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In this study, a total of 248 ground beef samples were analyzed for the presence of Shiga toxin-producing Escherichia coli (STEC). Out of these samples, only one (0.4%) tested positive for STEC. Further analysis using PCR confirmed the presence of all tested genes associated with STEC, including stx1, stx2, eae, ehx, uid, rfbO157, and fliCH7 in this isolate. Interestingly, no STEC strains were detected in the remaining 100 beef cut samples or the 100 chicken cut samples, indicating the absence of detectable STEC contamination in those specific samples. The isolated strain exhibited significant cytotoxic activity in Vero cells, indicating its ability to produce cytotoxic Shiga toxins. To further investigate the strain, whole-genome sequencing (WGS) analyses were performed. The resistome analysis revealed the absence of acquired antimicrobial resistance genes, indicating a pan-susceptible phenotype. However, this strain presented chromosomal mutations in gyrA, gyrB, parC, parE, pmrA, pmrB, and folP. Plasmid analysis identified the presence of two plasmids, namely IncFIB(AP001918) and IncFII. The multi-locus sequence typing (MLST) identified the strain as belonging to sequence type (ST) 11, which is associated with E. coli O157:H7 strains. The virulome analysis confirmed the presence of several canonical virulence markers, including stx1, stx2, eae-g01-gamma, ehxA, stx1a-O157, and stx2a-O157. Overall, this study identified for the first time a rare occurrence of STEC contamination in ground beef, with the isolated strain belonging to the highly virulent O157:H7 serotype. These findings contribute to our understanding of STEC prevalence and characteristics in food samples, highlighting the importance of effective food safety measures to prevent potential health risks associated with STEC contamination.
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This study focuses on the genomic characterization of a multidrug-resistant Escherichia coli strain responsible for a severe gastrointestinal infection in a 33-year-old male. The patient initially received sulfamethoxazole/trimethoprim treatment, which proved ineffective. Fecal culture confirmed the presence of E. coli displaying a MDR profile to ampicillin, nalidixic acid, ciprofloxacin, sulfamethoxazole, trimethoprim, and tetracycline. Serotyping identified the strain as ONT:H19. Virulence analysis indicated a highly virulent profile with numerous virulence markers. Plasmid analysis uncovered various plasmids carrying both antimicrobial resistance and virulence genes. MLST assigned the strain to ST10955. Phylogenomic analysis revealed similarity to an older Brazilian isolate, suggesting the persistence of a common lineage with evolving antimicrobial resistance. This report highlights the first identification of a multidrug-resistant ST10955 E. coli strain with a wide resistome and virulence potential, emphasizing the importance of ongoing surveillance of E. coli strains due to their potential for severe infections, resistance development, and virulence.
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Farmacorresistencia Bacteriana Múltiple , Infecciones por Escherichia coli , Escherichia coli , Genoma Bacteriano , Filogenia , Humanos , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Escherichia coli/patogenicidad , Escherichia coli/clasificación , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/diagnóstico , Adulto , Masculino , Farmacorresistencia Bacteriana Múltiple/genética , Genoma Bacteriano/genética , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Heces/microbiología , Plásmidos/genética , Tipificación de Secuencias Multilocus , Factores de Virulencia/genética , Enfermedades Gastrointestinales/microbiología , Enfermedades Gastrointestinales/diagnóstico , Virulencia/genética , Serotipificación , BrasilAsunto(s)
Antibacterianos , Carbapenémicos , Citrobacter freundii , Colistina , Infecciones por Enterobacteriaceae , Colistina/farmacología , Humanos , Citrobacter freundii/efectos de los fármacos , Citrobacter freundii/genética , Citrobacter freundii/aislamiento & purificación , Antibacterianos/farmacología , Infecciones por Enterobacteriaceae/microbiología , Infecciones por Enterobacteriaceae/tratamiento farmacológico , Carbapenémicos/farmacología , Pruebas de Sensibilidad Microbiana , Farmacorresistencia Bacteriana , Salud GlobalAsunto(s)
Antibacterianos , Farmacorresistencia Bacteriana , Fosfomicina , Infecciones por Klebsiella , Klebsiella pneumoniae , Pruebas de Sensibilidad Microbiana , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/efectos de los fármacos , Fosfomicina/farmacología , Humanos , Antibacterianos/farmacología , Infecciones por Klebsiella/microbiología , Infecciones por Klebsiella/tratamiento farmacológico , Farmacorresistencia Bacteriana/genética , Genes Bacterianos/genéticaRESUMEN
Food safety remains a significant global public health concern, with the risk of unsafe food varying worldwide. The economies of several low- and middle-income countries (LMICs) heavily rely on livestock, posing a challenge to ensuring the production of safe food. This review discusses our understanding of pre-harvest critical issues related to food safety in LMICs, specifically focusing on animal-derived food. In LMICs, food safety regulations are weak and inadequately enforced, primarily concentrating on the formal market despite a substantial portion of the food sector being dominated by informal markets. Key critical issues at the farm level include animal health, a low level of good agriculture practices, and the misuse of antimicrobials. Effectively addressing foodborne diseases requires a comprehensive One Health framework. Unfortunately, the application of the One Health approach to tackle food safety issues is notably limited in LMICs. In conclusion, considering that most animal-source foods from LMICs are marketed through informal channels, food safety legislation and policies need to account for this context. Interventions aimed at reducing foodborne bacterial pathogens at the farm level should be scalable, and there should be strong advocacy for the proper implementation of pre-harvest interventions through a One Health approach.
