemoproteidae) are cosmopolitan blood parasites, which have been neglected for over 100-years, but attracted attention recently due to reports of severe and even lethal haemoproteosis in birds and vectors. Approximately 150 species of avian Haemoproteus have been described and named, but molecular data suggest that hundreds of independently evolving molecular lineages might occur, indicating the existence of a remarkable undescribed species diversity. It is timely to develop a methodology, which allow the application of available genetic data in taxonomy of haemosporidians on species levels. This study aimed to test a hypothesis suggesting that DNA haplotype networks might aid in targeting genetically distinct, but still undescribed parasites, and might be used to direct taxonomic studies on haemosporidian species levels. Mainly, we tested a prediction that the lineage hTUPHI01, a common Haemoproteus parasite of Turdus philomelos, might be a new species, which is morphologically similar and genetically closely related to the parasites of Haemoproteus minutus group. Blood samples of T. philomelos naturally infected with this parasite lineage were collected and studied using microscopic examination of blood films and PCR-based methods. Haemoproteus asymmetricus n. sp. was found in this bird, described and characterised molecularly using partial cytochrome b (cytb) sequences. The new species shared some features with parasites of the H. minutus group, as was predicted by the DNA haplotype network. Due to the visualisation of closely related lineages as well as the evaluation of their host and geographic distributions, DNA haplotype networks can be recommended as the helpful methodology, able to direct and speed practical work on parasite species taxonomy and pathogen biodiversity. The combined molecular phylogenetic and morphological approaches showed that the well-supported clades in Bayesian phylogenetic trees based on the partial cytb gene sequences contain morphologically remarkably different Haemoproteus parasite species, which however, share some basic biological features. Phylogenetic analysis can be used for prediction of these basic features in still undescribed parasites. This study calls for further fusion of advanced molecular and microscopy approaches for better understanding haemosporidian parasite biology.


Asunto(s)
Enfermedades de las Aves/parasitología , Aves/parasitología , Haemosporida/citología , Haemosporida/genética , Infecciones Protozoarias en Animales/parasitología , Animales , Teorema de Bayes , Enfermedades de las Aves/sangre , Aves/sangre , Citocromos b/genética , ADN Protozoario , Pruebas Diagnósticas de Rutina , Gametogénesis , Genes Protozoarios , Genoma de Protozoos , Haemosporida/clasificación , Haplotipos , Tipificación Molecular , Filogenia , Reacción en Cadena de la Polimerasa
10.
Medicine (Baltimore) ; 100(13): e25362, 2021 Apr 02.
Artículo en Inglés | MEDLINE | ID: mdl-33787640

RESUMEN

ABSTRACT: We investigated the vaginal flora diversity of preschool-aged (ie, 4-6-year-old) girls in southwest China.Fourteen preschool-aged girls were enrolled in this study. The statuses and differences in their vaginal flora were evaluated by Gram staining, bacterial culturing, and sequencing analysis.Gram staining and microbial culturing showed that the main vaginal flora of the preschool-aged girls were Gram-negative bacilli, whereas the main vaginal flora of healthy adult controls were large Gram-positive bacilli such as Lactobacillus crispatus. Shannon and Simpson indexes indicated that the bacterial diversity tended to decrease with age. The species abundance heat map showed that the vaginal microecology of the girls differed slightly at different ages but mainly comprised Pseudomonas, Methylobacterium, Sphingomona,s and Escherichia. The functional abundance heat map indicated that the bacterial functions increased with age.The vaginal microecology of preschool-aged girls differs from that of adults. A comprehensive understanding of the vaginal flora diversity of preschool-aged girls will aid in clinically diagnosing vulvovaginitis in preschool-aged girls.


