Your browser doesn't support javascript.
loading
Show: 20 | 50 | 100
Results 1 - 20 de 946
Filter
1.
Comp Immunol Microbiol Infect Dis ; 113: 102234, 2024 Oct.
Article in English | MEDLINE | ID: mdl-39276760

ABSTRACT

The genus Citrobacter comprises clinically important human pathogens but has been less frequently associated with wildlife infections. Citrobacter pasteurii was first identified as causing human diarrhea and remains rarely documented. In this study, a Gram-negative bacterial strain, named A318, was identified as causing diarrhea in a black lion tamarin. This strain was biochemically identified as Trabulsiella guamensis, a species of unusual nature, and was submitted to whole-genome characterization. Curiously, phylogenomic analysis showed that A318 strain belonged to the genus Citrobacter, with confirmation of the species C. pasteurii by average nucleotide identity (99.02 %) and digital DNA-DNA hybridization (93.80 %) analyzes. Cases of misidentification of C. pasteurii as Citrobacter youngae were detected and corrected in this study. In addition to the genome sequence of the type strain of C. pasteurii, only two others from the Australian cockle and Portuguese silver gull are publicly available. Single nucleotide polymorphism differences among all C. pasteurii indicated a highly diverse population. No acquired antimicrobial resistance genes and plasmid replicons were found. Therefore, our findings emphasize the importance of gold-standard methods for accurate identification and underscores the importance of continued surveillance and research to mitigate the risks posed by zoonotic and zooanthroponotic pathogens.


Subject(s)
Citrobacter , Genome, Bacterial , Phylogeny , Animals , Citrobacter/genetics , Citrobacter/isolation & purification , Citrobacter/classification , Brazil , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/veterinary , Endangered Species , Diarrhea/microbiology , Diarrhea/veterinary , Whole Genome Sequencing , Polymorphism, Single Nucleotide
2.
J Appl Microbiol ; 135(8)2024 Aug 05.
Article in English | MEDLINE | ID: mdl-39143035

ABSTRACT

AIMS: This study aimed to investigate the presence of beta-lactams resistance genes and the clonal relationship of clinical isolates of Enterobacterales obtained from patients with and without COVID-19, in a hospital in northeastern Brazil. METHODS AND RESULTS: The study analyzed 45 carbapenem-resistant clinical isolates using enterobacterial repetitive intergenic consensus (ERIC-PCR), PCR, and amplicon sequencing to detect resistance genes (blaKPC, blaGES, blaNDM, blaVIM, and blaIMP). The main species were Klebsiella pneumoniae, Serratia marcescens, and Proteus mirabilis. Detected genes included blaNDM (46.66%), blaKPC (35.55%), and both (17.79%). ERIC-PCR showed multiclonal dissemination and high genetic variability. The main resistance gene was blaNDM, including blaNDM-5 and blaNDM-7. CONCLUSIONS: The presence of Enterobacterales carrying blaKPC and blaNDM in this study, particularly K. pneumoniae, in infections and colonizations of patients with COVID-19 and non-COVID-19, highlights genetic variability and resistance to carbapenems observed in multiple species of this order.


Subject(s)
COVID-19 , Enterobacteriaceae Infections , SARS-CoV-2 , beta-Lactamases , Humans , COVID-19/microbiology , Brazil , beta-Lactamases/genetics , SARS-CoV-2/genetics , Enterobacteriaceae Infections/microbiology , Genetic Variation , Anti-Bacterial Agents/pharmacology , Microbial Sensitivity Tests , Enterobacteriaceae/genetics , Enterobacteriaceae/drug effects , Enterobacteriaceae/isolation & purification , Carbapenems/pharmacology , Hospitals , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Klebsiella pneumoniae/drug effects
3.
Microb Pathog ; 193: 106778, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38972366

ABSTRACT

Antimicrobial resistance and biofilm formation by microbial pathogens pose a significant challenge to poultry production systems due to the persistent risk of dissemination and compromise of bird health and productivity. In this context, the study aimed to investigate the occurrence of different multiresistance phenotypes and the biofilm-forming ability of Enterobacteriaceae isolated from broiler chicken excreta in poultry production units in Ceará, Brazil. Samples were collected from three distinct broiler breeding facilities and subjected to isolation, identification, antibiotic susceptibility testing, phenotypic screening for ß-lactamases enzymes, and biofilm formation evaluation. Seventy-one strains were identified, being Escherichia coli (37 %) and Proteus mirabilis (32 %), followed by Klebsiella pneumoniae (11 %), Providencia stuartii (9 %), Klebsiella aerogenes (6 %), Alcaligenes faecalis (4 %), and Salmonella sp. (1 %). A significant proportion (87 %) of multiresistant strains were detected. For the phenotypic evaluation of ß-lactamases production, strains with resistance to second and third-generation cephalosporins and carbapenems were tested. About 4 of 6 and 10 of 26 were positive for inducible chromosomal AmpC ß-lactamase and extended-spectrum ß-lactamase (ESBL), respectively. Regarding biofilm formation, it was observed that all MDR strains were capable of forming biofilm. In this sense the potential of these MDR bacteria to develop biofilms becomes a significant concern, representing a real threat to both human and animal health, as biofilms offer stability, antimicrobial protection, and facilitate genetic transfer.