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Herein we report the draft genome sequences of Salmonella enterica subsp. enterica serovars Saintpaul ST50 and Worthington ST592 isolated from raw milk samples in Northeastern Brazil. The 4,696,281 bp S. Saintpaul ST50 genome contained 4,628 genes in 33 contigs, while S. Worthington ST592 genome was 4,890,415 bp in length, comprising 4,951 genes in 46 contigs. S. Worthington ST592 carried a conserved Col(pHAD28) plasmid which contains the antimicrobial resistance determinants tet(C), acc(6')-Iaa, and a nonsynonymous point mutation in ParC (p.T57S). The data could support further evolutionary and epidemiologic studies involving Salmonella organisms.
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Colistina , Proteínas de Escherichia coli , Animales , Colistina/farmacología , Escherichia coli/genética , Brasil/epidemiología , Antibacterianos/farmacología , Salmonella/genética , Farmacorresistencia Bacteriana , Proteínas de Escherichia coli/genética , Plásmidos , Pruebas de Sensibilidad MicrobianaRESUMEN
Antibiotic resistance in Citrobacter freundii is a public health concern. This study evaluated the closed genome of a C. freundii isolated from the stool of a hospitalized patient initially related to a Salmonella outbreak. Confirmation of the isolate was determined by whole-genome sequencing. Nanopore sequencing was performed using a MinION with a Flongle flow cell. Assembly using SPAdes and Unicycler yielded a closed genome annotated by National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline. Genomic analyses employed MLST 2.0, ResFinder4.1, PlasmidFinder2.1, and VFanalyzer. Phylogenetic comparison utilized the Center for Food Safety and Applied Nutrition (CFSAN)-single nucleotide polymorphism pipeline and Genetic Algorithm for Rapid Likelihood Inference. Antimicrobial susceptibility was tested by broth microdilution following Clinical and Laboratory Standards Institute criteria. Multi-locus sequence type in silico analysis assigned the C. freundii as sequence type 64 and the blaCMY-41 gene was detected in resistome investigation. The susceptibility to antibiotics, determined using Sensititre® plates, revealed resistance to aztreonam, colistin, cefoxitin, amoxicillin/clavulanic acid, sulfisoxazole, ampicillin, and streptomycin. The genetic relatedness of the C. freundii CFSAN077772 with publicly available C. freundii genomes revealed a close relationship to a C. freundii SRR1186659, isolated in 2009 from human stool in Tanzania. In addition, C. freundii CFSAN077772 is nested in the same cluster with C. freundii clinical strains isolated in Denmark, Mexico, Myanmar, and Canada, suggesting a successful intercontinental spread.
