RESUMEN
While conducting genomic surveillance of carbapenemase-producing Enterobacteriaceae (CPE) from patient colonisation and clinical infections at Birmingham's Queen Elizabeth Hospital (QE), we identified an N-type plasmid lineage, pQEB1, carrying several antibiotic resistance genes, including the carbapenemase gene bla KPC-2. The pQEB1 lineage is concerning due to its conferral of multidrug resistance, its host range and apparent transmissibility, and its potential for acquiring further resistance genes. Representatives of pQEB1 were found in three sequence types (STs) of Citrobacter freundii, two STs of Enterobacter cloacae, and three species of Klebsiella. Hosts of pQEB1 were isolated from 11 different patients who stayed in various wards throughout the hospital complex over a 13 month period from January 2023 to February 2024. At present, the only representatives of the pQEB1 lineage in GenBank were carried by an Enterobacter hormaechei isolated from a blood sample at the QE in 2016 and a Klebsiella pneumoniae isolated from a urine sample at University Hospitals Coventry and Warwickshire (UHCW) in May 2023. The UHCW patient had been treated at the QE. Long-read whole-genome sequencing was performed on Oxford Nanopore R10.4.1 flow cells, facilitating comparison of complete plasmid sequences. We identified structural variants of pQEB1 and defined the molecular events responsible for them. These have included IS26-mediated inversions and acquisitions of multiple insertion sequences and transposons, including carriers of mercury or arsenic resistance genes. We found that a particular inversion variant of pQEB1 was strongly associated with the QE Liver speciality after appearing in November 2023, but was found in different specialities and wards in January/February 2024. That variant has so far been seen in five different bacterial hosts from six patients, consistent with recent and ongoing inter-host and inter-patient transmission of pQEB1 in this hospital setting.
Asunto(s)
Brotes de Enfermedades , Plásmidos , beta-Lactamasas , Humanos , Plásmidos/genética , beta-Lactamasas/genética , Infecciones por Enterobacteriaceae/microbiología , Infecciones por Enterobacteriaceae/epidemiología , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Klebsiella pneumoniae/efectos de los fármacos , Proteínas Bacterianas/genética , Enterobacter cloacae/genética , Enterobacter cloacae/aislamiento & purificación , Enterobacter cloacae/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Infección Hospitalaria/microbiología , Antibacterianos/farmacología , Citrobacter freundii/genética , Citrobacter freundii/aislamiento & purificación , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Hospitales , EnterobacterRESUMEN
BACKGROUND: Antimicrobial resistance is a major global public health issue. Infections caused by resistant species are associated with higher mortality rates, longer hospital stays, medication failure, and rising medical costs. The World Health Organisation has declared multidrug resistance-associated infections as an epidemic of public health concern. OBJECTIVE: This study aimed to evaluate the antimicrobial resistance profile and associated factors of hospital-acquired Gram-negative bacterial pathogens among hospitalized patients in Northeast Ethiopia. MATERIALS AND METHODS: A health facility-based cross-sectional study was conducted among hospitalized patients from March 2021 to February 2022. About 810 clinical specimens were collected, transported, and processed from admitted patients following the standard bacteriological procedures. The clinical samples were inoculated onto blood agar, MacConkey agar, and chocolate agar. Furthermore, the species identification was done using gram reactions, colony morphology, and color and biochemical tests. Antimicrobial susceptibility tests, extended-spectrum beta-lactamase, and carbapenemase production were performed as per the clinical laboratory standard institute guidelines. For analysis, the information was entered into Epi-data and exported to SPSS. A P value of < 0.05 with a 95% confidence interval was considered as a statistically significant association. RESULTS: Out of 810 clinical specimens, 285/810 (35.2%) developed bacterial infections. From the isolated bacteria, E. coli was the predominant bacteria accounting for 78/285 (27.4%) followed by K. pneumoniae, 69/285(24.42%), whereas P. vulgaris accounted for the least, 7/285 (2.5%). Overall, 132/285 (46.3%) and 99/285 (34.7%) of culture-positive patients were infected by extended-spectrum beta-lactamase and carbapenemase-producing bacteria. The overall multidrug resistance rate of the isolated bacteria was 89.4%. The highest antibiotic resistance rates were detected for doxycycline (92.9%), amoxicillin-clavulanic acid (83.9%), and ampicillin (93%). The least antibiotic resistance rate was observed for meropenem at 41.1% and amikacin at 1.7%, respectively. CONCLUSIONS AND RECOMMENDATIONS: In the study area, significant health concerns include a range of hospital-acquired bacterial infections associated with elevated rates of multidrug resistance, Extended-spectrum beta-lactamase (ESBL), and carbapenemase-producing bacterial pathogens. Consequently, it is recommended to conduct drug-susceptibility testing of isolates and molecular detection at a national level to optimize antibiotic usage for treating prevalent bacterial infections in this area.