Subject(s)
Anti-Bacterial Agents , Biofilms , Chickens , Drug Resistance, Multiple, Bacterial , Enterobacteriaceae , Farms , Feces , Microbial Sensitivity Tests , beta-Lactamases , Animals , Biofilms/growth & development , Biofilms/drug effects , Brazil , beta-Lactamases/genetics , beta-Lactamases/metabolism , Feces/microbiology , Enterobacteriaceae/drug effects , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/genetics , Anti-Bacterial Agents/pharmacology , Chickens/microbiology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Poultry/microbiology , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/veterinary
4.
Eur J Clin Microbiol Infect Dis ; 43(9): 1741-1751, 2024 Sep.
Article in English | MEDLINE | ID: mdl-38958809

ABSTRACT

PURPOSE: Data on short courses of antibiotic therapy for Enterobacterales bacteremia in high-risk neutropenic patients are limited. The aim of the study was to describe and compare the frequency of bacteremia relapse, 30-day overall and infection-related mortality, Clostridiodes difficile infection and length of hospital stay since bacteremia among those who received antibiotic therapy for 7 or 14 days. METHODS: This is a multicenter, prospective, observational cohort study in adult high-risk neutropenic patients with hematologic malignancies or hematopoietic stem cell transplant and monomicrobial Enterobacterales bacteremia. They received appropriate empirical antibiotic therapy, had a clinical response within 7 days, and infection source control. Clinical, epidemiological and outcomes variables were compared based on 7 or 14 days of AT. RESULTS: Two hundred patients were included (100, 7-day antibiotic therapy; 100, 14-day antibiotic therapy). Escherichia coli was the pathogen most frequently isolated (47.5%), followed by Klebsiella sp. (40.5%). Among those patients that received 7-day vs. 14-day antibiotic course, a clinical source of bacteremia was found in 54% vs. 57% (p = 0.66), multidrug-resistant Enterobacterales isolates in 28% vs. 30% (p = 0.75), and 40% vs. 47% (p = 0.31) received combined empirical antibiotic therapy. Overall mortality was 3% vs. 1% (p = 0.62), in no case related to infection; bacteremia relapse was 7% vs. 2% (p = 0.17), and length of hospital stay since bacteremia had a median of 9 days (IQR: 7-15) vs. 14 days (IQR: 13-22) (p = < 0.001). CONCLUSIONS: These data suggest that seven-day antibiotic therapy might be adequate for patients with high-risk neutropenia and Enterobacterales bacteremia, who receive appropriate empirical therapy, with clinical response and infection source control.


Subject(s)
Anti-Bacterial Agents , Bacteremia , Enterobacteriaceae Infections , Neutropenia , Humans , Bacteremia/drug therapy , Bacteremia/microbiology , Bacteremia/mortality , Anti-Bacterial Agents/therapeutic use , Anti-Bacterial Agents/administration & dosage , Male , Female , Middle Aged , Prospective Studies , Neutropenia/complications , Enterobacteriaceae Infections/drug therapy , Enterobacteriaceae Infections/mortality , Enterobacteriaceae Infections/microbiology , Adult , Aged , Enterobacteriaceae/drug effects , Treatment Outcome , Length of Stay , Hematologic Neoplasms/complications , Young Adult
6.
Genes (Basel) ; 15(6)2024 Jun 20.
Article in English | MEDLINE | ID: mdl-38927749

ABSTRACT

BACKGROUND: Currently, the Enterobacteriaceae species are responsible for a variety of serious infections and are already considered a global public health problem, especially in underdeveloped countries, where surveillance and monitoring programs are still scarce and limited. Analyses were performed on the complete genome of an extensively antibiotic-resistant strain of Enterobater hormaechei, which was isolated from a patient with non-Hodgkin's lymphoma, who had been admitted to a hospital in the city of Manaus, Brazil. METHODS: Phenotypical identification and susceptibility tests were performed in automated equipment. Total DNA extraction was performed using the PureLink genomic DNA mini-Kit. The genomic DNA library was prepared with Illumina Microbial Amplicon Prep and sequenced in the MiSeq Illumina Platform. The assembly of the whole-genome and individual analyses of specific resistance genes extracted were carried out using online tools and the Geneious Prime software. RESULTS: The analyses identified an extensively resistant ST90 clone of E. hormaechei carrying different genes, including blaCTX-M-15, blaGES-2, blaTEM-1A, blaACT-15, blaOXA-1 and blaNDM-1, [aac(3)-IIa, aac(6')-Ian, ant(2″)-Ia], [aac(6')-Ib-cr, (qnrB1)], dfrA25, sul1 and sul2, catB3, fosA, and qnrB, in addition to resistance to chlorhexidine, which is widely used in patient antisepsis. CONCLUSIONS: These findings highlight the need for actions to control and monitor these pathogens in the hospital environment.


