Your browser doesn't support javascript.
loading
Mostrar: 20 | 50 | 100
Resultados 1 - 20 de 872
Filtrar
1.
Microb Pathog ; 195: 106816, 2024 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-39032675

RESUMO

Salmonella is a zoonotic pathogen posing a serious risk to the farming industry and public health due to food animals serving as reservoirs for future contamination and spread of Salmonella. The present study is designed to monitor the contamination status of Salmonella in duck farms and the main control points during breeding. 160 strains of duck-derived Salmonella were isolated from the 736 samples (cloacal swabs, feces, water, feed, soil, air and dead duck embryos) collected in southwest Shandong Province and the province's surrounding area. The percentage of Salmonella-positive samples collected was 21.74 % (160/736), and the greatest prevalence from duck embryo samples (40.00 %, 36/90). These Salmonella were classified into 23 serotypes depending on their O and H antigens, in which S. Typhimurium (30.15 %), S. Kottbus (13.97 %) and S. Enteritidis (10.29 %) were the prevailing serotypes. Subsequently, the molecular subtyping was done. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis showed that 41 strains of S. Typhimurium and 14 strains of S. Enteritidis were classified into 13 and 3 genotypes, respectively. 19 S. Kottbus isolates from different sources featured ST1546, ST198, ST321, and ST1690 by multilocus sequence typing (MLST) analysis, among which ST1546 belongs to S. Kottbus was a new ST. The minimum spanning tree analysis based on the two CRISPR loci and seven MLST loci from all S. Typhimurium, S. Enteritidis and S. Kottbus isolates revealed that duck embryos, feed and water were key control points to the spread of Salmonella along the breeding chain. Meanwhile, the emergence of S. Kottbus in duck flocks was considered a potential public health hazard.


Assuntos
Patos , Fazendas , Fezes , Genótipo , Doenças das Aves Domésticas , Salmonelose Animal , Salmonella , Sorogrupo , Animais , Patos/microbiologia , China/epidemiologia , Salmonelose Animal/microbiologia , Salmonelose Animal/epidemiologia , Salmonella/genética , Salmonella/isolamento & purificação , Salmonella/classificação , Doenças das Aves Domésticas/microbiologia , Doenças das Aves Domésticas/epidemiologia , Fezes/microbiologia , Salmonella typhimurium/genética , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/classificação , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas/genética , Prevalência , Filogenia , Salmonella enteritidis/genética , Salmonella enteritidis/isolamento & purificação , Salmonella enteritidis/classificação , Tipagem de Sequências Multilocus , Sorotipagem
2.
Microbiology (Reading) ; 170(4)2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38753417

RESUMO

Salmonella enterica subsp. enterica Typhimurium and its monophasic variant I 1;4,[5],12:i:- (MVST) are responsible for thousands of reported cases of salmonellosis each year in Canada, and countries worldwide. We investigated S. Typhimurium and MVST isolates recovered from raw shellfish harvested in Atlantic Canada by the Canadian Food Inspection Agency (CFIA) over the past decade, to assess the potential impact of these isolates on human illness and to explore possible routes of shellfish contamination. Whole-genome sequence analysis was performed on 210 isolates of S. Typhimurium and MVST recovered from various food sources, including shellfish. The objective was to identify genetic markers linked to ST-99, a sequence type specifically associated with shellfish, which could explain their high prevalence in shellfish. We also investigated the genetic similarity amongst CFIA ST-99 isolates recovered in different years and geographical locations. Finally, the study aimed to enhance the molecular serotyping of ST-99 isolates, as they are serologically classified as MVST but are frequently misidentified as S. Typhimurium through sequence analysis. To ensure recovery of ST-99 from shellfish was not due to favourable growth kinetics, we measured the growth rates of these isolates relative to other Salmonella and determined that ST-99 did not have a faster growth rate and/or shorter lag phase than other Salmonella evaluated. The CFIA ST-99 isolates from shellfish were highly clonal, with up to 81 high-quality single nucleotide variants amongst isolates. ST-99 isolates both within the CFIA collection and those isolated globally carried numerous unique deletions, insertions and mutations in genes, including some considered important for virulence, such as gene deletions in the type VI secretion system. Interestingly, several of these genetic characteristics appear to be unique to North America. Most notably was a large genomic region showing a high prevalence in genomes from Canadian isolates compared to those from the USA. Although the functions of the majority of the proteins encoded within this region remain unknown, the genes umuC and umuD, known to be protective against UV light damage, were present. While this study did not specifically examine the effects of mutations and insertions, results indicate that these isolates may be adapted to survive in specific environments, such as ocean water, where wild birds and/or animals serve as the natural hosts. Our hypothesis is reinforced by a global phylogenetic analysis, which indicates that isolates obtained from North American shellfish and wild birds are infrequently connected to isolates from human sources. These findings suggest a distinct ecological niche for ST-99, potentially indicating their specialization and adaptation to non-human hosts and environments, such as oceanic habitats.


