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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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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.
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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 MicrobianaRESUMO
In recent years, Salmonella enterica subsp. enterica serovar Mbandaka (S. Mbandaka) has been increasingly isolated from laying hens and shell eggs around the world. Moreover, this serovar has been identified as the causative agent of several salmonellosis outbreaks in humans. Surprisingly, little is known about the characteristics of this emerging serovar, and therefore, we investigated antimicrobial resistance, virulence, and prophage genes of six selected Brazilian strains of Salmonella Mbandaka using Whole Genome Sequencing (WGS). Multi-locus sequence typing revealed that the tested strains belong to Sequence Type 413 (ST413), which has been linked to recent multi-country salmonellosis outbreaks in Europe. A total of nine resistance genes were detected, and the most frequent ones were aac(6')-Iaa, sul1, qacE, blaOXA-129, tet(B), and aadA1. A point mutation in ParC at the 57th position (threonine â serine) associated with quinolone resistance was present in all investigated genomes. A 112,960 bp IncHI2A plasmid was mapped in 4/6 strains. This plasmid harboured tetracycline (tetACDR) and mercury (mer) resistance genes, genes contributing to conjugative transfer, and genes involved in plasmid maintenance. Most strains (four/six) carried Salmonella genomic island 1 (SGI1). All S. Mbandaka genomes carried seven pathogenicity islands (SPIs) involved in intracellular survival and virulence: SPIs 1-5, 9, and C63PI. The virulence genes csgC, fimY, tcfA, sscA, (two/six), and ssaS (one/six) were absent in some of the genomes; conversely, fimA, prgH, and mgtC were present in all of them. Five Salmonella bacteriophage sequences (with homology to Escherichia phage phiV10, Enterobacteria phage Fels-2, Enterobacteria phage HK542, Enterobacteria phage ST64T, Salmonella phage SW9) were identified, with protein counts between 31 and 54, genome lengths of 24.7 bp and 47.7 bp, and average GC content of 51.25%. In the phylogenetic analysis, the genomes of strains isolated from poultry in Brazil clustered into well-supported clades with a heterogeneous distribution, primarily associated with strains isolated from humans and food. The phylogenetic relationship of Brazilian S. Mbandaka suggests the presence of strains with high epidemiological significance and the potential to be linked to foodborne outbreaks. Overall, our results show that isolated strains of S. Mbandaka are multidrug-resistant and encode a rather conserved virulence machinery, which is an epidemiological hallmark of Salmonella strains that have successfully disseminated both regionally and globally.
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The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.
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This study aimed to investigate the genomic and epidemiological features of a methicillin-resistant Staphylococcus aureus sequence type 1 (MRSA ST1) strain associated with caprine subclinical mastitis. An S. aureus strain was isolated from goat's milk with subclinical mastitis in Paraiba, Northeastern Brazil, by means of aseptic procedures and tested for antimicrobial susceptibility using the disk-diffusion method. Whole genome sequencing was performed using the Illumina MiSeq platform. After genome assembly and annotation, in silico analyses, including multilocus sequence typing (MLST), antimicrobial resistance and stress-response genes, virulence factors, and plasmids detection were performed. A comparative SNP-based phylogenetic analysis was performed using publicly available MRSA genomes. The strain showed phenotypic resistance to cefoxitin, penicillin, and tetracycline and was identified as sequence type 1 (ST1) and spa type 128 (t128). It harbored the SCCmec type IVa (2B), as well as the lukF-PV and lukS-PV genes. The strain was phylogenetically related to six community-acquired MRSA isolates (CA-MRSA) strains associated with human clinical disease in North America, Europe, and Australia. This is the first report of a CA-MRSA strain associated with milk in the Americas. The structural and epidemiologic features reported in the MRSA ST1 carrying a mecA-SCCmec type IVa suggest highly complex mechanisms of horizontal gene transfer in MRSA. The SNP-based phylogenetic analysis suggests a zooanthroponotic transmission, i.e., a strain of human origin.