Subject(s)
Drug Resistance, Multiple, Bacterial , Enterobacter , Genome, Bacterial , Lymphoma, Non-Hodgkin , Whole Genome Sequencing , Humans , Enterobacter/genetics , Enterobacter/drug effects , Enterobacter/isolation & purification , Lymphoma, Non-Hodgkin/genetics , Lymphoma, Non-Hodgkin/microbiology , Lymphoma, Non-Hodgkin/drug therapy , Drug Resistance, Multiple, Bacterial/genetics , Whole Genome Sequencing/methods , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/drug therapy , Enterobacteriaceae Infections/genetics , Microbial Sensitivity Tests , Brazil
7.
Eur J Clin Microbiol Infect Dis ; 43(7): 1407-1417, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38733425

ABSTRACT

PURPOSE: To evaluate the performance of the rapid colorimetric polymyxin B microelution (RCPEm) in determining polymyxin B resistance directly from Enterobacterales-positive blood cultures. METHODS: A set volume of positive blood culture bottles (diluted 1:10) was inoculated into a glucose-broth-phenol red solution (NP solution), where a polymyxin B disk was previously eluted (final concentration of 3 µg/mL). Test was read each 1 h for up to 4 h. Color change from red/orange to yellow indicated resistant isolates. Results were compared to the reference method, broth microdilution (BMD), performed from colonies grown on solid media from the same blood culture bottle. RESULTS: One hundred fifty-two Enterobacterales-positive blood cultures were evaluated, 22.4% (34/152) of them resistant to polymyxin B (including 6.6% with borderline MICs). When performing directly from positive blood cultures (RCPEm-BC), specificity and sensitivity were 99.1% and 94.1%, respectively. Of note, 79.4% (27/34) of truly resistant isolates required 3 h of incubation, compared to the 18 ± 2 h incubation that microtiter plates of BMD demand before reading can be performed. CONCLUSIONS: RCPEm directly from blood cultures has great potential to be part of the routine of clinical microbiology laboratories to establish polymyxin B susceptibility, impacting outcome of patients with bloodstream infections caused by carbapenem-resistant Enterobacterales.


Subject(s)
Anti-Bacterial Agents , Blood Culture , Colorimetry , Microbial Sensitivity Tests , Polymyxin B , Polymyxin B/pharmacology , Humans , Colorimetry/methods , Microbial Sensitivity Tests/methods , Anti-Bacterial Agents/pharmacology , Blood Culture/methods , Enterobacteriaceae/drug effects , Enterobacteriaceae/isolation & purification , Sensitivity and Specificity , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/diagnosis , Drug Resistance, Bacterial , Bacteremia/microbiology , Bacteremia/diagnosis
8.
Virology ; 595: 110100, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38714025

ABSTRACT

Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.


Subject(s)
Bacteriophages , Enterobacter cloacae , Genome, Viral , Genomics , Host Specificity , Enterobacter cloacae/virology , Enterobacter cloacae/genetics , Bacteriophages/genetics , Bacteriophages/physiology , Bacteriophages/classification , Bacteriophages/isolation & purification , Phage Therapy , Enterobacteriaceae Infections/microbiology , Bacteriolysis
9.
BMC Vet Res ; 20(1): 174, 2024 May 03.
Article in English | MEDLINE | ID: mdl-38702700

ABSTRACT

Antimicrobial resistance is considered one of the most critical threat for both human and animal health. Recently, reports of infection or colonization by carbapenemase-producing Enterobacterales in companion animals had been described. This study report the first molecular characterization of NDM-producing Enterobacterales causing infections in companion animals from Argentina. Nineteen out of 3662 Enterobacterales isolates analyzed between October 2021 and July 2022 were resistant to carbapenemes by VITEK2C and disk diffusion method, and suspected to be carbapenemase-producers. Ten isolates were recovered from canine and nine from feline animals. Isolates were identified as K. pneumoniae (n = 9), E. coli (n = 6) and E. cloacae complex (n = 4), and all of them presented positive synergy among EDTA and carbapenems disks, mCIM/eCIM indicative of metallo-carbapenemase production and were also positive by PCR for blaNDM gene. NDM variants were determined by Sanger sequencing method. All 19 isolates were resistant to ß-lactams and aminoglycosides but remained susceptible to colistin (100%), tigecycline (95%), fosfomycin (84%), nitrofurantoin (63%), minocycline (58%), chloramphenicol (42%), doxycycline (21%), enrofloxacin (5%), ciprofloxacin (5%) and trimethoprim/sulfamethoxazole (5%). Almost all isolates (17/19) co-harbored blaCTX-M plus blaCMY, one harbored blaCTX-M alone and the remaining blaCMY. E. coli and E. cloacae complex isolates harbored blaCTX-M-1/15 or blaCTX-M-2 groups, while all K. pneumoniae harbored only blaCTX-M-1/15 genes. All E. coli and E. cloacae complex isolates harbored blaNDM-1, while in K. pneumoniae blaNDM-1 (n = 6), blaNDM-5 (n = 2), and blaNDM-1 plus blaNDM-5 (n = 1) were confirmed. MLST analysis revealed the following sequence types by species, K. pneumoniae: ST15 (n = 5), ST273 (n = 2), ST11, and ST29; E. coli: ST162 (n = 3), ST457, ST224, and ST1196; E. cloacae complex: ST171, ST286, ST544 and ST61. To the best of our knowledge, this is the first description of NDM-producing E. cloacae complex isolates recovered from cats. Even though different species and clones were observed, it is remarkable the finding of some major clones among K. pneumoniae and E. coli, as well as the circulation of NDM as the main carbapenemase. Surveillance in companion pets is needed to detect the spread of carbapenem-resistant Enterobacterales and to alert about the dissemination of these pathogens among pets and humans.