Assuntos
Tipagem de Sequências Multilocus , Salmonella typhimurium , Frutos do Mar , Frutos do Mar/microbiologia , Salmonella typhimurium/genética , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/classificação , Canadá , Sequenciamento Completo do Genoma , Animais , Humanos , Genoma Bacteriano , Microbiologia de Alimentos , Filogenia
3.
Microbiol Spectr ; 12(5): e0004724, 2024 May 02.
Artigo em Inglês | MEDLINE | ID: mdl-38546218

RESUMO

Surface waters are considered ecological habitats where Salmonella enterica can persist and disseminate to fresh produce production systems. This study aimed to explore the genomic profiles of S. enterica serotypes Typhimurium, Newport, and Infantis from surface waters in Chile, Mexico, and Brazil collected between 2019 and 2022. We analyzed the whole genomes of 106 S. Typhimurium, 161 S. Newport, and 113 S. Infantis isolates. Our phylogenetic analysis exhibited distinct groupings of isolates by their respective countries except for a notable case involving a Chilean S. Newport isolate closely related to two Mexican isolates, showing 4 and 13 single nucleotide polymorphisms of difference, respectively. The patterns of the most frequently detected antimicrobial resistance genes varied across countries and serotypes. A strong correlation existed between integron carriage and genotypic multidrug resistance (MDR) across serotypes in Chile and Mexico (R > 0.90, P < 0.01), while integron(s) were not detected in any of the Brazilian isolates. By contrast, we did not identify any strong correlation between plasmid carriage and genotypic MDR across diverse countries and serotypes.IMPORTANCEUnveiling the genomic landscape of S. enterica in Latin American surface waters is pivotal for ensuring public health. This investigation sheds light on the intricate genomic diversity of S. enterica in surface waters across Chile, Mexico, and Brazil. Our research also addresses critical knowledge gaps, pioneering a comprehensive understanding of surface waters as a reservoir for multidrug-resistant S. enterica. By integrating our understanding of integron carriage as biomarkers into broader MDR control strategies, we can also work toward targeted interventions that mitigate the emergence and dissemination of MDR in S. enterica in surface waters. Given its potential implications for food safety, this study emphasizes the critical need for informed policies and collaborative initiatives to address the risks associated with S. enterica in surface waters.


Assuntos
Farmacorresistência Bacteriana Múltipla , Filogenia , Salmonella enterica , Salmonella typhimurium , Sorogrupo , Salmonella enterica/genética , Salmonella enterica/isolamento & purificação , Salmonella enterica/classificação , Salmonella enterica/efeitos dos fármacos , Brasil , Farmacorresistência Bacteriana Múltipla/genética , México , Salmonella typhimurium/genética , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/classificação , Integrons/genética , Genoma Bacteriano , Chile , Genômica , Antibacterianos/farmacologia , América Latina , Microbiologia da Água , Polimorfismo de Nucleotídeo Único , Plasmídeos/genética , Testes de Sensibilidade Microbiana
4.
Infect Genet Evol ; 93: 104977, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34174480

RESUMO

Salmonella Typhimurium has been transmitted between humans and animals. Although, Brazil has been one of the largest pork meat exporters worldwide, there are few studies that characterized epidemiologically S. Typhimurium strains from swine. The aims of this work were to study the phylogenetic relationship of S. Typhimurium genomes isolated from swine in Brazil among themselves and with other genomes isolated from several sources and countries using wgMLST and cgMLST and to perform the search of Salmonella pathogenicity islands (SPIs). In addition, for S. Typhimurium strains from swine to compare the virulence and antimicrobial resistance genes by VFDB and ResFinder, genetic content by BLAST Atlas and orthologous proteins clusters by OrthoVenn. The constructed phylogenetic trees by wgMLST and cgMLST grouped the majority (92.3% and 80.7%, respectively) of the strains isolated from swine in Brazil into the same group. All the isolates contained important SPIs (SPI-1, SPI-2, SPI-3, SPI-5 and SPI-9). A total of 100 and 31 virulence and resistance genes were detected in the S. Typhimurium strains isolated from swine, respectively. The BLAST Atlas and orthologous proteins analysis found regions of phages and differences in metabolic, regulatory and cellular processes among S. Typhimurium LT2 and S. Typhimurium isolates from swine. In conclusion, molecular typing based in the wgMLST and cgMLST suggested that the S. Typhimurium isolates from swine studied were genetically related. The pathogenic potential of the strains studied was corroborated by the presence of important SPIs and virulence genes. The high number of antimicrobial resistance genes detected is worrying and reinforced their potential risk in swine in Brazil. The comparison by BLAST Atlas suggested differences in mobile genetic elements among S. Typhimurium LT2 and S. Typhimurium isolates from swine in Brazil. The orthologous proteins analysis revealed unique genes related to important cellular processes in the strains from swine.


