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Introduction: Foodborne infections, which are frequently linked to bacterial contamination, are a serious concern to public health on a global scale. Whether agricultural farming practices help spread genes linked to antibiotic resistance in bacteria associated with humans or animals is a controversial question. Methods: This study applied a long-read Oxford Nanopore MinION-based sequencing to obtain the complete genome sequence of a multi-drug resistant Escherichia coli strain (L1PEag1), isolated from commercial cape gooseberry fruits (Physalis peruviana L.) in Ecuador. Using different genome analysis tools, the serotype, Multi Locus Sequence Typing (MLST), virulence genes, and antimicrobial resistance (AMR) genes of the L1PEag1 isolate were determined. Additionally, in vitro assays were performed to demonstrate functional genes. Results: The complete genome sequence of the L1PEag1 isolate was assembled into a circular chromosome of 4825.722 Kbp and one plasmid of 3.561 Kbp. The L1PEag1 isolate belongs to the B2 phylogroup, sequence type ST1170, and O1:H4 serotype based on in silico genome analysis. The genome contains 4,473 genes, 88 tRNA, 8 5S rRNA, 7 16S rRNA, and 7 23S rRNA. The average GC content is 50.58%. The specific annotation consisted of 4,439 and 3,723 genes annotated with KEEG and COG respectively, 3 intact prophage regions, 23 genomic islands (GIs), and 4 insertion sequences (ISs) of the ISAs1 and IS630 families. The L1PEag1 isolate carries 25 virulence genes, and 4 perfect and 51 strict antibiotic resistant gene (ARG) regions based on VirulenceFinder and RGI annotation. Besides, the in vitro antibiotic profile indicated resistance to kanamycin (K30), azithromycin (AZM15), clindamycin (DA2), novobiocin (NV30), amikacin (AMK30), and other antibiotics. The L1PEag1 isolate was predicted as a human pathogen, matching 464 protein families (0.934 likelihood). Conclusion: Our work emphasizes the necessity of monitoring environmental antibiotic resistance, particularly in commercial settings to contribute to develop early mitigation techniques for dealing with resistance diffusion.
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Background: Infectious illnesses are a serious health concern in Indonesia. Widespread use of self-medication by the community increases the risk of developing multi-drug resistant (MDR) bacteria. This study assessed the potential of sappan wood as an inhibitor of extended-spectrum beta-lactamase (ESBL) encoded by blaSHV, blaTEM and blaCTX-M genes. Method: In silico testing was conducted to develop an effective and economical starting strategy. Thereby, this study significantly advances the development of novel treatments to combat antibiotic resistance. Using clavulanic acid as the benchmark medicine, the potency of the beta-lactamase inhibitor brazilein was predicted. Using the Molegro Virtual Docker computer tool, docking was performed to estimate the chemical and physical properties of the compounds, as well as the biological activity of brazilein toward the required receptor. The receptors used were SHV-1 beta-lactamase, PDB code: 2H0T; TEM-1 beta-lactamase, PDB code: 4OQG and CTX-M-14 beta-lactamase, PDB code: 6VHS. Data analysis was performed by comparing the binding energies of the docking results between the ligands and the target receptor. The more stable the bond that formed between the ligand and the target receptor, the lower the bond energy. Results: The in silico test results on the blaSHV gene were as follows: binding energy of ligand MA4_400[A] = -100.699, brazilein = -82.206, clavulanic acid = -79.3704; in the blaTEM gene: ligand bond energy 2UL_301[B] = -107.681, brazilein = -82.0296, clavulanic acid = -103.3; in the blaCTX-M gene: X57_301[A] ligand bond energy = -86.6197, and brazilein = -88.1586, clavulanic acid = -101.933. Conclusion: The findings of this study demonstrate the significant potential of brazilein sappan wood to block the beta-lactamase activity of blaCTX-M.