Subject(s)
Anti-Bacterial Agents , Cat Diseases , Dog Diseases , Enterobacteriaceae Infections , beta-Lactamases , Animals , Cats , Dogs , Cat Diseases/microbiology , Cat Diseases/epidemiology , beta-Lactamases/genetics , Argentina/epidemiology , Enterobacteriaceae Infections/veterinary , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/epidemiology , Anti-Bacterial Agents/pharmacology , Dog Diseases/microbiology , Dog Diseases/epidemiology , Microbial Sensitivity Tests , Pets , Enterobacteriaceae/drug effects , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/genetics , Enterobacteriaceae/enzymology , Escherichia coli/drug effects , Escherichia coli/genetics , Klebsiella pneumoniae/drug effects , Klebsiella pneumoniae/genetics , Klebsiella pneumoniae/isolation & purification , Klebsiella pneumoniae/enzymology
10.
Microbiology (Reading) ; 170(4)2024 Apr.
Article in English | MEDLINE | ID: mdl-38661713

ABSTRACT

Introduction. Leclercia adecarboxylata is a member of Enterobacterales, often considered an opportunistic pathogen. Recent reports have highlighted L. adecarboxylata as an emerging pathogen harbouring virulence and resistance determinants.Gap statement. Little information exists on virulence and resistance determinants in L. adecarboxylata strains isolated from environmental, food, and clinical samples.Aim. To determine the presence of resistance and virulence determinants and plasmid features in L. adecarboxylata strains isolated from environmental, food, and clinical samples, as well as their phylogenetic relationship.Results. All strains tested showed resistance to ß-lactams and quinolones but were sensitive to aminoglycosides and nitrofurans. However, even though fosfomycin resistance is considered a characteristic trait of L. adecarboxylata, the resistance phenotype was only observed in 50 % of the strains; bla TEM was the most prevalent BLEE gene (70 %), while the quinolone qnrB gene was observed in 60 % of the strains. Virulence genes were differentially observed in the strains, with adhesion-related genes being the most abundant, followed by toxin genes. Finally, all strains carried one to seven plasmid bands ranging from 7 to 125 kbps and harboured several plasmid addiction systems, such as ParDE, VagCD, and CcdAB in 80 % of the strains.Conclusions. L. adecarboxylata is an important emerging pathogen that may harbour resistance and virulence genes. Additionally, it has mobilizable genetic elements that may contribute to the dissemination of genetic determinants to other bacterial genera.


Subject(s)
Anti-Bacterial Agents , Enterobacteriaceae , Microbial Sensitivity Tests , Phylogeny , Plasmids , Virulence Factors , Anti-Bacterial Agents/pharmacology , Plasmids/genetics , Virulence/genetics , Enterobacteriaceae/genetics , Enterobacteriaceae/drug effects , Enterobacteriaceae/pathogenicity , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/classification , Virulence Factors/genetics , Humans , Enterobacteriaceae Infections/microbiology , Phenotype , Drug Resistance, Bacterial/genetics , Quinolones/pharmacology , beta-Lactams/pharmacology , Drug Resistance, Multiple, Bacterial/genetics , Food Microbiology
11.
Infect Genet Evol ; 121: 105596, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38643959

ABSTRACT

Foodstuffs are a well-documented source of multidrug-resistant bacteria, and hospitalized patients are usually susceptible to hospital infections owing to their immune status. Therefore, this study aimed to investigate the presence of beta-lactamase-producing Enterobacterales in ready-to-eat foods consumed by hospitalized patients. For this purpose, 51 vegetable and meat samples were collected over 2 months and analyzed. Enterobacterales isolates were identified and subjected to antimicrobial susceptibility testing, followed by beta-lactamase gene screening, pH tolerance assays, and whole-genome sequencing (WGS). Isolates harboring genes encoding extended-spectrum beta-lactamases, cephalosporinases, or carbapenemases were detected, and all isolates tolerated pH levels similar to those in the human gastrointestinal tract. The blaKPC-2 carriers were characterized by WGS and lineages closely related to those causing human infections were identified. These results showed that dietary intake is an alternative route for the transmission of antimicrobial-resistant bacteria, which must be considered when designing effective strategies for infection control.