Assuntos
Farmacorresistência Bacteriana/genética , Salmonelose Animal/microbiologia , Salmonella typhimurium/genética , Doenças dos Suínos/microbiologia , Animais , Ilhas Genômicas , Tipagem Molecular , Filogenia , Salmonella typhimurium/classificação , Salmonella typhimurium/patogenicidade , Sus scrofa , Suínos , Virulência/genética
5.
BMC Microbiol ; 21(1): 49, 2021 02 16.
Artigo em Inglês | MEDLINE | ID: mdl-33593291

RESUMO

BACKGROUND: Salmonella enterica serovar Typhimurium is an intestinal pathogen capable of infecting a wide range of animals. It initiates infection by invading intestinal epithelial cells using a type III secretion system encoded within Salmonella pathogenicity island 1 (SPI-1). The SPI-1 genes are regulated by multiple interacting transcription factors. The master regulator is HilD. HilE represses SPI-1 gene expression by binding HilD and preventing it from activating its target promoters. Previous work found that acetate and nutrients synergistically induce SPI-1 gene expression. In the present study, we investigated the role of HilE, nominally a repressor of SPI-1 gene expression, in mediating this response to acetate and nutrients. RESULTS: HilE is necessary for activation of SPI-1 gene expression by acetate and nutrients. In mutants lacking hilE, acetate and nutrients no longer increase SPI-1 gene expression but rather repress it. This puzzling response is not due to the BarA/SirA two component system, which governs the response to acetate. To identify the mechanism, we profiled gene expression using RNAseq in the wild type and a ΔhilE mutant under different growth conditions. Analysis of these data suggested that the Rcs system, which regulates gene expression in response to envelope stress, is involved. Consistent with this hypothesis, acetate and nutrients were able to induce SPI-1 gene expression in mutants lacking hilE and the Rcs system. CONCLUSIONS: While the exact mechanism is unknown, these results demonstrate the HilE, nominally a repressor of SPI-1 gene expression, can also function as an activator under the growth conditions investigated. Collectively, these results provide new insights regarding SPI-1 gene regulation and demonstrate that HilE is more complex than initially envisioned.


Assuntos
Proteínas de Bactérias/genética , Expressão Gênica , Proteínas Repressoras/genética , Salmonella typhimurium/genética , Fatores de Transcrição/genética , Proteínas de Bactérias/metabolismo , Regulação Bacteriana da Expressão Gênica , Proteínas Repressoras/metabolismo , Salmonella typhimurium/classificação , Sorogrupo , Fatores de Transcrição/metabolismo
6.
mBio ; 12(1)2021 01 12.
Artigo em Inglês | MEDLINE | ID: mdl-33436434

RESUMO

Enterobacterial pathogens infect the gut by a multistep process, resulting in colonization of both the lumen and the mucosal epithelium. Due to experimental constraints, it remains challenging to address how luminal and epithelium-lodged pathogen populations cross-feed each other in vivo Enteroids are cultured three-dimensional miniature intestinal organs with a single layer of primary intestinal epithelial cells (IECs) surrounding a central lumen. They offer new opportunities to study enterobacterial infection under near-physiological conditions, at a temporal and spatial resolution not attainable in animal models, but remain poorly explored in this context. We employed microinjection, time-lapse microscopy, bacterial genetics, and barcoded consortium infections to describe the complete infection cycle of Salmonella enterica serovar Typhimurium in both human and murine enteroids. Flagellar motility and type III secretion system 1 (TTSS-1) promoted Salmonella Typhimurium targeting of the intraepithelial compartment and breaching of the epithelial barrier. Strikingly, however, TTSS-1 also potently boosted colonization of the enteroid lumen. By tracing the infection over time, we identified a cycle(s) of TTSS-1-driven IEC invasion, intraepithelial replication, and reemergence through infected IEC expulsion as a key mechanism for Salmonella Typhimurium luminal colonization. These findings suggest a positive feed-forward loop, through which IEC invasion by planktonic bacteria fuels further luminal population expansion, thereby ensuring efficient colonization of both the intraepithelial and luminal niches.IMPORTANCE Pathogenic gut bacteria are common causes of intestinal disease. Enteroids-cultured three-dimensional replicas of the mammalian gut-offer an emerging model system to study disease mechanisms under conditions that recapitulate key features of the intestinal tract. In this study, we describe the full life cycle of the prototype gut pathogen Salmonella enterica serovar Typhimurium within human and mouse enteroids. We map the consecutive steps and define the bacterial virulence factors that drive colonization of luminal and epithelial compartments, as well as breaching of the epithelial barrier. Strikingly, our work reveals how bacterial colonization of the epithelium potently fuels expansion also in the luminal compartment, through a mechanism involving the death and expulsion of bacterium-infected epithelial cells. These findings have repercussions for our understanding of the Salmonella infection cycle. Moreover, our work provides a comprehensive foundation for the use of microinjected enteroids to model gut bacterial diseases.