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INTRODUCTION: Novel beta-lactam/beta-lactamase inhibitor (BIBLI) combinations are commercially available and have been used for treating carbapenem-resistant Klebsiella pneumoniae (CRKP) infections. Continuous surveillance of susceptibility profiles and resistance mechanism identification are necessary to monitor the evolution of resistance within these agents. OBJECTIVE: The purpose of this study was to evaluate the susceptibility rates of ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam in CRKP isolated from patients with bloodstream infections who underwent screening for a randomized clinical trial in Brazil. METHODS: Minimum inhibitory concentrations (MICs) were determined for meropenem, ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam using the gradient diffusion strip method. Carbapenemase genes were detected by multiplex real-time polymerase chain reaction. Klebsiella pneumoniae carbapenemase (KPC)-producing isolates showing resistance to any BLBLI and New Delhi Metallo-beta-lactamase (NDM)-producing isolates with susceptibility to any BLBLI isolates were further submitted for whole-genome sequencing. RESULTS: From a total of 69 CRKP isolates, 39 were positive for blaKPC, 19 for blaNDM and 11 for blaKPC and blaNDM. KPC-producing isolates demonstrated susceptibility rates above 94â¯% for all BLBLIs. Two isolates with resistance to meropenem/vaborbactam demonstrated a Gly and Asp duplication at the porin OmpK36 as well as a truncated OmpK35. All NDM-producing isolates, including KPC and NDM coproducers, demonstrated susceptibility rates to ceftazidime/avibactam, imipenem/relebactam and meropenem/vaborbactam of 0â¯%, 9.1-21.1â¯% and 9.1-26.3â¯%, respectively. Five NDM-producing isolates that presented susceptibility to BLBLIs also had porin alterations CONCLUSIONS: This study showed that, although high susceptibility rates to BLBLIs were found, KPC-2 isolates were able to demonstrate resistance probably as a result of porin mutations. Additionally, NDM-1 isolates showed susceptibility to BLBLIs in vitro.
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Antibacterianos , Compostos Azabicíclicos , Enterobacteriáceas Resistentes a Carbapenêmicos , Ceftazidima , Combinação de Medicamentos , Infecções por Klebsiella , Klebsiella pneumoniae , Testes de Sensibilidade Microbiana , Inibidores de beta-Lactamases , beta-Lactamases , Humanos , Brasil , Klebsiella pneumoniae/efeitos dos fármacos , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/isolamento & purificação , Inibidores de beta-Lactamases/farmacologia , Infecções por Klebsiella/microbiologia , Compostos Azabicíclicos/farmacologia , Ceftazidima/farmacologia , beta-Lactamases/genética , Antibacterianos/farmacologia , Enterobacteriáceas Resistentes a Carbapenêmicos/efeitos dos fármacos , Enterobacteriáceas Resistentes a Carbapenêmicos/genética , Enterobacteriáceas Resistentes a Carbapenêmicos/isolamento & purificação , Proteínas de Bactérias/genética , Meropeném/farmacologia , Imipenem/farmacologia , Bacteriemia/microbiologia , Ácidos Borônicos/farmacologia , Compostos Heterocíclicos com 1 AnelRESUMO
BACKGROUND: Enzymatic degradation mediated by beta-lactamases constitutes one of the primary mechanisms of resistance to beta-lactam antibiotics in gram-negative bacteria. This enzyme family comprises four molecular classes, categorized into serine beta-lactamases (Classes A, C, and D) and zinc-dependent metallo-beta-lactamases (Class B). Gram-negative bacteria producing beta-lactamase are of significant concern, particularly due to their prevalence in nosocomial infections. A comprehensive understanding of the evolution and dissemination of this enzyme family is essential for effective control of these pathogens. In this study, we conducted the prospecting, phylogenetic analysis, and in silico analysis of beta-lactamases and homologous proteins identified in 1827 bacterial genomes with phenotypic data on beta-lactam resistance. These genomes were distributed among Klebsiella pneumoniae (45%), Acinetobacter baumannii (31%), Pseudomonas aeruginosa (14%), Escherichia coli (6%), and Enterobacter spp. (4%). Using an HMM profile and searching for conserved domains, we mined 2514, 8733, 5424, and 2957 proteins for molecular classes A, B, C, and D, respectively. This set of proteins encompasses canonical subfamilies of beta-lactamases as well as hypothetical proteins and other functional groups. Canonical beta-lactamases were found to be phylogenetically distant from hypothetical proteins, which, in turn, are closer to other representatives of the penicillin-binding-protein (PBP-like) and metallo-beta-lactamase (MBL) families. The catalytic amino acid residues characteristic of beta-lactamases were identified from the sequence alignment and revealed that motifs are less conserved in homologous groups than in beta-lactamases. After comparing the frequency of protein groups in genomes of resistant strains with those of sensitive ones applying Fisher's exact test and relative risk, it was observed that some groups of homologous proteins to classes B and C are more common in the genomes of resistant strains, particularly to carbapenems. We identified the beta-lactamase-like domain widely distributed in gram-negative species of the ESKAPEE group, which highlights its importance in the context of beta-lactam resistance. Some hypothetical homologous proteins have been shown to potentially possess promiscuous activity against beta-lactam antibiotics, however, they do not appear to expressly determine the resistance phenotype. The selective pressure due to the widespread use of antibiotics may favor the optimization of these functions for specialized resistance enzymes.