Asunto(s)
Antibacterianos , Infección Hospitalaria , Farmacorresistencia Bacteriana Múltiple , Bacterias Gramnegativas , Infecciones por Bacterias Gramnegativas , Pruebas de Sensibilidad Microbiana , Humanos , Etiopía/epidemiología , Estudios Transversales , Masculino , Femenino , Adulto , Persona de Mediana Edad , Antibacterianos/farmacología , Infección Hospitalaria/microbiología , Infección Hospitalaria/epidemiología , Bacterias Gramnegativas/efectos de los fármacos , Bacterias Gramnegativas/aislamiento & purificación , Bacterias Gramnegativas/clasificación , Bacterias Gramnegativas/genética , Adulto Joven , Adolescente , Infecciones por Bacterias Gramnegativas/microbiología , Infecciones por Bacterias Gramnegativas/epidemiología , Infecciones por Bacterias Gramnegativas/tratamiento farmacológico , Farmacorresistencia Bacteriana Múltiple/genética , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Anciano , Niño , Preescolar , Lactante , Hospitalización/estadística & datos numéricos , Proteínas Bacterianas/genética , Anciano de 80 o más AñosRESUMEN
There have been increasing reports of Klebsiella pneumoniae resistant to ß-lactam antibiotics. This study aimed to determine the prevalence of some selected carbapenemase genes among clinical isolates of Klebsiella pneumoniae recovered from patients attending a private tertiary hospital in Southwestern Nigeria. The study was conducted over two months (February-March 2024). A total of 50 clinical isolates of Klebsiella pneumoniae from different clinical specimens were obtained from the Medical Microbiology Department, Babcock University Teaching Hospital (BUTH). The clinical isolates were then characterized using standard microbiological procedures and were tested for susceptibility to meropenem and other classes of antibiotics according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Polymerase Chain Reaction (PCR) detection for OXA-48 and NDM-1 carbapenemase genes was performed on the 50 clinical isolates. PCR analysis showed that 9 (18%) clinical isolates were positive for the OXA-48 gene, 22 (44%) were positive for the NDM-1 gene, 4 (8%) possessed both the OXA-48 and NDM-1 genes, and 23 (46%) possessed neither the OXA-48 nor NDM-1 genes. Antibiotic Susceptibility Testing (AST) revealed that all the clinical isolates were resistant to meropenem. In conclusion, this study demonstrates the presence of OXA-48 and NDM-1 genes in clinical isolates of Klebsiella pneumoniae recovered from patients attending a private tertiary hospital in Southwestern Nigeria, highlighting the role of ESBL (extended-spectrum beta-lactamase) as a major resistance mechanism alongside other mechanisms. Population-based surveillance programs should be implemented to monitor the prevalence and epidemiology of Klebsiella pneumoniae infections at the community level, facilitating early detection of outbreaks and identification of emerging antimicrobial resistance patterns. CORE TIP: This study highlights the significant prevalence of NDM-1 and OXA-48 carbapenemase genes among Klebsiella pneumoniae clinical isolates in a private tertiary hospital in Southwestern Nigeria, with 44% and 18% of isolates harboring these genes, respectively. Notably, 46% of isolates were resistant to carbapenems despite lacking these genes, suggesting alternative resistance mechanisms. The findings underscore the urgent need for enhanced surveillance, infection control measures, and antibiotic stewardship programs to combat the spread of multidrug-resistant Klebsiella pneumoniae in healthcare settings.