Assuntos
Células Epiteliais/microbiologia , Infecções por Salmonella/microbiologia , Salmonella enterica/classificação , Salmonella typhimurium/classificação , Sorogrupo , Animais , Modelos Animais de Doenças , Epitélio , Humanos , Mucosa Intestinal/microbiologia , Camundongos , Salmonelose Animal/microbiologia , Salmonella enterica/genética , Salmonella enterica/crescimento & desenvolvimento , Salmonella typhimurium/genética , Salmonella typhimurium/crescimento & desenvolvimento , Sistemas de Secreção Tipo III , Fatores de Virulência
7.
Microb Genom ; 7(6)2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-31682222

RESUMO

Salmonella enterica serovar Typhimurium is the leading cause of salmonellosis in Australia, and the ability to identify outbreaks and their sources is vital to public health. Here, we examined the utility of whole-genome sequencing (WGS), including complete genome sequencing with Oxford Nanopore technologies, in examining 105 isolates from an endemic multi-locus variable number tandem repeat analysis (MLVA) type over 5 years. The MLVA type was very homogeneous, with 90 % of the isolates falling into groups with a five SNP cut-off. We developed a new two-step approach for outbreak detection using WGS. The first clustering at a zero single nucleotide polymorphism (SNP) cut-off was used to detect outbreak clusters that each occurred within a 4 week window and then a second clustering with dynamically increased SNP cut-offs were used to generate outbreak investigation clusters capable of identifying all outbreak cases. This approach offered optimal specificity and sensitivity for outbreak detection and investigation, in particular of those caused by endemic MLVA types or clones with low genetic diversity. We further showed that inclusion of complete genome sequences detected no additional mutational events for genomic outbreak surveillance. Phylogenetic analysis found that the MLVA type was likely to have been derived recently from a single source that persisted over 5 years, and seeded numerous sporadic infections and outbreaks. Our findings suggest that SNP cut-offs for outbreak cluster detection and public-health surveillance should be based on the local diversity of the relevant strains over time. These findings have general applicability to outbreak detection of bacterial pathogens.


Assuntos
Surtos de Doenças , Doenças Endêmicas , Genômica , Epidemiologia Molecular , Infecções por Salmonella/epidemiologia , Infecções por Salmonella/microbiologia , Salmonella typhimurium/classificação , Salmonella typhimurium/genética , Austrália/epidemiologia , DNA Bacteriano/genética , Humanos , Repetições Minissatélites , Tipagem Molecular , Filogenia , Polimorfismo de Nucleotídeo Único , Saúde Pública , Intoxicação Alimentar por Salmonella/epidemiologia , Sorogrupo , Sequenciamento Completo do Genoma
8.
PLoS Negl Trop Dis ; 14(11): e0008796, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-33232324

RESUMO

Salmonella is a major cause of foodborne disease globally. Pigs can carry and shed non-typhoidal Salmonella (NTS) asymptomatically, representing a significant reservoir for these pathogens. To investigate Salmonella carriage by African domestic pigs, faecal and mesenteric lymph node samples were taken at slaughter in Nairobi, Busia (Kenya) and Chikwawa (Malawi) between October 2016 and May 2017. Selective culture, antisera testing and whole genome sequencing were performed on samples from 647 pigs; the prevalence of NTS carriage was 12.7% in Busia, 9.1% in Nairobi and 24.6% in Chikwawa. Two isolates of S. Typhimurium ST313 were isolated, but were more closely related to ST313 isolates associated with gastroenteritis in the UK than bloodstream infection in Africa. The discovery of porcine NTS carriage in Kenya and Malawi reveals potential for zoonotic transmission of diarrhoeal strains to humans in these countries, but not for transmission of clades specifically associated with invasive NTS disease in Africa.


Assuntos
Doenças Transmitidas por Alimentos/epidemiologia , Gastroenterite/epidemiologia , Carne de Porco/microbiologia , Salmonelose Animal/epidemiologia , Salmonella typhimurium/classificação , Salmonella typhimurium/isolamento & purificação , Animais , Zoonoses Bacterianas/epidemiologia , Zoonoses Bacterianas/microbiologia , Zoonoses Bacterianas/transmissão , Farmacorresistência Bacteriana Múltipla/genética , Doenças Transmitidas por Alimentos/microbiologia , Gastroenterite/microbiologia , Gastroenterite/veterinária , Humanos , Quênia/epidemiologia , Linfonodos/microbiologia , Malaui/epidemiologia , Testes de Sensibilidade Microbiana , Tipagem Molecular , Salmonelose Animal/transmissão , Salmonella typhimurium/genética , Suínos/parasitologia , Sequenciamento Completo do Genoma
9.
PLoS Comput Biol ; 16(10): e1008401, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-33125373