Asunto(s)
Bacterias/aislamiento & purificación , Microbiota/genética , Vagina/microbiología , Vulvovaginitis/diagnóstico , Adulto , Factores de Edad , Bacterias/genética , Estudios de Casos y Controles , Niño , Preescolar , China , ADN Bacteriano/aislamiento & purificación , Femenino , Voluntarios Sanos , Humanos , Tipificación Molecular/métodos , Análisis de Secuencia de ADN , Frotis Vaginal , Vulvovaginitis/microbiología
11.
Acta Trop ; 217: 105857, 2021 May.
Artículo en Inglés | MEDLINE | ID: mdl-33582142

RESUMEN

Borrelia miyamotoi is a relapsing fever spirochete that can cause chills, fatigue, headache, myalgia, arthralgia, and even meningitis, damaging human health. B. miyamotoi has a wide distribution since its discovery in Ixodes persulcatus in 1994. The human B. miyamotoi disease was first described in Russia in 2011. However, the epidemiological information in China is limited. Here, we report the molecular detection of B. miyamotoi in the northeast of Inner Mongolia, China. A total of 774 adult ticks and 771 blood samples of patients were collected, from April 2017 to August 2019 in the northeast of Inner Mongolia, and tested for B. miyamotoi using real time-PCR. Gene sequences of 16S rRNA, fla, and glpQ were obtained to reconstruct the phylogenetic relationship of B. miyamotoi from humans and ticks. The results showed the total prevalence of B. miyamotoi in ticks was 1.3% of 774 ticks, with rates of 2.6% in I. persulcatus, 0.78% in Dermacentor nuttalli, 1.3% in D. silvarum, and 0.4% in Haemaphysalis longicornis. Thirteen (1.7%) patients were confirmed as positive for B. miyamotoi. Patients were mainly 50-60-years old and had a history of tick contact. They presented flu-like symptoms, including fever, headache, poor spirit, dizziness, nausea, vomiting, hypodynamic, chest distress, and myalgia. Phylogenetic analysis showed that the B. miyamotoi in the present study belonged to the Siberian type, distinct from European and American types and the I. ovatus isolate from Japan. This is the first report of B. miyamotoi detection in both ticks and humans in the northeast of Inner Mongolia, China, indicating B. miyamotoi is present in the area. These findings suggest that people have a risk of infection with B. miyamotoi in this region, where it should be included the differential diagnosis of tick-borne diseases.


Asunto(s)
Borrelia/clasificación , Borrelia/genética , Enfermedades por Picaduras de Garrapatas/epidemiología , Enfermedades por Picaduras de Garrapatas/microbiología , Garrapatas/microbiología , Adulto , Animales , Borrelia/aislamiento & purificación , China/epidemiología , ADN Bacteriano/genética , Femenino , Flagelina/genética , Humanos , Ixodes , Japón , Masculino , Persona de Mediana Edad , Tipificación Molecular , Hidrolasas Diéster Fosfóricas/genética , Filogenia , ARN Ribosómico 16S/genética , Reacción en Cadena en Tiempo Real de la Polimerasa , Enfermedades por Picaduras de Garrapatas/sangre
12.
Comp Immunol Microbiol Infect Dis ; 75: 101623, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33607397

RESUMEN

PCR ribotypes (RTs027 and 078) are known causes of Clostridioides difficile infection (CDI) in humans. Molecular typing and characterization of 39 C. difficile strains isolated from samples from humas and animals in 2016-2018 indicated an overlap of RTs between community-acquired patients (CA-CDI) and domestic animals from the same geographical area; 14 RTs were identified: 12 RTs were positive for toxins A/B; RT078, RT080 and RT126 were also positive for binary toxin (CDT). Most of the RTs from the animals (RTs020, 078, 106, 126) were also detected in the samples from humans. Strains grouped into three clusters: cluster I included prevalently human strains, mainly RT 018; clusters II and III included strains from humans and animals, mainly RT078 and RT020. The CA-CDI strains suggested animals as a reservoir of C. difficile isolated together with other microorganisms from animals, highlighting the association of enteric pathogens as a cause of infection and death.