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Antibacterianos , Proteínas Bacterianas , Infecciones por Klebsiella , Klebsiella pneumoniae , Pruebas de Sensibilidad Microbiana , Centros de Atención Terciaria , beta-Lactamasas , beta-Lactamasas/genética , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/enzimología , Humanos , Centros de Atención Terciaria/estadística & datos numéricos , Infecciones por Klebsiella/microbiología , Infecciones por Klebsiella/epidemiología , Nigeria/epidemiología , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Masculino , Femenino , Persona de Mediana Edad , Adulto , Anciano , Adulto JovenRESUMEN
BACKGROUND: Extended-spectrum ß-lactamase -producing Enterobacterales (ESBL-E) are important zoonotic pathogens that can cause serious clinical infections, also in horses. Preventing the spread of ESBL-E, especially in the equine hospital environment, is key to reducing the number of difficult-to-treat infections. Estimating the local prevalence of ESBL-E in horses is crucial to establish targeted infection control programs at equine hospitals. We conducted a prevalence and risk factor study in equine patients on admission to an equine teaching hospital in Finland through a rectal ESBL-E screening specimen of the horse and a questionnaire. RESULTS: The prevalence of ESBL-E in admitted horses was 3% (5/161, 95% CI 1-7%); none of the tested factors remained statistically significant in multivariate analysis, although antimicrobial treatment within three months was borderline significant (p = 0.052). Extended-spectrum ß-lactamase -producing Klebsiella pneumoniae ST6179:CTX-M-15 was detected in three horses using whole-genome sequencing, which in combination with patient records suggested nosocomial transmission. Escherichia coli isolates were ST1250:CTX-M-1 (n = 1), ST1079:CTX-M-1 (n = 1), and ST1245:CTX-M-14 (n = 1). Multiple virulence genes were detected in the ESBL-E isolates. In the ESBL-E positive horses enrolled in a one-year follow-up study, ESBL-E were unlikely to be isolated in rectal screening specimens after the initial positive specimen. CONCLUSIONS: The prevalence of ESBL-E in horses visiting a veterinary teaching hospital in Finland is low, indicating an overall low prevalence estimate in the country's equine population. No statistically significant risk factors were identified, likely due to the low number of cases. The duration of ESBL-E carriage is likely to be very short in horses.
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Infecciones por Enterobacteriaceae , Enfermedades de los Caballos , Hospitales Veterinarios , beta-Lactamasas , Animales , Caballos , Enfermedades de los Caballos/microbiología , Enfermedades de los Caballos/epidemiología , beta-Lactamasas/metabolismo , beta-Lactamasas/genética , Prevalencia , Factores de Riesgo , Finlandia/epidemiología , Infecciones por Enterobacteriaceae/veterinaria , Infecciones por Enterobacteriaceae/epidemiología , Infecciones por Enterobacteriaceae/microbiología , Masculino , Femenino , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/aislamiento & purificación , Infección Hospitalaria/epidemiología , Infección Hospitalaria/veterinaria , Infección Hospitalaria/microbiología , Escherichia coli/enzimología , Escherichia coli/aislamiento & purificación , Enterobacteriaceae/enzimología , Enterobacteriaceae/aislamiento & purificación , Enterobacteriaceae/efectos de los fármacos , Antibacterianos/farmacologíaRESUMEN
BACKGROUND: Environmental reservoirs of antibiotic resistance pose a threat to human and animal health. Aquatic biofilms impacted by wastewater effluent (WW) are known environmental reservoirs for antibiotic resistance; however, the relative importance of biotic factors and abiotic factors from WW on the abundance of antibiotic resistance genes (ARGs) within aquatic biofilms remains unclear. Additionally, experimental evidence is limited within complex aquatic microbial communities as to whether genes bearing low sequence similarity to validated reference ARGs are functional as ARGs. RESULTS: To disentangle the effects of abiotic and biotic factors on ARG abundances, natural biofilms were previously grown in flume systems with different proportions of stream water and either ultrafiltered or non-ultrafiltered WW. In this study, we conducted deep shotgun metagenomic sequencing of 75 biofilm, stream, and WW samples from these flume systems and compared the taxonomic and functional microbiome and resistome composition. Statistical analysis revealed an alignment of the resistome and microbiome composition and a significant association with experimental treatment. Several ARG classes exhibited an increase in normalized metagenomic abundances in biofilms grown with increasing percentages of non-ultrafiltered WW. In contrast, sulfonamide and extended-spectrum beta-lactamase ARGs showed greater abundances in biofilms grown in ultrafiltered