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Citrobacter freundii , Infecciones por Enterobacteriaceae , Humanos , Citrobacter freundii/genética , beta-Lactamasas/genética , Tipificación de Secuencias Multilocus , Filogenia , Infecciones por Enterobacteriaceae/epidemiología , Antibacterianos/farmacología , Genómica , Pruebas de Sensibilidad MicrobianaRESUMEN
The mechanism of colonisation of the chicken intestine by Salmonella remains poorly understood, while the severity of infections vary enormously depending on the serovar and the age of the bird. Several metabolism and virulence genes have been identified in Salmonella Heidelberg; however, information on their roles in infection, particularly in the chicken infection model, remains scarce. In the present publication, we investigated three Salmonella Heidelberg mutants containing deletions in misL, ssa, and pta-ackA genes by using signature-tagged mutagenesis. We found that mutations in these genes of S. Heidelberg result in an increase in fitness in the chicken model. The exception was perhaps the pta-ackA mutant where colonisation was slightly reduced (2, 7, 14, and 21 days post-infection) although some birds were still excreting at the end of the experiment. Our results suggest that for intestinal colonisation of the chicken caecum, substrate-level phosphorylation is likely to be more important than the MisL outer membrane protein or even the secretion system apparatus. These findings validate previous work that demonstrated the contribution of ackA and pta mutants to virulence in chickens, suggesting that the anaerobic metabolism genes such as pta-ackA could be a promising mitigation strategy to reduce S. Heidelberg virulence.
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Pollos , Salmonelosis Animal , Animales , Fosforilación , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Fosfato Acetiltransferasa/genética , Fosfato Acetiltransferasa/metabolismo , Anaerobiosis , Virulencia , Salmonella , Salmonelosis Animal/microbiologíaAsunto(s)
Fosfomicina , Infecciones Estafilocócicas , Humanos , Fosfomicina/farmacología , Staphylococcus aureus/genética , Prevalencia , Infecciones Estafilocócicas/tratamiento farmacológico , Infecciones Estafilocócicas/epidemiología , Antibacterianos/farmacología , Antibacterianos/uso terapéuticoRESUMEN
Shiga toxin-producing Escherichia coli (STEC) is an important pathogen with public health implications, including its potential association with vegetables. In this study, we investigated the presence of STEC in vegetables obtained from organic producers located in São Paulo city, Brazil. As part of a routine surveillance study conducted over (years of isolation), a total of 200 samples of organic vegetables were screened using biochemical and PCR methods. Among the vegetable samples tested, 30 (15%) were positive for non-Shiga toxin-producing E. coli. While no STEC was detected in the organic vegetables in this study, the presence of non-STEC in vegetables raises concerns about the lack of proper hygiene practices during vegetable handling. This contamination represents a public health risk, particularly considering that these isolates can still be pathogenic, and vegetables are often consumed raw. To address this important issue, continuous monitoring of these farms is recommended to ensure the quality and safety of organic vegetables produced for both domestic consumption and exportation.
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Infecciones por Escherichia coli , Proteínas de Escherichia coli , Escherichia coli Shiga-Toxigénica , Humanos , Escherichia coli Shiga-Toxigénica/genética , Brasil , Proteínas de Escherichia coli/genética , Reacción en Cadena de la Polimerasa , Infecciones por Escherichia coli/microbiologíaRESUMEN
The global dissemination of extended-spectrum-ß-lactamase (ESBL)-producing Escherichia coli has been considered a critical issue within a One Health framework. The aim of this study was to perform a genomic investigation of an ESBL-producing E. coli strain belonging to the globally spread sequence type/clonal complex ST90/CC23, isolated from gastrointestinal tract of a dog, in Brazil. Besides CTX-M-15 ESBL, this E. coli isolate carried mutations conferring resistance to human and veterinary fluoroquinolones (GyrA [Ser83Leu, Asp87Asn], ParC [Ser80Ile] and ParE [Ser458Ala]), and resistance determinants to disinfectants and pesticides. Noteworthy, phylogenomic analysis revealed that this multidrug E. coli strain clustered with ST90 lineages isolated from human, dog, and livestock in Brazil. The phylogenetic tree also revealed that this E. coli strain shares a common ancestor with isolates from the United States, Russia, Germany, and China, highlighting the potential global spreading of this clone. In summary, we report genomic data of CTX-M-15-positive E.coli ST90 colonizing a pet. Colonization of companion animals by critical resistant pathogens highlights the need for close monitoring to better understand the epidemiology and genetic factors contributing for successful adaptation of global clones at the human-animal interface.