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Bactérias Gram-Negativas , Filogenia , beta-Lactamases , beta-Lactamases/metabolismo , beta-Lactamases/genética , beta-Lactamases/química , Bactérias Gram-Negativas/efeitos dos fármacos , Bactérias Gram-Negativas/genética , Bactérias Gram-Negativas/enzimologia , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , beta-Lactamas/farmacologia , beta-Lactamas/metabolismo , Antibacterianos/farmacologia , Genoma Bacteriano , Resistência beta-Lactâmica/genética , Antibióticos beta LactamRESUMO
In 2014, Brazil detected New Delhi metallo-ß-lactamase (NDM)-producing Enterobacterales from a Providencia rettgeri isolate obtained through surveillance swabs in the Southern region. Subsequently, various species have reported several NDM enzymes. However, comprehensive data on the current epidemiology of NDM-producing P. rettgeri in Brazil remains limited. This study, aimed to provide a detailed characterization of the phenotypic, genotypic, and epidemiological profile of clinical isolates of P. rettgeri NDM. From April 2020 to December 2022, 18 carbapenem-resistant P. rettgeri strains, previously identified using Vitek2®, were isolated at the University Hospital of Londrina. Resistance and virulence genes were assessed through genetic analysis using ERIC PCR and NextSeq (Illumina) sequencing. Statistical analysis was conducted using SPSS version 2.0. Genomic analysis confirmed the presence of ß-lactamase blaNDM-1 and blaOXA-1. All isolates showed the presence of the NDM encoding gene and genetic similarity above 90% between isolates. Clinical parameters of patients infected with P. rettgeri exhibited significant association with mechanical ventilation, prior use of carbapenems, and polymyxins. We also report a significant association between P. rettgeri infection and death outcome. This study characterizes NDM-1 metallo-ß-lactmases isolates, among P. rettgeri isolates from patients at the University Hospital (HU), during the COVID-19 pandemic. The emergence of this novel resistance mechanism among P. rettgeri poses a significant challenge, limiting the therapeutic options for infections in our hospital.
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Β-lactamases-producing Escherichia coli are a widely distributed source of antimicrobial resistance (AMR), for animals and humans. Little is known about the sensitivity profile and genetic characteristics of E. coli strains isolated from domestic cats. We report a cross-sectional study that evaluated E. coli strains isolated from domestic cats in Panama. For this study the following antibiotics were analyzed: ampicillin, amoxicillin-clavulanate cefepime, cefotaxime, cefoxitin, ceftazidime, aztreonam, imipenem, gentamicin, kanamycin, streptomycin, tetracycline, ciprofloxacin, nalidixic acid, trimethoprim-sulfamethoxazole, and chloramphenicol. The data obtained were classified as resistant, intermediate, or sensitive. MDR strains were established when the strain presented resistance to at least one antibiotic from three or more antimicrobial classes. Forty-eight E. coli isolates were obtained, of which 80% presented resistance to at least one of the antibiotics analyzed, while only 20% were sensitive to all (p = 0.0001). The most common resistance was to gentamicin (58%). Twenty-nine percent were identified as multidrug-resistant isolates and 4% with extended spectrum beta-lactamase phenotype. The genes blaTEM (39%), blaMOX(16%), blaACC (16%) and blaEBC (8%) were detected. Plasmid-mediated resistance qnrB (25%) and qnrA (13%) are reported. The most frequent sequence types (STs) being ST399 and we reported 5 new STs. Our results suggest that in intestinal strains of E. coli isolated from domestic cats there is a high frequency of AMR.
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Antibacterianos , Farmacorresistência Bacteriana Múltipla , Escherichia coli , Testes de Sensibilidade Microbiana , Animais , Gatos/microbiologia , Escherichia coli/genética , Escherichia coli/efeitos dos fármacos , Escherichia coli/isolamento & purificação , Farmacorresistência Bacteriana Múltipla/genética , Antibacterianos/farmacologia , Fenótipo , beta-Lactamases/genética , Estudos Transversais , Infecções por Escherichia coli/microbiologia , Infecções por Escherichia coli/veterinária , Variação GenéticaRESUMO
The use, misuse, and overuse of antimicrobials is one of the main public health threats of the 21st century. We investigated the risk factor of the presence of extended-spectrum, cephalosporin-resistant Enterobacterales in feces of non-domestic and domestic birds and other domestic animals in Piauí State, northeast Brazil. We collected a total of 387 cloacal and rectal swab samples of free-living birds, domestic birds, and domestic mammals in five municipalities: Amarante, Água Branca, Lagoa Alegre, Parnaíba, and Teresina. A total of 59/387 (15.2%) of these samples harbored extended spectrum beta-lactamase (ESBL)-producing Enterobacterales. Using the MALDI-TOF technique, we identified fifty-seven samples as Escherichia coli and two samples as Klebsiella pneumoniae. Teresina and Parnaíba had the highest prevalence of animals with resistant bacteria (32.1% and 27.1%, respectively) and highest exposure risk factor (OR of 16.06 and 8.58, respectively, and p < 0.001 for all). Multidrug-resistant, ESBL-producing Enterobacterales were observed in 72.8% of the samples (43/59). For the free-living birds, the positive samples belonged to a great kiskadee (Pitangus sulphuratus) and a semipalmated sandpiper (Calidris pusilla) in migratory and resident species, respectively. For domestic animals, the swine samples showed the highest prevalence of antimicrobial resistance. The lack of access to veterinary care and information regarding antimicrobial therapy, along with the easy access to antimicrobials without medical prescription, favors the inadequate use of antimicrobials in Piauí.