RESUMO

Modelling the emergence of foodborne pathogens is a crucial step in the prediction and prevention of disease outbreaks. Unfortunately, the mechanisms that drive the evolution of such continuously adapting pathogens remain poorly understood. Here, we combine molecular genotyping with network science and Bayesian inference to infer directed genotype networks-and trace the emergence and evolutionary paths-of Salmonella Typhimurium (STM) from nine years of Australian disease surveillance data. We construct networks where nodes represent STM strains and directed edges represent evolutionary steps, presenting evidence that the structural (i.e., network-based) features are relevant to understanding the functional (i.e., fitness-based) progression of co-evolving STM strains. This is argued by showing that outbreak severity, i.e., prevalence, correlates to: (i) the network path length to the most prevalent node (r = -0.613, N = 690); and (ii) the network connected-component size (r = 0.739). Moreover, we uncover distinct exploration-exploitation pathways in the genetic space of STM, including a strong evolutionary drive through a transition region. This is examined via the 6,897 distinct evolutionary paths in the directed network, where we observe a dominant 66% of these paths decrease in network centrality, whilst increasing in prevalence. Furthermore, 72.4% of all paths originate in the transition region, with 64% of those following the dominant direction. Further, we find that the length of an evolutionary path strongly correlates to its increase in prevalence (r = 0.497). Combined, these findings indicate that longer evolutionary paths result in genetically rare and virulent strains, which mostly evolve from a single transition point. Our results not only validate our widely-applicable approach for inferring directed genotype networks from data, but also provide a unique insight into the elusive functional and structural drivers of STM bacteria.


Assuntos
Genoma Bacteriano/genética , Intoxicação Alimentar por Salmonella/microbiologia , Salmonella typhimurium , Austrália , Teorema de Bayes , Evolução Molecular , Genômica , Genótipo , Humanos , Modelos Genéticos , Salmonella typhimurium/classificação , Salmonella typhimurium/genética , Salmonella typhimurium/patogenicidade
10.
PLoS One ; 15(10): e0240978, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-33125394

RESUMO

International lineages, such as Salmonella Typhimurium sequence type (ST) 19, are most often associated with foodborne diseases and deaths in humans. In this study, we compared the whole-genome sequences of five S. Typhimurium strains belonging to ST19 recovered from clinical human stool samples in North Carolina, United States. Overall, S. Typhimurium strains displayed multidrug-resistant profile, being resistance to critically and highly important antimicrobials including ampicillin, ticarcillin/clavulanic acid, streptomycin and sulfisoxazole, chloramphenicol, tetracycline, respectively. Interestingly, all S. Typhimurium strains carried class 1 integron (intl1) and we were able to describe two genomic regions surrounding blaCARB-2 gene, size 4,062 bp and 4,422 bp for S. Typhimurium strains (HS5344, HS5437, and HS5478) and (HS5302 and HS5368), respectively. Genomic analysis for antimicrobial resistome confirmed the presence of clinically important genes, including blaCARB-2, aac(6')-Iaa, aadA2b, sul1, tetG, floR, and biocide resistance genes (qacEΔ1). S. Typhimurium strains harbored IncFIB plasmid containing spvRABCD operon, as well as rck and pef virulence genes, which constitute an important apparatus for spreading the virulence plasmid. In addition, we identified several virulence genes, chromosomally located, while the phylogenetic analysis revealed clonal relatedness among these strains with S. enterica isolated from human and non-human sources obtained in European and Asian countries. Our results provide new insights into this unusual class 1 integron in virulent S. Typhimurium strains that harbors a pool of genes acting as potential hotspots for horizontal gene transfer providing readily adaptation to new surrounds, as well as being crucially required for virulence in vivo. Therefore, continuous genomic surveillance is an important tool for safeguarding human health.


Assuntos
Farmacorresistência Bacteriana Múltipla , Infecções por Salmonella/microbiologia , Salmonella typhimurium/classificação , Fatores de Virulência/genética , beta-Lactamases/genética , Antibacterianos/farmacologia , Genoma Bacteriano , Humanos , Integrons , Testes de Sensibilidade Microbiana , Filogenia , Plasmídeos/genética , Salmonella typhimurium/genética , Salmonella typhimurium/isolamento & purificação , Salmonella typhimurium/patogenicidade , Estados Unidos , Sequenciamento Completo do Genoma
11.
Sci Rep ; 10(1): 14428, 2020 09 02.
Artigo em Inglês | MEDLINE | ID: mdl-32879348

RESUMO

Salmonella enterica serotype Typhimurium (S. Typhimurium) boasts a broad host range and can be transmitted between livestock and humans. While members of this serotype can acquire resistance to antimicrobials, the temporal dynamics of this acquisition is not well understood. Using New York State (NYS) and its dairy cattle farms as a model system, 87 S. Typhimurium strains isolated from 1999 to 2016 from either human clinical or bovine-associated sources in NYS were characterized using whole-genome sequencing. More than 91% of isolates were classified into one of four major lineages, two of which were largely susceptible to antimicrobials but showed sporadic antimicrobial resistance (AMR) gene acquisition, and two that were largely multidrug-resistant (MDR). All four lineages clustered by presence and absence of elements in the pan-genome. The two MDR lineages, one of which resembled S. Typhimurium DT104, were predicted to have emerged circa 1960 and 1972. The two largely susceptible lineages emerged earlier, but showcased sporadic AMR determinant acquisition largely after 1960, including acquisition of cephalosporin resistance-conferring genes after 1985. These results confine the majority of AMR acquisition events in NYS S. Typhimurium to the twentieth century, largely within the era of antibiotic usage.