WW compared to non-ultrafiltered WW. Overall, our results pointed toward the dominance of biotic factors over abiotic factors in determining ARG abundances in WW-impacted stream biofilms and suggested gene family-specific mechanisms for ARGs that exhibited divergent abundance patterns. To investigate one of these specific ARG families experimentally, we biochemically characterized a new beta-lactamase from the Planctomycetota (Phycisphaeraceae). This beta-lactamase displayed activity in the cleavage of cephalosporin analog despite sharing a low sequence identity with known ARGs. CONCLUSIONS: This discovery of a functional planctomycete beta-lactamase ARG is noteworthy, not only because it was the first beta-lactamase to be biochemically characterized from this phylum, but also because it was not detected by standard homology-based ARG tools. In summary, this study conducted a metagenomic analysis of the relative importance of biotic and abiotic factors in the context of WW discharge and their impact on both known and new ARGs in aquatic biofilms. Video Abstract.
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Biopelículas , Metagenómica , Ríos , Aguas Residuales , beta-Lactamasas , Biopelículas/efectos de los fármacos , Aguas Residuales/microbiología , beta-Lactamasas/genética , Ríos/microbiología , Microbiota/efectos de los fármacos , Bacterias/genética , Bacterias/clasificación , Bacterias/efectos de los fármacos , Bacterias/aislamiento & purificación , Antibacterianos/farmacología , Planctomycetales/genética , Planctomycetales/efectos de los fármacos , Metagenoma , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismoRESUMEN
Fosfomycin (FOS) is an effective antibiotic against multidrug-resistant Enterobacterales, but its effectiveness is reducing. Little is known on the current prevalence of FosA enzymes in low-risk pathogens, such as Citrobacter freundii. The aim of the study was the molecular characterization of a carbapenemase- and FosA-producing C. freundii collected in Italy. AK867, collected in 2023, showed an XDR profile, retaining susceptibility only to colistin. AK867 showed a FOS MIC >128 mg/L by ADM. Based on WGS, AK867 belonged to ST116 and owned a wide resistome, including fosA3, blaKPC-2, and blaVIM-1. fosA3 was carried by a conjugative pKPC-CAV1312 plasmid of 320,480 bp, on a novel composite transposon (12,907 bp). FosA3 transposon shared similarities with other fosA3-harboring pKPC-CAV1312 plasmids among Citrobacter spp. We report the first case of FosA3 production in clinical carbapenemase-producing C. freundii ST116. The incidence of FosA3 enzymes is increasing among Enterobacterales, affecting even low-virulence pathogens, as C. freundii.
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Antibacterianos , Proteínas Bacterianas , Citrobacter freundii , Infecciones por Enterobacteriaceae , Fosfomicina , beta-Lactamasas , Humanos , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Citrobacter freundii/genética , Citrobacter freundii/enzimología , Citrobacter freundii/efectos de los fármacos , Elementos Transponibles de ADN , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Enterobacteriaceae/microbiología , Fosfomicina/farmacología , Italia/epidemiología , Pruebas de Sensibilidad Microbiana , Plásmidos/genética , Secuenciación Completa del GenomaRESUMEN
BACKGROUND: Urolithiasis combined with ESBL-producing E. coli is often difficult to control and leads to higher postoperative infection-related complications. This study was aim to explore the efficacy and necessity for early use of carbapenem antibiotics perioperatively in urolithiasis patients with urinary tract infections caused by ESBL-producing E. coli. METHODS: The study included a total of 626 patients who were separated into two groups: Group I (the ESBL-producing E. coli group) and Group II (the non-ESBL-producing E. coli group). Antibiotic susceptibility testing was performed and the two groups induced postoperative infection-related events were recorded. the efficacy of perioperative antibiotics was evaluated. RESULTS: All strains of E. coli in our research were sensitive to Carbapenems antibiotics. In addition to Carbapenems, the resistance rates of ESBL-producing E. coli to 6 other commonly used antibiotics were higher than those of non-ESBL-producing strains. Based on the preoperative antibiotic susceptibility test for the ESBL-producing E. coli group and the qSOFA score, the Carbapenems were more effective than the ß-lactamase inhibitors (p = 0.08), while for the non-ESBL-producing E. coli group, there was no difference in the treatment effects between Carbapenems, ß-lactamase inhibitors, Ceftazidime and Quinolones (p = 0.975). CONCLUSIONS: Carbapenem antibiotics significantly reduced the incidence of postoperative infection-related events compared with other types of antibiotics for ESBL-producing E. coli infections in patient with urolithiasis.