Subject(s)
Food Microbiology , beta-Lactamases , beta-Lactamases/genetics , beta-Lactamases/metabolism , Humans , Enterobacteriaceae/genetics , Enterobacteriaceae/drug effects , Whole Genome Sequencing , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , Microbial Sensitivity Tests , Enterobacteriaceae Infections/microbiology , Fast Foods/microbiology , Meat/microbiology , Phylogeny
12.
Prev Vet Med ; 227: 106205, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38678816

ABSTRACT

Mastitis is the most common disease of dairy cattle and can be manifested in clinical and subclinical forms. The overuse of antimicrobials in the treatment and prevention of mastitis favours antimicrobial resistance and milk can be a potential route of dissemination. This study aimed to evaluate the biological quality of bulk tank milk (BTM) and the microbiological quality and signs of mastitis of freshly milked raw milk. In addition, to evaluate antimicrobial resistance in Enterobacteriaceae and Staphylococcus spp. isolated from freshly milked raw milk. None of the farms were within the official Brazilian biological quality limits for BTM. Freshly milked raw milk with signs of clinical (CMM), subclinical (SCMM) and no signs (MFM) of mastitis were detected in 6.67%, 27.62% and 65.71% samples, respectively. Most samples of freshly milked raw milk showed acceptable microbiological quality, when evaluating the indicators total coliforms (78.10%), Escherichia coli (88.57%) and Staphylococcus aureus (100%). Klebsiella oxytoca and S. aureus were the most prevalent microorganisms in SCMM and MFM samples. Antimicrobial resistance and multidrug resistance (MDR) were observed in 65.12% and 13.95% of Enterobacteriaceae and 84.31% and 5.88% of Staphylococcus spp., respectively, isolated from both SCMM and MFM samples. Enterobacteriaceae resistant to third-generation cephalosporin (3GCR) (6.98%) and carbapenems (CRE) (6.98%) and methicillin-resistant S. aureus (MRSA) (4.88%) were observed. Antimicrobial-resistant bacteria can spread resistance genes to previously susceptible bacteria. This is a problem that affects animal, human and environmental health and should be evaluated within the one-health concept.


Subject(s)
Anti-Bacterial Agents , Drug Resistance, Bacterial , Enterobacteriaceae , Mastitis, Bovine , Milk , Staphylococcus , Animals , Cattle , Milk/microbiology , Mastitis, Bovine/microbiology , Enterobacteriaceae/drug effects , Enterobacteriaceae/isolation & purification , Female , Staphylococcus/drug effects , Brazil , Anti-Bacterial Agents/pharmacology , Enterobacteriaceae Infections/veterinary , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/drug therapy , Staphylococcal Infections/veterinary , Staphylococcal Infections/microbiology , Staphylococcal Infections/drug therapy , Asymptomatic Infections , Microbial Sensitivity Tests/veterinary
14.
Lett Appl Microbiol ; 77(2)2024 Feb 01.
Article in English | MEDLINE | ID: mdl-38327245

ABSTRACT

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.


Subject(s)
Citrobacter freundii , Enterobacteriaceae Infections , Humans , Citrobacter freundii/genetics , beta-Lactamases/genetics , Multilocus Sequence Typing , Phylogeny , Enterobacteriaceae Infections/epidemiology , Anti-Bacterial Agents/pharmacology , Genomics , Microbial Sensitivity Tests
15.
Arch Pathol Lab Med ; 148(10): 1145-1151, 2024 Oct 01.
Article in English | MEDLINE | ID: mdl-38197133

ABSTRACT

CONTEXT.­: Carbapenem-resistant Enterobacterales are disseminated worldwide and associated with infections with high rates of morbidity and mortality. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is a useful tool for identification of pathogens directly from blood cultures in clinical microbiology laboratories. Furthermore, it has been applied for the detection of carbapenemase production, by evaluating carbapenem hydrolysis. OBJECTIVE.­: To determine meropenem hydrolysis to detect carbapenemase production directly from positive blood cultures, using logRQ to establish a quantitative measure of hydrolysis. DESIGN.­: We evaluated 100 Enterobacterales from positive blood cultures, with 81 carrying a carbapenemase gene (blaKPC, blaGES, blaNDM-1, blaIMP, blaVIM, and blaOXA-48-like), as determined by real-time multiplex polymerase chain reaction with high-resolution melting (HRM-qPCR). Bacterial proteins extracted from positive blood culture bottles were incubated in a meropenem solution (2-4 hours) followed by centrifugation for MALDI-TOF MS analysis. The intensity of peaks of the hydrolyzed and nonhydrolyzed forms were used to calculate the logRQ value. RESULTS.­: Overall, sensitivity was 86.8% and specificity, 89.5%. Of note, sensitivity varied depending on enzyme type. For blaKPC-positive isolates, sensitivity was 97.9%, while it reduced significantly for blaNDM-1 and blaOXA-48-like isolates: 62.5% (10 of 16) and 66.7% (6 of 9), respectively. Indeed, logRQ was higher in blaKPC-positive isolates (0.37-1.97) than in blaNDM-1 (-1.37 to 0.83) and blaOXA-48-like isolates (-1.08 to 1.79). CONCLUSIONS.­: This is an inexpensive and rapid test to identify carbapenemase activity directly from blood culture bottles, which contributes to early adequate antimicrobial therapy and implementation of infection control measures.