Assuntos
Farmacorresistência Bacteriana Múltipla , Evolução Molecular , Salmonella typhimurium/genética , Animais , Antibacterianos/farmacologia , Bovinos/microbiologia , Cefalosporinas/farmacologia , Humanos , New York , Filogenia , Salmonella typhimurium/classificação , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/patogenicidade , Sorogrupo
12.
Microbiol Immunol ; 64(10): 679-693, 2020 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-32803887

RESUMO

Salmonella enterica serovar Typhimurium (S. Typhimurium [STM]) is a leading cause of nontyphoidal salmonellosis (NTS) worldwide. The pathogenesis of NTS has been studied extensively using a streptomycin-pretreated mouse colitis model with the limited numbers of laboratory STM strains. However, the pathogenicity of the clinically isolated STM (STMC) strains endemic in Thailand in mice has not been explored. The aim of this study was to compare the pathogenicity of STMC strains collected from Northern Thailand with the laboratory STM (IR715) in mice. Five STMC isolates were obtained from the stool cultures of patients with acute NTS admitted to Maharaj Nakorn Chiang Mai Hospital in 2016 and 2017. Detection of virulence genes and sequence type (ST) of the strains was performed. Female C57BL/6 mice were pretreated with streptomycin sulfate 1 day prior to oral infection with STM. On Day 4 postinfection, mice were euthanized, and tissues were collected to analyze the bacterial numbers, tissue inflammation, and cecal histopathological score. We found that all five STMC strains are ST34 and conferred the same or reduced pathogenicity compared with that of IR715 in mice. A strain-specific effect of ST34 on mouse gut colonization was also observed. Thailand STM ST34 exhibited a significant attenuated systemic infection in mice possibly due to the lack of spvABC-containing virulence plasmid.


Assuntos
Colite/patologia , Gastroenterite/patologia , Salmonelose Animal/patologia , Salmonella typhimurium/patogenicidade , Adolescente , Adulto , Idoso , Animais , Antibacterianos/farmacologia , Proteínas de Bactérias/genética , Células CACO-2 , Linhagem Celular , Criança , Pré-Escolar , Modelos Animais de Doenças , Testes de Sensibilidade a Antimicrobianos por Disco-Difusão , Farmacorresistência Bacteriana Múltipla/genética , Feminino , Gastroenterite/microbiologia , Humanos , Lactente , Masculino , Camundongos , Camundongos Endogâmicos C57BL , Pessoa de Meia-Idade , Tipagem de Sequências Multilocus , Plasmídeos/genética , Células RAW 264.7 , Salmonella typhimurium/classificação , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/isolamento & purificação , Tailândia , Virulência/genética , Adulto Jovem
13.
PLoS One ; 15(7): e0235641, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32614888

RESUMO

We sequenced 25 isolates of phenotypically multidrug-resistant Salmonella Indiana (n = 11), Typhimurium (n = 8), and Enteritidis (n = 6) using both MinION long-read [SQK-LSK109 and flow cell (R9.4.1)] and MiSeq short-read (Nextera XT and MiSeq Reagent Kit v2) sequencing technologies to determine the advantages of each approach in terms of the characteristics of genome structure, antimicrobial resistance (AMR), virulence potential, whole-genome phylogeny, and pan-genome. The MinION reads were base-called in real-time using MinKnow 3.4.8 integrated with Guppy 3.0.7. The long-read-only assembly, Illumina-only assembly, and hybrid assembly pipelines of Unicycler 0.4.8 were used to generate the MinION, MiSeq, and hybrid assemblies, respectively. The MinION assemblies were highly contiguous compared to the MiSeq assemblies but lacked accuracy, a deficiency that was mitigated by adding the MiSeq short reads through the Unicycler hybrid assembly which corrected erroneous single nucleotide polymorphisms (SNPs). The MinION assemblies provided similar predictions of AMR and virulence potential compared to the MiSeq and hybrid assemblies, although they produced more total false negatives of AMR genotypes, primarily due to failure in identifying tetracycline resistance genes in 11 of the 19 MinION assemblies of tetracycline-resistant isolates. The MinION assemblies displayed a large genetic distance from their corresponding MiSeq and hybrid assemblies on the whole-genome phylogenetic tree, indicating that the lower read accuracy of MinION sequencing caused incorrect clustering. The pan-genome of the MinION assemblies contained significantly more accessory genes and less core genes compared to the MiSeq and hybrid assemblies, suggesting that although these assemblies were more contiguous, their sequencing errors reduced accurate genome annotations. Our research demonstrates that MinION sequencing by itself provides an efficient assessment of the genome structure, antimicrobial resistance, and virulence potential of Salmonella; however, it is not sufficient for whole-genome phylogenetic and pan-genome analyses. MinION in combination with MiSeq facilitated the most accurate genomic analyses.