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Carbapenémicos , Infecciones por Escherichia coli , Escherichia coli , Urolitiasis , beta-Lactamasas , Humanos , Carbapenémicos/uso terapéutico , Escherichia coli/efectos de los fármacos , Urolitiasis/tratamiento farmacológico , Femenino , Masculino , Persona de Mediana Edad , beta-Lactamasas/metabolismo , Infecciones por Escherichia coli/tratamiento farmacológico , Anciano , Antibacterianos/uso terapéutico , Infecciones Urinarias/tratamiento farmacológico , Atención Perioperativa , Adulto , Estudios Retrospectivos , Pruebas de Sensibilidad Microbiana , Resultado del TratamientoRESUMEN
OBJECTIVES: To determine the prevalence, trends, and potential nosocomial transmission events of the hidden reservoir of rectal carriage of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). METHODS: From 2013 to 2022, yearly point prevalence surveys were conducted in a large Dutch teaching hospital. On the day of the survey, all admitted patients were screened for ESBL-E rectal carriage using peri-anal swabs and a consistent and sensitive selective culturing method. All Enterobacterales phenotypically suspected of ESBL production were analysed using whole genome sequencing for ESBL gene detection and clonal relatedness analysis. RESULTS: On average, the ESBL-E prevalence was 4.6% (188/4,119 patients), ranging from 2.1 to 6.6% per year. The ESBL-prevalence decreased on average 5.5% per year. After time trend correction, the prevalence in 2016 and 2020 was lower compared to the other year. Among the ESBL-E, Escherichia coli (80%) and CTX-M genes (85%) predominated. Potential nosocomial transmission events could be found in 5.9% (11/188) of the ESBL-E carriers. CONCLUSIONS: The ESBL-E rectal carriage prevalence among hospitalized patients was 4.6% with a downward trend from 2013 to 2022. The decrease in ESBL-E prevalence in 2020 could have been due to the COVID-19 pandemic and subsequent countrywide measures as no nosocomial transmission events were detected in 2020. However, the persistently low ESBL-E prevalences in 2021 and 2022 suggest that the decline in ESBL-E prevalence goes beyond the COVID-19 pandemic, indicating that overall ESBL-E carriage rates are declining over time. Continuous monitoring of ESBL-E prevalence and transmission rates can aid infection control policy to keep antibiotic resistance rates in hospitals low.