Subject(s)
Anti-Bacterial Agents , Bacterial Proteins , Blood Culture , Carbapenems , Meropenem , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , beta-Lactamases , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , Humans , Blood Culture/methods , Bacterial Proteins/genetics , Bacterial Proteins/metabolism , beta-Lactamases/genetics , beta-Lactamases/metabolism , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , Meropenem/pharmacology , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae Infections/diagnosis , Enterobacteriaceae Infections/drug therapy , Microbial Sensitivity Tests , Enterobacteriaceae/drug effects , Enterobacteriaceae/genetics , Enterobacteriaceae/isolation & purification , Carbapenem-Resistant Enterobacteriaceae/isolation & purification , Carbapenem-Resistant Enterobacteriaceae/drug effects , Carbapenem-Resistant Enterobacteriaceae/genetics , Hydrolysis , Sensitivity and Specificity
16.
Microbiol Immunol ; 68(1): 1-5, 2024 Jan.
Article in English | MEDLINE | ID: mdl-37859304

ABSTRACT

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.


Subject(s)
Enterobacteriaceae Infections , Escherichia coli , Humans , Klebsiella/genetics , Brazil/epidemiology , Anti-Bacterial Agents/pharmacology , beta-Lactamases/genetics , Enterobacteriaceae Infections/epidemiology , Genomics , Microbial Sensitivity Tests , Polymyxins/pharmacology
17.
Article in Spanish | LILACS, BNUY, UY-BNMED | ID: biblio-1556817

ABSTRACT

Introducción: La diarrea con sangre es un motivo frecuente de admisión hospitalaria en niños, con gastroenteritis aguda; en la mayoría de los casos se tratan de infecciones leves y autolimitadas, pero pueden producirse complicaciones graves. Objetivos: Describir la etiología y características clínico- evolutivas de los niños menores de 15 años hospitalizados por diarrea con sangre en el Hospital Pediátrico, Centro Hospitalario Pereira Rossell entre los años 2012- 2023. Materiales y métodos: Estudio retrospectivo mediante revisión de historias y registros de laboratorio. Variables: demográficas, estado nutricional, hidratación, motivos de hospitalización, ingreso unidades de cuidados intensivos (UCI), enteropatógenos, tratamientos, evolución. Resultados: Se incluyeron 229 niños, mediana de edad de 8 meses; sexo masculino 61%; eutróficos 88%, bien hidratados 55%, con comorbilidades 11%, prematurez 6,5%. El motivo de hospitalización fue diarrea con sangre/disentería sin otro síntoma 45%. Se solicitó coprovirológico/coprocultivo en 98% y detección por técnicas de ácidos nucleicos en materia fecal 5,2%. Se identificó al menos un agente patógeno en 34,3%: Shigella sp. 38%; Salmonella sp. 19,5%; coinfecciones en 12%. Se indicaron antibióticos a 86%; ceftriaxona 62%, azitromicina 35%. Ingresaron a UCI 6,5% (15), presentaron complicaciones 10/14, fallo renal agudo 5 y alteraciones del medio interno 3. La mayoría presentó buena evolución. Conclusiones: La diarrea con sangre/disentería continúa siendo una causa importante de hospitalización afectando en su mayoría a niños sanos menores de 5 años. Los patógenos detectados con mayor frecuencia fueron bacterias principalmente Shigella sp., Salmonella sp. y E coli diarreogénicas. Se reportó alta prescripción de antibióticos, cumpliendo en la mayoría de los casos con las recomendaciones.