Asunto(s)
Infecciones por Clostridium , Animales , Infecciones por Clostridium/epidemiología , Infecciones por Clostridium/veterinaria , Humanos , Italia/epidemiología , Tipificación Molecular/veterinaria , Ribotipificación/veterinaria
13.
Nat Med ; 27(3): 440-446, 2021 03.
Artículo en Inglés | MEDLINE | ID: mdl-33531709

RESUMEN

The first severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in South Africa was identified on 5 March 2020, and by 26 March the country was in full lockdown (Oxford stringency index of 90)1. Despite the early response, by November 2020, over 785,000 people in South Africa were infected, which accounted for approximately 50% of all known African infections2. In this study, we analyzed 1,365 near whole genomes and report the identification of 16 new lineages of SARS-CoV-2 isolated between 6 March and 26 August 2020. Most of these lineages have unique mutations that have not been identified elsewhere. We also show that three lineages (B.1.1.54, B.1.1.56 and C.1) spread widely in South Africa during the first wave, comprising ~42% of all infections in the country at the time. The newly identified C lineage of SARS-CoV-2, C.1, which has 16 nucleotide mutations as compared with the original Wuhan sequence, including one amino acid change on the spike protein, D614G (ref. 3), was the most geographically widespread lineage in South Africa by the end of August 2020. An early South African-specific lineage, B.1.106, which was identified in April 2020 (ref. 4), became extinct after nosocomial outbreaks were controlled in KwaZulu-Natal Province. Our findings show that genomic surveillance can be implemented on a large scale in Africa to identify new lineages and inform measures to control the spread of SARS-CoV-2. Such genomic surveillance presented in this study has been shown to be crucial in the identification of the 501Y.V2 variant in South Africa in December 2020 (ref. 5).


Asunto(s)
/epidemiología , /genética , Conjuntos de Datos como Asunto , Genoma Viral , Humanos , Tipificación Molecular , Mutación , Pandemias , Filogenia , Filogeografía , Reacción en Cadena en Tiempo Real de la Polimerasa , /aislamiento & purificación , Análisis de Secuencia de ARN , Sudáfrica/epidemiología , Secuenciación Completa del Genoma
14.
Indian J Med Microbiol ; 39(1): 73-80, 2021 Jan.
Artículo en Inglés | MEDLINE | ID: mdl-33460733

RESUMEN

BACKGROUND: In the initial few months of the COVID-19 pandemic, two distinct strains of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) were identified (L and S strain) based on a tightly linked SNP between two widely separated nucleotides at location 8782 (ORF1ab T8517C) and position 28,144 (ORF8: C251T, codon S84L). MATERIALS AND METHODS: A Type Specific Primer based one step RT-PCR (TSP-PCR) test to distinguish the L and S type strains of SARS-CoV-2 without the need for viral genome sequencing, was developed. The study also analyzed 18,221 whole genome sequences (WGS) available up to April 2020 to know the prevalence of L and S type of strains. Phylogenetic and recombination analysis of SARS-CoV-2 genome with nearest animal and human coronaviruses were analyzed using MEGA X and SimPlot version 3.5.1 software respectively. RESULTS: The rapid TSP-PCR distinguished the L and S type strains of SARS-CoV-2 by amplifying a specific 326 bp and 256 bp fragment of the L and S type strain respectively. The test was used to analyzed 120 random SARS-CoV-2 positive samples from Assam, India among which 118 were found to be of L-type strains only. On analysis of 18,221 WGS, it was found that L type was the predominant strain with an overall prevalence ∼90%. However, pockets of high prevalence of S-type strains (>35%) were still in circulation in Washington region in April 2020. The study did not detect any significant recombination events between closely related coronavirus and SARS-CoV-2. CONCLUSION: TSP-based PCR for identification of circulating strains of SARS-CoV-2, will add in rapid identification of strains of COVID-19 pandemic to understand the spread of the virus, its transmissibility and adaptation into human population. Though, the S-type strains have decreased drastically across the globe since April 2020, the role of TSP-PCR in geographical niches where such strains are still prevalent may help in rapidly distinguishing the strains and study its evolution.