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Portador Sano , Infección Hospitalaria , Infecciones por Enterobacteriaceae , Enterobacteriaceae , Hospitales de Enseñanza , Secuenciación Completa del Genoma , beta-Lactamasas , Humanos , beta-Lactamasas/genética , Países Bajos/epidemiología , Prevalencia , Infecciones por Enterobacteriaceae/epidemiología , Infecciones por Enterobacteriaceae/microbiología , Infecciones por Enterobacteriaceae/transmisión , Portador Sano/epidemiología , Portador Sano/microbiología , Masculino , Femenino , Enterobacteriaceae/genética , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/enzimología , Anciano , Infección Hospitalaria/epidemiología , Infección Hospitalaria/microbiología , Persona de Mediana Edad , Adulto , Recto/microbiología , Anciano de 80 o más Años , Adulto JovenRESUMEN
The global proliferation of carbapenemase-producing bacteria (CPB) has garnered significant attention worldwide. Early diagnosis of CPB and accurate identification of carbapenemases are crucial for preventing the spread of CPB and ensuring targeted antibiotic therapy. Therefore, efficient and accurate identification of carbapenemases is paramount in clinically treating diseases associated with CPB. In this study, 58 CPB strains were collected and detected using the DNA endonuclease-targeted CRISPR trans reporter (DETECTR) method, a rapid detection platform based on CRISPR-Cas12a gene editing and isothermal amplification. Additionally, four conventional methods (the APB/EDTA method, PCR, NG-test Carba 5, and GeneXpert Carba-R) were employed and compared against whole genome sequencing (WGS) results, considered the gold standard, to evaluate their efficacy in detecting carbapenemases. Detection by the APB/EDTA method revealed that 29 strains were positive for Class A serine endopeptidases, while 29 strains were positive for Class B metalloenzymes. The classification of these zymotypes was consistent with the sequencing result. All target carbapenemases for KPC were identified with 100% sensitivity using NG-test Carba 5, PCR, DETECTR, and GeneXpert Carba-R. In the case of NDM, both Xpert Carba-R and DETECTR showed a sensitivity of 100%. In contrast, NG-test Carba 5 and PCR had a slightly lower sensitivity of 96.7%, each missing one target carbapenemase. n this study, the APB/EDTA method is capable of identifying the zymotype classification but not the specific resistant genes, while Xpert Carba-R and DETECTR are able to detect all target carbapenemases.
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Proteínas Bacterianas , beta-Lactamasas , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Humanos , Técnicas de Amplificación de Ácido Nucleico/métodos , Sensibilidad y Especificidad , Reacción en Cadena de la Polimerasa/métodos , Secuenciación Completa del Genoma , Sistemas CRISPR-CasRESUMEN
Escherichia coli, a rod-shaped Gram-negative bacterium, is a significant causative agent of severe clinical bacterial infections. This study aimed to analyze the epidemiology of extended-spectrum ß-lactamase (ESBL)-producing mcr-1 -positive E. coli in Shandong, China. We collected 668 non-duplicate ESBL-producing E. coli strains from clinical samples at Shandong Provincial Hospital between January and December 2018, and estimated their minimum inhibitory concentrations (MICs) using a VITEK® 2 compact system and broth microdilution. Next-generation sequencing and bioinformatic analyses identified the mcr-1 gene and other resistance genes in the polymyxin B-resistant strains. The conjugation experiment assessed the horizontal transfer capacity of the mcr-1 gene. Of the strains collected, 24 polymyxin B-resistant strains were isolated with a positivity rate of 3.59% and among the 668 strains, 19 clinical strains carried the mobile colistin resistance gene mcr-1, with a positivity rate of approximately 2.8%. All 19 clinical strains were resistant to ampicillin, cefazolin, ceftriaxone, ciprofloxacin, levofloxacin, and polymyxin B. Seventeen strains successfully transferred the mcr-1 gene into E. coli J53. All transconjugants were resistant to polymyxin B, and carried the drug resistance gene mcr-1. The 19 clinical strains had 14 sequence types (STs), with ST155 (n = 4) being the most common. The whole-genome sequencing results of pECO-POL-29_mcr1 revealed that no ISApl1 insertion sequences were found on either side of the mcr-1 gene. Our study uncovered the molecular epidemiology of mcr-1-carrying ESBL-producing E. coli in the region and suggested horizontal transmission mediated by plasmids as the main mode of mcr-1 transmission.