Introduction: Bloody diarrhea is a common reason for hospital admission in children with acute gastroenteritis; In most cases these are mild and self-limiting infections, but serious complications can occur. Goals: To describe the etiology and clinical-evolutionary characteristics of children under 15 years of age hospitalized for bloody diarrhea at the Pediatric Hospital, Centro Hospitalario Pereira Rossell between the years 2012-2023. Materials and methods: Retrospective study through review of histories and laboratory records. Variables: demographics, nutritional status, hydration, reason for hospitalization, intensive care unit (ICU) admission, enteropathogens, treatments, evolution. Results: 229 children were included, median age 8 months; male sex 61%; eutrophic 88%, well hydrated 55%, with comorbidities 11%, prematurity 6.5%. The reason for hospitalization was bloody diarrhea/dysentery without other symptoms 45%. Coprovirological/coproculture was requested in 98% and detection by nucleic acid techniques in fecal matter was requested in 5,2%. At least one pathogenic agent was identified in 34,3%: Shigella sp. 38%; Salmonella sp 19,5%; coinfections in 12%. Antibiotics were indicated for 86%; ceftriaxone 62%, azithromycin 35%. Were admitted to the ICU 6,5% (15), 10/14 had complications, 5 had acute kidney failure and 3 had alterations in the internal environment. The majority had a good evolution. Conclusions: Bloody diarrhea/dysentery continues to be an important cause of hospitalization, affecting mostly healthy children under 5 years of age. The most frequently detected pathogens were bacteria, mainly Shigella sp., Salmonella sp. and diarrheagenic E coli. High prescription of antibiotics was reported, complying in most cases with the recommendations.


Introdução: A diarreia com sangue é um motivo comum de internação hospitalar em crianças com gastroenterite aguda; Na maioria dos casos, estas são infecções leves e autolimitadas, mas podem ocorrer complicações graves. Metas: Descrever a etiologia e as características clínico-evolutivas de crianças menores de 15 anos internadas por diarreia sanguinolenta no Hospital Pediátrico Centro Hospitalario Pereira Rossell entre os anos de 2012-2023. Materiais e métodos: Estudo retrospectivo por meio de revisão de histórias e registros laboratoriais. Variáveis: dados demográficos, estado nutricional, hidratação, motivo da internação, internação em unidade de terapia intensiva (UTI), enteropatógenos, tratamentos, evolução. Resultados: foram incluídas 229 crianças, mediana de idade 8 meses; sexo masculino 61%; eutrófico 88%, bem hidratado 55%, com comorbidades 11%, prematuridade 6,5%. O motivo da internação foi diarreia sanguinolenta/disenteria sem outros sintomas 45%. O estudo coprovirologico/coprocultivo foi solicitado em 98% e a detecção por técnicas de ácidos nucleicos em matéria fecal foi solicitada em 5,2%. Pelo menos um agente patogênico foi identificado em 34,3%: Shigella sp. 38%; Salmonella sp. 19,5%; coinfecções em 12%. Os antibióticos foram indicados para 86%; ceftriaxona 62%, azitromicina 35%. Foram internados em UTI 6,5% (15), 10/14 apresentaram complicações, 5 tiveram insuficiência renal aguda e 3 apresentaram alterações no meio interno, a maioria teve boa evolução. Conclusões: A diarreia/disenteria com sangue continua a ser uma causa importante de hospitalização, afetando sobretudo crianças saudáveis ​​com menos de 5 anos de idade. Os patógenos mais frequentemente detectados foram bactérias, principalmente Shigella sp., Salmonella sp. e E. coli diarreiogênica. Foi relatada elevada prescrição de antibióticos, cumprindo na maioria dos casos as recomendações.


Subject(s)
Humans , Male , Female , Infant, Newborn , Infant , Child, Preschool , Child , Adolescent , Rotavirus Infections/complications , Campylobacter Infections/complications , Diarrhea, Infantile/etiology , Diarrhea, Infantile/blood , Dysentery/etiology , Dysentery/blood , Enterobacteriaceae Infections/complications , Rotavirus Infections , Rotavirus Infections/drug therapy , Campylobacter Infections/diagnosis , Campylobacter Infections/drug therapy , Child, Hospitalized/statistics & numerical data , Retrospective Studies , Enterobacteriaceae Infections/diagnosis , Enterobacteriaceae Infections/drug therapy
18.
Rev. chil. infectol ; Rev. chil. infectol;40(6): 589-598, dic. 2023. tab, graf
Article in Spanish | LILACS | ID: biblio-1530002

ABSTRACT

INTRODUCCIÓN: Las bacteriemias por Enterobacterales productores de carbapenemasa KPC (EPC-KPC) presentan una mortalidad elevada y opciones terapéuticas limitadas. OBJETIVOS: Describir y comparar la evolución de los pacientes con bacteriemia por EPC-KPC tratados con ceftazidima/avibactam (CA) frente a otros antimicrobianos (OA). PACIENTES Y MÉTODOS: Estudio prospectivo y retrospectivo de casos y controles. Se incluyeron pacientes adultos con bacteriemia por EPC-KPC, con una proporción entre casos tratados con CA y controles tratados con OA. de 1:2. Se analizaron variables clínicas, epidemiológicas y de evolución. RESULTADOS: Se incluyeron 48 pacientes (16 CA y 32 OA). Los casos se encontraban más frecuentemente neutropénicos (50 vs.16%, p = 0,012); asimismo, presentaron medianas de score de APACHE II más altas y de score de Pitt más bajas. El 65% de la cohorte total presentó un foco clínico y Klebsiellapneumoniae fue el microorganismo más frecuentemente aislado. Los casos recibieron una mayor proporción de tratamiento antimicrobiano empírico adecuado (81 vs. 53%, p = 0,05). La antibioterapia dirigida en casos y controles fue combinada en 38 y 91%, p = 0,009. Los casos presentaron menor mortalidad al día 7 y al día 30 relacionada a infección (0 vs. 22%, p = 0,04 y 0 vs. 34%, p = 0,008). Solo los controles desarrollaron shock, ingresaron a la unidad de cuidados intensivos y presentaron bacteriemia de brecha. CONCLUSIÓN: CA mostró beneficio clínico frente a OA para el tratamiento de pacientes con bacteriemia por EPC-KPC.