Asunto(s)
/diagnóstico , Cartilla de ADN , Tipificación Molecular/métodos , Reacción en Cadena de la Polimerasa , /genética , /epidemiología , Genoma Viral , Humanos , Sistemas de Lectura Abierta , Filogenia , Reacción en Cadena de la Polimerasa/métodos , Vigilancia en Salud Pública , ARN Viral , Análisis de Secuencia de ADN
15.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33507141

RESUMEN

Cryptosporidium species are responsible for causing the majority of parasite-related gastrointestinal infections in the UK. This report describes an outbreak of 12 laboratory-confirmed cryptosporidiosis cases identified as part of a Scottish swimming pool investigation, with 9 primary and 3 secondary cases occurring over an 8-week period. Molecular speciation was successful for 11/12 cases, which revealed 10 Cryptosporidium hominis cases and 1 Cryptosporidium parvum case. Of the 10 C. hominis cases, further typing identified 7 as being an unusual sub-type, IbA6G3, which is the first description in the UK of this rare variant. The remaining three C. hominis cases were identified as the common IbA10G2 subtype. Following implementation of control measures on two occasions, no further cases were reported. This report highlights the importance of molecular typing to identify and characterize outbreaks, and emphasizes the need to adhere to swimming pool guidance. It also raises awareness of the potential for outbreaks to involve multiple species/sub-types, and emphasizes the importance of strong public health leadership to ensure effective multi-agency investigations and management of outbreaks.


Asunto(s)
Criptosporidiosis , Cryptosporidium/aislamiento & purificación , Brotes de Enfermedades , Piscinas , Criptosporidiosis/epidemiología , Criptosporidiosis/parasitología , Cryptosporidium/clasificación , Humanos , Tipificación Molecular , Escocia
16.
Medicine (Baltimore) ; 100(2): e24090, 2021 Jan 15.
Artículo en Inglés | MEDLINE | ID: mdl-33466172

RESUMEN

OBJECTIVE: To understood the pathogen detection status and clinical characteristics of suspected pertussis in children and to observe the drug sensitivity and drug resistance genes of Bordetella pertussis (B. pertussis). METHODS: Three hundred fifty-one cases were collected and their nasopharyngeal swab samples were analyzed by culture and fluorescent quantitative polymerase chain reaction. The susceptibility to erythromycin, clindamycin, ampicillin, levofloxacin, and sulfamethoxazole-trimethoprim were tested by E-test for the positive strains, and the susceptibility to erythromycin was also tested for the KB disk diffusion method. The 23S rRNA gene of the positive strains was amplified and sequenced, and statistical analysis was performed in conjunction with clinical data. RESULTS: The positive rate of bacterial culture was 16.8% (59/351), and the positive rate of PCR was 62.4% (219/351). Two cases were positive about bacterial culture and negative for PCR. There were 221 confirmed cases of pertussis. The E-test results showed that the rate of the sensitivity of the 55 strains of pertussis to erythromycin and clindamycin was 50.9% (28/55), the minimum antibiotic concentration50 (MIC50) and MIC90 values were 0.094/>256 and 0.75/>256 mg/L, respectively, and the MIC50/MIC90 to ampicillin, levofloxacin, and sulfamethoxazole were 0.125/0.19, 0.38/0.5, and 0.125/0.25 mg/L, respectively. The KB disk diffusion method showed 27 of the 55 strains 49.1% (27/55) was resistant to erythromycin; all of the resistant strains had the 23S rRNA gene A2047G mutation, and their MIC of erythromycin was >256 mg/L. CONCLUSION: The diagnosis of pertussis by a fluorescent quantitative polymerase chain reaction method is more sensitive than that of bacterial culture. The resistance of B. pertussis to erythromycin was prominent. All of the strains of B. pertussis resistant to erythromycin in our center had the A2047G mutation of the 23S rRNA gene.


Asunto(s)
Bordetella pertussis/efectos de los fármacos , Bordetella pertussis/genética , Farmacorresistencia Bacteriana/genética , Pruebas de Sensibilidad Microbiana/métodos , Tos Ferina/microbiología , Antibacterianos/farmacología , Niño , Preescolar , China , Técnicas de Cultivo , Eritromicina/farmacología , Femenino , Humanos , Lactante , Masculino , Tipificación Molecular , Mutación , Reacción en Cadena de la Polimerasa , ARN Ribosómico 23S/genética , Tos Ferina/diagnóstico
17.
Acta Trop ; 216: 105820, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33400915