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Antibacterianos , Infecciones por Escherichia coli , Proteínas de Escherichia coli , Escherichia coli , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Polimixina B , Centros de Atención Terciaria , beta-Lactamasas , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Polimixina B/farmacología , Humanos , China/epidemiología , beta-Lactamasas/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Antibacterianos/farmacología , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/epidemiología , Farmacorresistencia Bacteriana/genética , Plásmidos/genética , Farmacorresistencia Bacteriana Múltiple/genéticaRESUMEN
Antibiotic resistance poses a persistent threat to modern medicine due to the emergence of novel antibiotic-resistant strains. Therefore, a timely understanding of antibiotic resistance and the virulence biology of pathogenic bacteria, particularly those of public health significance, is crucial for implementing effective mitigation strategies. This study aimed to investigate the virulence profiles of ten S. aureus isolates (NDa to NDj) and ten E. coli isolates (ND1 to ND10) originating from livestock and poultry, and to assess how various cell surface properties and biofilm formation abilities influence antibiotic resistance phenotypes. Antibiotic resistance profiling through phenotypic (AST) and genotypic methods (PCR) confirmed that NDa to NDe were methicillin-resistant S. aureus (MRSA) and ND1 to ND5 were extended-spectrum ß-lactamase (ESBL) producing E. coli isolates. Virulence properties such as hemolytic activity, coagulase activity, and nuclease activity were found to be independent of the antibiotic resistance phenotype in S. aureus. In contrast, biofilm formation phenotype was observed to influence antibiotic resistance phenotypes, with MRSA and ESBL E. coli isolates demonstrating higher biofilm formation potency. Chemical and enzymatic analysis of S. aureus and E. coli biofilms revealed proteins and polysaccharides as major components, followed by nucleic acids. Furthermore, cell surface properties such as auto-aggregation and hydrophobicity were notably higher in isolates with strong to medium biofilm-forming capabilities (ESBL and MRSA isolates), corroborated by genomic confirmation of various genes associated with biofilm, adhesion, and colonization. In conclusion, this study highlights that surface hydrophobicity and biofilm formation ability of MRSA (NDa to NDe) and ESBL E. coli (ND1 to ND5) isolates may influence antibiotic resistance phenotypes.
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Antibacterianos , Biopelículas , Escherichia coli , Ganado , Staphylococcus aureus Resistente a Meticilina , Pruebas de Sensibilidad Microbiana , Aves de Corral , Factores de Virulencia , beta-Lactamasas , Biopelículas/crecimiento & desarrollo , Biopelículas/efectos de los fármacos , Animales , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/patogenicidad , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Staphylococcus aureus Resistente a Meticilina/genética , Staphylococcus aureus Resistente a Meticilina/efectos de los fármacos , Staphylococcus aureus Resistente a Meticilina/patogenicidad , Staphylococcus aureus Resistente a Meticilina/enzimología , Staphylococcus aureus Resistente a Meticilina/aislamiento & purificación , Aves de Corral/microbiología , Factores de Virulencia/genética , Factores de Virulencia/metabolismo , Ganado/microbiología , Virulencia , Antibacterianos/farmacología , Propiedades de Superficie , Genotipo , Fenotipo , Infecciones Estafilocócicas/microbiologíaRESUMEN
Objective: This study aimed to comprehensively investigate hypervirulent carbapenem-resistant Klebsiella pneumoniae (CR-hvKP) in the Ningbo region. Importantly, we sought to elucidate its molecular characteristics and pathogenic mechanisms. This information will provide evidence-based insights for preventing and controlling nosocomial infections and facilitate improved clinical diagnosis and treatment in this region. Methods: 96 carbapenem-resistant Klebsiella pneumoniae strains were collected from the Ningbo region between January 2021 and December 2022. Whole genome sequencing and bioinformatic methods were employed to identify and characterize CR-hvKP strains at the molecular level. The minimum inhibitory concentrations (MICs) of common clinical antibiotics were determined using the VITEK-2 Compact automatic microbiological analyzer. Plasmid conjugation experiments evaluated the transferability of resistance plasmids. Finally, mouse virulence assays were conducted to explore the pathogenic mechanisms. Results: Among the 96 strains, a single CR-hvKP strain, designated CR-hvKP57, was identified, with an isolation frequency of 1.04%. Whole-genome sequencing revealed the strain to be ST23 serotype with a K1 capsule. This strain harbored three plasmids. Plasmid 1, a pLVPK-like virulence plasmid, carried multiple virulence genes, including rmpA, rmpA2, iroB, iucA, and terB. Plasmid 2 contained transposable element sequences such as IS15 and IS26. Plasmid 3, classified as a resistance plasmid, harbored the bla KPC-3 carbapenem resistance gene. Mouse virulence assays demonstrated a high mortality rate associated with CR-hvKP57 infection. Additionally, there was a significant increase in IL-1ß, IL-6, and TNF-α levels in response to CR-hvKP57 infection, indicating varying degrees of inflammatory response. Western blot experiments further suggested that the pathogenic mechanism involves activation of the NF-κB signaling pathway. Conclusion: This study confirms the emergence of hypervirulent CR-hvKP in the Ningbo region, which likely resulted from the acquisition of a pLVPK-like virulence plasmid and a bla KPC-3 resistance plasmid by the ST23-K1 type Klebsiella pneumoniae. Our findings highlight the urgent need for more judicious use of antibiotics to limit the emergence of resistance. Additionally, strengthening infection prevention and control measures is crucial to minimize the spread of virulence and resistance plasmids.