Assuntos
Farmacorresistência Bacteriana Múltipla/genética , Genoma Bacteriano , Salmonella enterica/genética , Sequenciamento Completo do Genoma/métodos , Antibacterianos/farmacologia , Genótipo , Testes de Sensibilidade Microbiana , Fenótipo , Filogenia , Plasmídeos/genética , Plasmídeos/metabolismo , Mutação Puntual , Salmonella enterica/classificação , Salmonella enterica/efeitos dos fármacos , Salmonella enterica/patogenicidade , Salmonella enteritidis/classificação , Salmonella enteritidis/efeitos dos fármacos , Salmonella enteritidis/genética , Salmonella enteritidis/patogenicidade , Salmonella typhimurium/classificação , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/genética , Salmonella typhimurium/patogenicidade , Virulência
14.
Infect Genet Evol ; 85: 104436, 2020 11.
Artigo em Inglês | MEDLINE | ID: mdl-32569743

RESUMO

Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants). Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59. SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.


Assuntos
Polimorfismo de Nucleotídeo Único , Infecções por Salmonella/microbiologia , Salmonella typhimurium/classificação , Salmonella typhimurium/genética , Tipagem de Bacteriófagos , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , DNA Bacteriano , Eletroforese em Gel de Campo Pulsado , Hospitais Universitários , Humanos , Repetições Minissatélites , Tipagem de Sequências Multilocus , Filogenia , Infecções por Salmonella/epidemiologia , Salmonella typhimurium/isolamento & purificação , Análise de Sequência de DNA , Tunísia/epidemiologia , Sequenciamento Completo do Genoma
15.
Microb Genom ; 6(7)2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32320376

RESUMO

The partitioning of pathogenic strains isolated in environmental or human cases to their sources is challenging. The pathogens usually colonize multiple animal hosts, including livestock, which contaminate the food-production chain and the environment (e.g. soil and water), posing an additional public-health burden and major challenges in the identification of the source. Genomic data opens up new opportunities for the development of statistical models aiming to indicate the likely source of pathogen contamination. Here, we propose a computationally fast and efficient multinomial logistic regression source-attribution classifier to predict the animal source of bacterial isolates based on 'source-enriched' loci extracted from the accessory-genome profiles of a pangenomic dataset. Depending on the accuracy of the model's self-attribution step, the modeller selects the number of candidate accessory genes that best fit the model for calculating the likelihood of (source) category membership. The Accessory genes-Based Source Attribution (AB_SA) method was applied to a dataset of strains of Salmonella enterica Typhimurium and its monophasic variant (S. enterica 1,4,[5],12:i:-). The model was trained on 69 strains with known animal-source categories (i.e. poultry, ruminant and pig). The AB_SA method helped to identify 8 genes as predictors among the 2802 accessory genes. The self-attribution accuracy was 80 %. The AB_SA model was then able to classify 25 of the 29 S. enterica Typhimurium and S. enterica 1,4,[5],12:i:- isolates collected from the environment (considered to be of unknown source) into a specific category (i.e. animal source), with more than 85 % of probability. The AB_SA method herein described provides a user-friendly and valuable tool for performing source-attribution studies in only a few steps. AB_SA is written in R and freely available at https://github.com/lguillier/AB_SA.


Assuntos
Proteínas de Bactérias/genética , Biologia Computacional/métodos , Gado/classificação , Salmonella typhimurium/classificação , Animais , Bases de Dados Genéticas , Microbiologia de Alimentos , Gado/microbiologia , Modelos Logísticos , Modelos Teóricos , Salmonella typhimurium/genética , Interface Usuário-Computador
17.
Foodborne Pathog Dis ; 17(3): 202-208, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-31556704

RESUMO

The mcr-1 gene has been identified in bacterial isolates obtained from humans, animals, environment, and food, including Salmonella spp., which is one of the major foodborne pathogens worldwide. The aim of this study was to evaluate the presence of mcr-1 gene in Salmonella spp. from food produced in Brazil and to characterize the isolates harboring this gene. A total of 490 Salmonella spp. isolates from the Brazilian National Program for the Control of Foodborne Pathogens were screened for the presence of mcr-1 gene by polymerase chain reaction (PCR). Whole genome sequencing (WGS) was performed in positive isolates to characterize the sequence type (ST), plasmid families and resistance genes. Antimicrobial susceptibility tests were performed by broth microdilution. Selected isolates were submitted to conjugation experiments using the Escherichia coli J53 as a receptor. We detected eight isolates harboring the mcr-1 gene; seven belonged to Salmonella enterica serovar Typhimurium and its monophasic variant 4,[5],12:i:-, and one belonged to serovar Saintpaul. Seven of the mcr-1 positive isolates displayed a high rate of resistance to other antibiotics in addition to colistin. Analysis of the WGS indicated that the ST 19 was the most common ST among the mcr-1 positive isolates. The mcr-1 gene was located in an IncX4 plasmid of ∼33 kb, with no additional resistance genes and with high identity with a plasmid obtained from a clinical isolate of E. coli mcr-1 positive in Brazil. All plasmids harboring the mcr-1 gene were able to conjugate. Our results suggest the spread of a single plasmid type in Brazil harboring the mcr-1 among Salmonella spp. The horizontal transfer of this mobile element has been contributing to the spread of the colistin resistance in the country.