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Over the last decade, New Delhi metallo-beta-lactamase (NDM) carbapenemase has silently spread in Brazil. In this study, we analyzed a large collection of Enterobacterales other than Klebsiella spp. received in our reference laboratory between 2013 and 2022. A total of 32 clinical isolates displaying different pulsed-field gel electrophoresis profiles, and represented by 11 species in the families Enterobacteriaceae (Citrobacter freundii, Citrobacter portucalensis, Enterobacter hormaechei, and Escherichia coli), Morganellaceae (Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, Providencia stuartii, and Raoultella ornithinolytica), and Yersiniaceae (Serratia marcescens) had their whole genomes sequenced and further analyzed. Antimicrobial susceptibility was determined by disk diffusion, except for polymyxin B, assessed by broth microdilution. The blaNDM-1 allele was predominant (n = 29), but blaNDM-5 was identified in an E. coli specimen with a novel ST, and the blaNDM-7 allele was found in E. hormaechei ST45 and E. coli ST1049. Polymyxin was active against all but one Enterobacteriaceae isolate: an mcr-1-producing E. coli presenting minimal inhibitory concentration (4 mg/L). Isolates producing extended-spectrum ß-lactamases were common: cefotaximase from Munich (CTX-M)-15 (n = 10), CTX-M-2 (n = 4), and CTX-M-8 (n = 3) were detected, and the mcr-1-producing E. coli was found to co-produce both CTX-M-8 and CTX-M-55 ß-lactamases. The mcr-9 gene was found in 5/8 E. hormaechei isolates, distributed in four different sequence types, all of them presenting susceptibility to polymyxin. This study showed that NDM-producing Enterobacterales other than Klebsiella are already spread in Brazil, in diversified species, and cocarrying important resistance genes. Prompt detection and effective implementation of measures to prevent further spread are mandatory for mitigating the dissemination of NDM carbapenemase in hospital settings and preserving the already limited antimicrobial therapy options.
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Infecções por Enterobacteriaceae , Escherichia coli , Humanos , Klebsiella/genética , Brasil/epidemiologia , Antibacterianos/farmacologia , beta-Lactamases/genética , Infecções por Enterobacteriaceae/epidemiologia , Genômica , Testes de Sensibilidade Microbiana , Polimixinas/farmacologiaRESUMO
Acinetobacter pittii 978-A_19 was obtained from a parrot with pneumonia. It is resistant to ampicillin, carbenicillin, cephalosporins, clindamycin, and trimethoprim + sulfamethoxazole. The genome encodes a new blaADC allele, a blaOXA-502 gene, possesses several virulence genes related to adherence and biofilm formation, and has types I, II, and IV secretion systems.
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Enterobacterales of clinical importance for humans and domestic animals are now commonly detected among wildlife worldwide. However, few studies have investigated their prevalence among bats, particularly in bat species living near humans. In this study, we assessed the occurrence of Extended-spectrum beta-lactamase-producing (ESBL) and carbapenemase-resistant (CR) Enterobacterales in rectal swabs of bats submitted to the Chilean national rabies surveillance program from 2021 to 2022. From the 307 swabs screened, 47 (15%) harboured cefotaxime-resistant Enterobacterales. Bats carrying these bacteria originated from 9 out of the 14 Chilean regions. Most positive samples were obtained from Tadarida brasiliensis (n = 42), but also Lasiurus varius, L. cinereus and Histiotus macrotus. No Enterobacterales were resistant to imipenem. All ESBL-Enterobacterales were confirmed as Rahnella aquatilis by MALDI-TOF. No other ESBL or CR Enterobacterales were detected. To our knowledge, this is the first screening of antibiotic-resistant bacteria in wild bats of Chile, showing the bat faecal carriage of R. aquatilis naturally resistant to cephalosporins, but also including acquired resistance to important antibiotics for public health such as amoxicillin with clavulanic acid. Our results suggest unknown selective pressures on R. aquatilis, but low or no carriage of ESBL or CR Escherichia coli and Klebsiella spp. Future studies should assess the zoonotic and environmental implications of R. aquatilis, which are likely present in the guano left by bats roosting in human infrastructures.