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OBJECTIVES: In contrast to other qnr families, qnrVC has been reported mainly in Vibrio spp. and inserted in class 1 integrons. This study aimed to identify the variants of qnrVC genes detected in Klebsiella pneumoniae carbapenemase-2-producing Enterobacter and Klebsiella strains isolated from Brazilian coastal waters and the genetic contexts associated with their occurrence. METHODS: qnrVC variants were identified by Sanger sequencing. Stains were typified by pulsed-field gel electrophoresis. Antimicrobial susceptibility testing, conjugation assays, and whole genome sequencing (WGS) were applied to identify the strains' antimicrobial resistance profile, qnrVC and blaKPC-2 co-transference, and qnrVC genetic context. RESULTS: qnrVC1 was identified in 15 Enterobacter and 3 Klebsiella, and qnrVC4 in 2 Enterobacter strains. Pulsed-field gel electrophoresis revealed 12 clonal profiles of Enterobacter and one of Klebsiella. Strains were resistant to aminoglycosides, beta-lactams, fosfomycin, quinolones, and sulfamethoxazole-trimethoprim. Co-transference of qnrVC and blaKPC-2 were obtained from five representative Enterobacter strains, which showed resistance to ampicillin and amoxicillin-clavulanate, and reduced susceptibility to extended-spectrum cephalosporins, meropenem, and ciprofloxacin. WGS analysis from representative strains revealed one K. quasipneumoniae subsp. similipneumoniae, one E. soli, four E. kobei, and seven isolates belonging to Enterobacter Taxon 3. Long-read WGS showed qnrVC and blaKPC-2 were carried by the same replicon on Klebsiella and Enterobacter strains, and the qnrVC association with not previously described genetic environments composed of insertion sequences and truncated genes. These contexts occurred in small- and high-molecular-weight plasmids belonging to IncFII, IncP6, pKPC-CAV1321, and IncU groups. CONCLUSION: Our results suggest that the dissemination of qnrVC among Enterobacterales in Brazilian coastal waters is associated with several genetic recombination events.
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Enterobacter , Klebsiella , Antibacterianos/farmacologia , Enterobacter/genética , Klebsiella/genética , Klebsiella pneumoniae/genéticaRESUMO
BACKGROUND AND AIM: Antimicrobial resistance poses a major threat to global public health. Foodstuff of animal origin can serve as potential vehicles for the dissemination of antimicrobial-resistant bacteria and resistance genes to consumers. In view of the lack of knowledge about antimicrobial resistance in bacteria associated with goat milk, the aim of this study was to report species-level identification and antimicrobial susceptibility profiles of a large collection of Staphylococcus spp. isolates recovered from raw goat milk in Brazil. MATERIALS AND METHODS: A total of 434 Staphylococcus spp. isolates originated from 510 goat milk samples in Northeast Brazil were investigated. The isolates were obtained by conventional microbiological methods. Species identification and antimicrobial susceptibility testing were performed by means of a semi-automated system using a panel for biochemical tests and broth microdilution method for 19 antimicrobial drugs. RESULTS: Although Staphylococcus aureus (22.6%) accounted for the majority of the isolates, a total of 13 different non-aureus staphylococci spp. were identified. High resistance rates against erythromycin (40.8%), and the beta-lactams ampicillin (45.9%) and penicillin (42.9%) were observed among S. aureus isolates. The most significant findings were related to the resistance against quinupristin-dalfopristin, a drug of last resort used in human medicine to treat infections caused by vancomycin-resistant S. aureus and enterococci. CONCLUSION: The high diversity of Staphylococcus spp. showing phenotypic resistance against different antimicrobial drugs encourages further investigations on the real impact of these bacteria as reservoirs of antimicrobial resistance genes to consumers. Furthermore, the potential impact of technological processes, such as pasteurization, fermentation, and maturation, on the maintenance and dissemination of antimicrobial resistance among the microbial populations in milk and dairy products must also be investigated.
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We investigated the effects of pathogens associated with subclinical intramammary infections on yield, composition and quality indicators of goat milk. By means of a longitudinal study, individual half udder milk samples (n = 132) were collected at different lactation periods and assessed for milk yield and physicochemical composition, somatic cell count (SCC), total bacteria count (TBC) and microbiological culture. Staphylococci species accounted for the great majority of the isolates (96.1%). Intramammary infections significantly reduced fat and total solids in goat milk and increased both SCC and TBC. However, these indicators were significantly higher in udder halves affected by S. aureus compared with other staphylococci species.