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Infecciones por Escherichia coli , Salud Única , Animales , Perros , Humanos , Escherichia coli , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/veterinaria , Infecciones por Escherichia coli/epidemiología , Filogenia , Mascotas , Antibacterianos/farmacología , Pruebas de Sensibilidad Microbiana , beta-Lactamasas/genéticaRESUMEN
Salmonella spp. is one of the major foodborne pathogens responsible for causing economic losses to the poultry industry and bringing consequences for public health as well. Both the pathogen survival ability in the intestinal environment during inflammation as well as their relationship with the host immune system, play a key role during infections in poultry. The objective of this study was to quantify the presence of the macrophages and CD4+/CD8+ cells populations using the immunohistochemistry technique, in commercial lineages of chickens experimentally infected by wild-type and mutant strains of Salmonella Enteritidis and Salmonella Typhimurium lacking ttrA and pduA genes. Salmonella Enteritidis ∆ttrA∆pduA triggered a higher percentage of the stained area than the wild-type, with exception of light laying hens. Salmonella Typhimurium wild-type strain and Salmonella Typhimurium ∆ttrA∆pduA infections lead to a similar pattern in which, at 1 and 14 dpi, the caecal tonsils and ileum of birds showed a more expressive stained area compared to 3 and 7 dpi. In all lineages studied, prominent infiltration of macrophages in comparison with CD4+ and CD8+ cells was observed. Overall, animals infected by the mutant strain displayed a positively stained area higher than the wild-type. Deletions in both ttrA and pduA genes resulted in a more intense infiltration of macrophages and CD4+ and CD8+ cells in the host birds, suggesting no pathogen attenuation, even in different strains of Salmonella.
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Pollos , Enfermedades de las Aves de Corral , Salmonelosis Animal , Salmonella enterica , Animales , Femenino , Inmunidad Celular , Enfermedades de las Aves de Corral/genética , Enfermedades de las Aves de Corral/inmunología , Salmonella enterica/genética , Salmonella enteritidis/genética , Salmonelosis Animal/inmunología , Salmonella typhimurium/genética , SerogrupoRESUMEN
Among the important recent observations involving anaerobic respiration was that an electron acceptor produced as a result of an inflammatory response to Salmonella Typhimurium generates a growth advantage over the competing microbiota in the lumen. In this regard, anaerobically, salmonellae can oxidize thiosulphate (S2O32-) converting it into tetrathionate (S4O62-), the process by which it is encoded by ttr gene cluster (ttrSRttrBCA). Another important pathway under aerobic or anaerobic conditions is the 1,2-propanediol-utilization mediated by the pdu gene cluster that promotes Salmonella expansion during colitis. Therefore, we sought to compare in this study, whether Salmonella Heidelberg strains lacking the ttrA, ttrApduA, and ttrACBSR genes experience a disadvantage during cecal colonization in broiler chicks. In contrast to expectations, we found that the gene loss in S. Heidelberg potentially confers an increase in fitness in the chicken infection model. These data argue that S. Heidelberg may trigger an alternative pathway involving the use of an alternative electron acceptor, conferring a growth advantage for S. Heidelberg in chicks.
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Pollos , Salmonelosis Animal , Animales , Pollos/metabolismo , Propilenglicol/metabolismo , Salmonella , Salmonella typhimurium , TiosulfatosRESUMEN
Methicillin-resistant staphylococci have become leading cause of infectious diseases in humans and animals, being categorized as high priority pathogens by the World Health Organization. Although methicillin-resistant Staphylococcus sciuri (recently moved to Mammaliicoccus sciuri) has been widely reported in companion animals, there is scarce information regarding their clinical impact and genomic features. Herein, we reported the occurrence and genomic characteristics of methicillin-resistant M. sciuri recovered from fatal infections in pets admitted to an intensive care unit of a veterinary hospital, in Brazil. Two M. sciuri strains were isolated from bronchoalveolar lavage samples collected from dog (strain SS01) and cat (strain SS02) presenting with sepsis and acute respiratory distress syndrome. Both isolates displayed a multidrug-resistant profile, whereas whole-genome sequencing analysis confirmed the presence of the mecA gene, along to genetic determinant conferring resistance to macrolides, streptogramins, aminoglycosides, and trimethoprim. For both strains, the mec and crr gene complex shared high identity (≥97%) with analogue sequences from a M. sciuri isolated from a human wound infection, in the Czech Republic. Strains were assigned to the sequence type ST52 and the novel ST74. Phylogenomic analysis revealed a broad host range association of these strains with several hosts and sources, including humans, animals, food, and the environment through different years and geographic locations. Our findings demonstrate that infections caused by mecA-positive M. sciuri strains can be a serious threat for veterinary intensive care patients and the medical staff, with additional implications for One Health approaches.