RESUMEN

Malaria vector control in Mali relies heavily on the use of long-lasting insecticidal nets (LLINs) and indoor residual spraying (IRS) in selected districts. As part of strengthening vector control strategies in Koulikoro district, the National Malaria Control Programme (NMCP) through the support from the US President's Malaria Initiative (PMI) has strategically driven the implementation of IRS, with the LLINs coverage also rising from 93.3% and 98.2%. Due to the increased reports of vector resistance to both pyrethroid and carbamates, there was a campaign for the use of pirimiphos-methyl, an organophosphate at Koulikoro between 2015 and 2016. In this study, the effect of IRS on malaria transmission was assessed, by comparing some key entomological indices between Koulikoro, where IRS was implemented and its neighboring district, Banamba that has never received IRS as vector control intervention. The study was conducted in two villages of each district (Koulikoro and Banamba). Pyrethrum spray catches and entry window trapping were used to collect mosquitoes on a monthly basis. WHO tube tests were carried out to assess mosquito susceptibility to insecticides. Mosquitoes were identified to species level by PCR and their infection to P. falciparum was detected by Enzyme Linked-Immuno-Sorbent Assay (ELISA). Of the 527 specimens identified, An. coluzzii was the most frequent species (95%) followed by An. gambiae (4%) and An. arabiensis (1%). Its density was rainfall dependent in the no-IRS area, and almost independent in the IRS area. The infection rate (IR) in the no-IRS area was 0.96%, while it was null in the IRS area. In the no-IRS area, the entomological inoculation rate (EIR) was 0.21 infective bites /person month with a peak in September. High resistance to pyrethroids and carbamates and susceptibility to organophosphates was observed at all sites. The introduction of pirimiphos-methyl based IRS for vector control resulted in a significant decrease in malaria transmission. An. gambiae s.l., the main malaria vector in the area, was resistant to pyrethroids and carbamates but remained susceptible to the organophosphate pirimiphos-methyl.


Asunto(s)
Anopheles/efectos de los fármacos , Anopheles/parasitología , Carbamatos/farmacología , Malaria/prevención & control , Malaria/transmisión , Compuestos Organotiofosforados/farmacología , Piretrinas/farmacología , Animales , Anopheles/genética , Vectores de Enfermedades , Femenino , Humanos , Mordeduras y Picaduras de Insectos/parasitología , Resistencia a los Insecticidas , Insecticidas/farmacología , Malí , Tipificación Molecular , Control de Mosquitos/métodos , Mosquitos Vectores/efectos de los fármacos , Mosquitos Vectores/genética , Reacción en Cadena de la Polimerasa
18.
Trop Anim Health Prod ; 53(1): 127, 2021 Jan 16.
Artículo en Inglés | MEDLINE | ID: mdl-33454847

RESUMEN

The frequency of Listeria monocytogenes isolates collected from a total of 1150 samples including food (n = 300), livestock (n = 50), and human clinical (n = 800) was evaluated during 2008-2016. Antimicrobial resistance patterns, virulence factors, and molecular characteristics of these isolates were analyzed using disk diffusion method, sequencing, serotyping, and pulsed-field gel electrophoresis (PFGE). The analysis of 44 L. monocytogenes isolates showed that 72.7% (32 of 44) of all the isolates belonged to Serotype 1/2c, and 15.9% (7 of 44) belonged to Serotype 3c. All 44 isolates were resistant to one or more antimicrobial agents with the most frequent resistance to penicillin (75%) and tetracycline (47.7%). Of the 44 L. monocytogenes strains, 100, 69.2, and 62.5% of livestock, human, and food strains were resistant to penicillin, respectively. Using pulsed-field gel electrophoresis (PFGE) technique, the isolates' genetic diversity was determined, and 28 PFGE patterns with 8 common (CT) and 20 single types (ST) were identified. This study highlights the high prevalence of Serotype 1/2c in clinical and livestock samples, while different serotypes were observed in food samples. The presence of rare serotypes such as 4c, belonging to the Lineage III, as well as 4e and 1/2c which are infrequent in Iran indicates that paying attention to uncommon serotypes, especially 1/2c, during the listeriosis outbreaks is necessary.