Assuntos
Contaminação de Alimentos , Microbiologia de Alimentos , Sequências Repetitivas Dispersas , Salmonella enterica/classificação , Salmonella enterica/efeitos dos fármacos , Animais , Antibacterianos/farmacologia , Brasil/epidemiologia , Conjugação Genética , DNA Bacteriano , Farmacorresistência Bacteriana , Escherichia coli/genética , Microbiologia de Alimentos/métodos , Genes Bacterianos , Testes de Sensibilidade Microbiana , Filogenia , Reação em Cadeia da Polimerase , Carne de Porco/microbiologia , Aves Domésticas/microbiologia , Salmonella enterica/isolamento & purificação , Salmonella typhimurium/classificação , Salmonella typhimurium/efeitos dos fármacos , Salmonella typhimurium/isolamento & purificação , Perus/microbiologia , Sequenciamento Completo do Genoma
18.
Emerg Microbes Infect ; 9(1): 1-4, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-31859589

RESUMO

CRISPR-based typing was performed to subtype isolates of S. Typhimurium and its monophasic variant Salmonella 4,[5],12:i:- from humans and animals between 2009 and 2017 in China. CRISPR typing classified all isolates into two lineages and four sub-lineages. All isolates from Lineage II and Lineage IB-1 were Salmonella Typhimurium. All of Salmonella 4,[5],12:i: - isolates were distributed in Lineage IA and Lineage IB-2, which all belonged to ST34 by MLST typing. Only Lineage IB-2 contained ST34 isolates from both Salmonella Typhimurium and Salmonella 4,[5],12:i:-. Among the isolates of ST34, TST4 was identified as the most common CRISPR type representing 86.5% of Salmonella 4,[5],12:i:- and 14.5 % of Salmonella Typhimurium mainly from pigs and humans. This study demonstrated that TST4-ST34 isolates were predominant in Salmonella 4,[5],12:i:-, and pig was the main reservoir for Salmonella 4,[5],12:i:- in China, which might have the potential to transmit to humans by pig production.


Assuntos
Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Reservatórios de Doenças , Técnicas de Genotipagem/métodos , Carne/microbiologia , Salmonella typhimurium/classificação , Salmonella typhimurium/isolamento & purificação , Sus scrofa , Animais , China , Diarreia/microbiologia , Eletroforese em Gel de Campo Pulsado , Humanos , Tipagem de Sequências Multilocus , Filogenia , Infecções por Salmonella/microbiologia , Salmonella typhimurium/genética
19.
Braz J Microbiol ; 51(1): 53-64, 2020 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-31728978

RESUMO

Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)-the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.


Assuntos
Microbiologia de Alimentos , Genoma Bacteriano , Filogenia , Salmonella typhimurium/classificação , Técnicas de Tipagem Bacteriana , Brasil , Fezes/microbiologia , Genômica , Genótipo , Humanos , Tipagem de Sequências Multilocus , RNA Ribossômico 16S/genética , Infecções por Salmonella/microbiologia , Fatores de Virulência/genética , Sequenciamento Completo do Genoma
20.
Braz. J. Pharm. Sci. (Online) ; 56: e18468, 2020. tab
Artigo em Inglês | LILACS | ID: biblio-1249147

RESUMO

Origanum vulgare L. (OVEO) essential oil has been considered a candidate antimicrobial for use in food conservation systems. However, studies on the influence of concomitant variations of different food components or physicochemical parameters on the antibacterial properties of OVEO are scarce. This study assessed the influence of concomitant variations in amounts of proteins - PTN (4.0, 6.0 or 8.0 g/100 mL) and lipids - LIP (3.75, 5.0 or 6.25 g/100 mL) and pH values (5.0, 5.5 or 6.0) in cultivation medium on the inhibitory effects of OVEO against Escherichia coli (EC) and Salmonella Typhimurium (ST). Lowest minimum inhibitory concentration values of OVEO against EC and ST were observed in media with the highest LIP amounts regardless the PTN amount and pH value. In absorbance based microtiter plate assay (MPA), for both EC and ST, OVEO caused the lowest Grmax values in medium containing the highest LIP and PTN amounts and lowest pH value. Highest Grmax values for EC and ST were observed in medium containing the lowest LIP and PTN amount and highest pH value. Grmax values estimated from viable counts of EC and ST in tested media with OVEO confirmed bacterial growth behavior similar to that observed in MPA. Overall, the LIP amount in media was as the most influential factor to enhance the antibacterial effects of OVEO. These results indicate that the concomitant influence of LIP and PTN amounts and pH values on the antibacterial effects of OVEO should be considered for optimizing its antimicrobial efficacy in foods.


Assuntos
Salmonella typhimurium/classificação , Óleos Voláteis/análise , Origanum/classificação , Escherichia coli/classificação , Lipídeos/efeitos adversos , Proteínas , Testes de Sensibilidade Microbiana/instrumentação , Crescimento Bacteriano , Eficácia , Alimentos , Concentração de Íons de Hidrogênio
SELEÇÃO DE REFERÊNCIAS
DETALHE DA PESQUISA