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Infecções Bacterianas/veterinária , Doenças das Cabras/microbiologia , Mastite/veterinária , Leite/química , Leite/microbiologia , Animais , Infecções Bacterianas/microbiologia , Carga Bacteriana/veterinária , Contagem de Células/veterinária , Feminino , Cabras , Lactação , Estudos Longitudinais , Glândulas Mamárias Animais/microbiologia , Mastite/microbiologia , Leite/citologia , Infecções Estafilocócicas/microbiologia , Infecções Estafilocócicas/veterinária , Staphylococcus aureus/isolamento & purificaçãoRESUMO
Anaplasma marginale, a tick-borne α-proteobacterium that causes significant economic losses for the cattle industry worldwide, has been increasingly detected in other animal species. This agent has been previously detected in buffaloes and goats co-grazed with cattle in Brazil. This study aimed to investigate the occurrence of A. marginale in a multispecies (goats, sheep and cattle) grazing farm in the State of Paraíba, northeastern Brazil. A total of 119 goats, 71 sheep, and five cattle were evaluated. An epidemiological questionnaire was applied to the farm owner addressing age, gender, and presence of ticks. Serum samples from goat, sheep and cattle were tested for anti-Anaplasma marginale antibodies by a commercial MSP5-based on indirect enzyme-linked immunosorbent assay (iELISA). EDTA-blood samples were screened for A. marginale- and A. ovis-infection by PCR using primers targeting Anaplasma spp. msp4 gene. Sequencing of the repeat region of the msp1α gene was used for genotyping A. marginale strains found in the present study. A total of 47/119 (39.5 %, 95 % CI: 31.1-48.4 %) goats and 2/71 (3%, 95 % CI: 0.7-9.7 %) sheep were seroreactive for A. marginale rMSP5 by the commercial iELISA. All cattle were seronegative for A. marginale. Anaplasma spp. msp4 PCR results revealed that two out of 119 (1.7 %; 95 % CI: 0.4-5.9 %) goats tested positive and all sheep and cattle samples were negative. It was not possible to sequence one sample. Therefore, the other sequencing sample found tandem repeats of A. marginale msp1α gene demonstrating that goat was infected with the genotype F/91. Rhipicephalus microplus ticks were found parasitizing goats but not on sheep or cattle. Considering that in Brazil A. marginale genotype F/91 and the MSP1a tandem repeat F has only been detected in goats so far, we hypothesized that this genotype may be related to goats.
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Anaplasma marginale/isolamento & purificação , Anaplasmose/epidemiologia , Doenças das Cabras/epidemiologia , Anaplasmose/microbiologia , Animais , Brasil/epidemiologia , Feminino , Doenças das Cabras/microbiologia , Cabras , Masculino , Prevalência , Estudos SoroepidemiológicosRESUMO
The prophylactic administration of ceftiofur to newly hatched chicks is a common practice in some hatcheries worldwide to mitigate early gastrointestinal infections caused by Enterobacteriaceae. In spite of the crucial role of the gut microbiome for the broiler's health, there is still limited information on how the microbial composition is affected by such procedure. We investigated the effects of posthatch prophylactic application of ceftiofur on the cecal microbiota of 14-day-old broilers fed regular or sanguinarine-supplemented diets. DNA samples were extracted from cecal contents, amplified for the V3-V4 regions of the microbial 16S rRNA gene, and sequenced in a high-throughput sequencing platform (Illumina MiSeq). After downstream bioinformatics and statistical analyses, our results demonstrated that both ceftiofur and sanguinarine treatments similarly increased the proportions of the phylum Bacteroidetes and the genera Bacteroides and Megamonas, whereas reduced the relative abundances of Firmicutes and Lachnospiraceae in the ceca of the birds. Such changes are probably associated with increased carbohydrate fermentation processes favoring the production of short-chain fatty acids. This was also corroborated by the functional prediction findings, which suggest an increase in some metabolic pathways associated with digestibility in broilers receiving ceftiofur. Considering that antimicrobial stewardship in animal production systems is strongly needed to mitigate the threat of antimicrobial resistance, our findings show that supplementation with a phytogenic feed additive can lead to a similar microbial composition in the ceca of commercial broiler chickens, suggesting that the use of alternative products could lead to functional modifications without increasing pressure for antimicrobial resistance.