Asunto(s)
Microbiología de Alimentos , Listeria monocytogenes , Listeriosis , Virulencia , Animales , Técnicas de Tipificación Bacteriana , Farmacorresistencia Bacteriana/genética , Electroforesis en Gel de Campo Pulsado , Humanos , Irán/epidemiología , Listeria monocytogenes/clasificación , Listeria monocytogenes/genética , Listeria monocytogenes/patogenicidad , Listeriosis/epidemiología , Listeriosis/veterinaria , Ganado/microbiología , Tipificación Molecular , Serotipificación
19.
Methods Mol Biol ; 2182: 187-196, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-32894497

RESUMEN

Salmonella is recognized as a major human foodborne pathogen and threat to public health world widely. It is important to carry out epidemiological investigations to determine the primary sources of bacterial contamination. Pulsed-field gel electrophoresis (PFGE) is an important method of the molecular typing, and play an important role in tracking the sources of infection and epidemic control. The PFGE is currently considered as "gold standard" of molecular typing methods for bacterial foodborne pathogen. Here, we describe the PFGE protocol to type the Salmonella from pork.


Asunto(s)
Técnicas de Tipificación Bacteriana/métodos , Electroforesis en Gel de Campo Pulsado/métodos , Tipificación Molecular/métodos , Salmonella/genética , ADN Bacteriano/genética , Carne de Cerdo/microbiología
20.
PLoS Pathog ; 16(12): e1009177, 2020 12.
Artículo en Inglés | MEDLINE | ID: mdl-33370400

RESUMEN

HIV-1 strains harboring immune escape mutations can persist in circulation, but the impact of selection by multiple HLA alleles on population HIV-1 dynamics remains unclear. In Japan, HIV-1 Reverse Transcriptase codon 135 (RT135) is under strong immune pressure by HLA-B*51:01-restricted and HLA-B*52:01-restricted T cells that target a key epitope in this region (TI8; spanning RT codons 128-135). Major population-level shifts have occurred at HIV-1 RT135 during the Japanese epidemic, which first affected hemophiliacs (via imported contaminated blood products) and subsequently non-hemophiliacs (via domestic transmission). Specifically, threonine accumulated at RT135 (RT135T) in hemophiliac and non-hemophiliac HLA-B*51:01+ individuals diagnosed before 1997, but since then RT135T has markedly declined while RT135L has increased among non-hemophiliac individuals. We demonstrated that RT135V selection by HLA-B*52:01-restricted TI8-specific T-cells led to the creation of a new HLA-C*12:02-restricted epitope TN9-8V. We further showed that TN9-8V-specific HLA-C*12:02-restricted T cells selected RT135L while TN9-8T-specific HLA-C*12:02-restricted T cells suppressed replication of the RT135T variant. Thus, population-level accumulation of the RT135L mutation over time in Japan can be explained by initial targeting of the TI8 epitope by HLA-B*52:01-restricted T-cells, followed by targeting of the resulting escape mutant by HLA-C*12:02-restricted T-cells. We further demonstrate that this phenomenon is particular to Japan, where the HLA-B*52:01-C*12:02 haplotype is common: RT135L did not accumulate over a 15-year longitudinal analysis of HIV sequences in British Columbia, Canada, where this haplotype is rare. Together, our observations reveal that T-cell responses to sequentially emerging viral escape mutants can shape long-term HIV-1 population dynamics in a host population-specific manner.


Asunto(s)
Variación Antigénica/inmunología , Infecciones por VIH , VIH-1 , Evasión Inmune/genética , Linfocitos T Citotóxicos/inmunología , Células Cultivadas , Evolución Clonal/inmunología , Epítopos de Linfocito T/genética , Infecciones por VIH/inmunología , Infecciones por VIH/virología , Seropositividad para VIH , VIH-1/clasificación , VIH-1/genética , VIH-1/inmunología , Células HeLa , Interacciones Huésped-Patógeno/genética , Interacciones Huésped-Patógeno/inmunología , Humanos , Tipificación Molecular , Mutación , Linfocitos T Citotóxicos/metabolismo , Carga Viral/inmunología , Replicación Viral/genética , Replicación Viral/inmunología
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