BACKGROUND: KPC-producing Enterobacterales bacteremia (KPCCPE) is associated with a high mortality rate and limited therapeutic options. AIM: To describe and compare the outcome of patients with KPC-CPE bacteremia treated with ceftazidime/avibactam (CA) versus other antibiotics (OA). METHODS: Prospective and retrospective cases and control study performed in adult patients with KPC-CPE bacteremia, with a 1:2 ratio between cases treated with CA. and controls treated with OA. Clinical, epidemiological, and outcome variables were analyzed. RESULTS: Forty-eight patients (16 CA and 32 OA) were included. Cases were more frequently neutropenic (50 vs. 16%, p = 0.012), presented higher median APACHE II score and lower Pitt score. Of the total cohort, 65% had a clinical source, and Klebsiella pneumoniae was the most frequently isolated microorganism. Cases received more adequate empirical antibiotic treatment (81 vs. 53%, p = 0.05). Targeted antibiotic therapy in cases and controls was combined in 38 and 91%, p = 0.009. Cases had a lower 7-day mortality and 30-day infection-related mortality (0 vs. 22%, p = 0.04 and 0 vs. 34%, p = 0.008). Only controls developed shock, were admitted to the intensive care unit, and had breakthrough bacteremia. CONCLUSION: CA. showed clinical benefit over OA in the treatment of patients with EPC-KPC bacteremia.


Subject(s)
Humans , Male , Female , Adult , Middle Aged , Aged , Ceftazidime/therapeutic use , Bacteremia/drug therapy , Enterobacteriaceae Infections/drug therapy , Azabicyclo Compounds/therapeutic use , Anti-Bacterial Agents/therapeutic use , Bacterial Proteins , beta-Lactamases , Case-Control Studies , Ceftazidime/administration & dosage , Clinical Evolution , Prospective Studies , Bacteremia/microbiology , Bacteremia/mortality , Drug Combinations , Enterobacteriaceae/isolation & purification , Enterobacteriaceae/drug effects , Enterobacteriaceae Infections/mortality , Azabicyclo Compounds/administration & dosage , beta-Lactamase Inhibitors , Anti-Bacterial Agents/administration & dosage
19.
Am J Trop Med Hyg ; 109(2): 356-367, 2023 08 02.
Article in English | MEDLINE | ID: mdl-37339767

ABSTRACT

Cedecea lapagei is a gram-negative, non-encapsulated, facultative anaerobic bacterium that has been reported in only a few cases with varying clinical presentations, drug susceptibility, and treatment since its first isolation in 1981. This study aimed to describe a case report of C. lapagei in Peru and systematically review the documented case reports of individuals infected with C. lapagei. A 59-year-old man who had become bedridden with Parkinson's disease and had epilepsy presented with a 1-week history of fever and sore throat and was admitted. Physical examination revealed an obtundation state and abolished vesicular murmur in the right hemithorax. During hospitalization, the patient was diagnosed with various infections, including tuberculosis, for which he received broad-spectrum antibiotics. In the absence of clinical improvement, a urine culture was performed showing C. lapagei (detected by BD Phoenix M50 system, Vernon Hills, IL). The patient received amoxicillin/clavulanate and was discharged. Case reports of C. lapagei were also searched in five databases on January 28, 2023. Twenty cases of C. lapagei were reported worldwide between 2006 and 2022, 16 of which involved adults. Fever was the most common manifestation (75%), and pneumonia was the primary form of presentation (45%). Moreover, 90% of the patients had at least one comorbidity, and 15% died. Also, most of the isolates were sensitive to ciprofloxacin (81%), meropenem (62%), and amikacin (60%). Overall, C. lapagei should be suspected in compromised hosts, particularly those with pneumonia. Although the bacterium can affect various organs and the antibiotic susceptibility pattern is variable, quinolones, tetracyclines, and carbapenems seem to be the first therapeutic option.


Subject(s)
Enterobacteriaceae Infections , Male , Adult , Humans , Middle Aged , Enterobacteriaceae Infections/microbiology , Peru , Base Composition , Phylogeny , RNA, Ribosomal, 16S , Sequence Analysis, DNA , Anti-Bacterial Agents/therapeutic use
SELECTION OF CITATIONS
SEARCH DETAIL