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Antibacterianos , Proteínas Bacterianas , Enterobacteriaceae Resistentes a los Carbapenémicos , Carbapenémicos , Infecciones por Klebsiella , Klebsiella pneumoniae , Pruebas de Sensibilidad Microbiana , Plásmidos , Secuenciación Completa del Genoma , beta-Lactamasas , Animales , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/patogenicidad , Klebsiella pneumoniae/efectos de los fármacos , Infecciones por Klebsiella/microbiología , Ratones , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Plásmidos/genética , Virulencia/genética , Humanos , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Enterobacteriaceae Resistentes a los Carbapenémicos/patogenicidad , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Carbapenémicos/farmacología , China , Factores de Virulencia/genética , Femenino , Modelos Animales de Enfermedad , MasculinoRESUMEN
Escherichia coli multi-locus sequence type ST131 is a globally distributed pandemic lineage that causes multidrug-resistant extra-intestinal infections. ST131 E. coli frequently produce extended-spectrum ß-lactamases (ESBLs), which confer resistance to many ß-lactam antibiotics and make infections difficult to treat. We sequenced the genomes of 154 ESBL-producing E. coli clinical isolates belonging to the ST131 lineage from patients at the University of Pittsburgh Medical Center (UPMC) between 2004 and 2018. Isolates belonged to the well described ST131 clades A (8%), B (3%), and C (89%). Time-dated phylogenetic analysis estimated that the most recent common ancestor (MRCA) for all clade C isolates emerged around 1989, consistent with previous studies. We identified multiple genes potentially under selection in clade C, including the cell wall assembly gene ftsI, the LPS biosynthesis gene arnC, and the yersiniabactin uptake receptor fyuA. Diverse ESBL-encoding genes belonging to the blaCTX-M, blaSHV, and blaTEM families were identified; these genes were found at varying numbers of loci and in variable numbers of copies across isolates. Analysis of ESBL flanking regions revealed diverse mobile elements that varied by ESBL type. Overall, our findings show that ST131 subclade C dominated among patients and uncover possible signals of ongoing adaptation within this ST131 lineage.
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Infecciones por Escherichia coli , Escherichia coli , Filogenia , beta-Lactamasas , beta-Lactamasas/genética , Escherichia coli/genética , Humanos , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/epidemiología , Evolución Molecular , Antibacterianos/farmacología , Farmacorresistencia Bacteriana Múltiple/genética , Proteínas de Escherichia coli/genética , Proteínas de Escherichia coli/metabolismo , Hospitales , Genoma Bacteriano , Pruebas de Sensibilidad MicrobianaRESUMEN
Antibiotic resistance is one of most important health concerns nowadays, and ß-lactamases are the most important resistance determinants. These enzymes, based on their structural and functional characteristics, are grouped in four categories (A, B, C and D). We have solved the structure of PIB-1, a Pseudomonas aeruginosa chromosomally-encoded ß-lactamase, in its apo form and in complex with meropenem and zinc. These crystal structures show that it belongs to the Class C ß-lactamase group, although it shows notable differences, especially in the Ω- and P2-loops, which are important for the enzymatic activity. Functional analysis showed that PIB-1 is able to degrade carbapenems but not cephalosporins, the typical substrate of Class C ß-lactamases, and that its catalytic activity increases in the presence of metal ions, especially zinc. They do not bind to the active-site but they induce the formation of trimers that show an increased capacity for the degradation of the antibiotics, suggesting that this oligomer is more active than the other oligomeric species. While PIB-1 is structurally a Class C ß-lactamase, the low sequence conservation, substrate profile and its metal-dependence, prompts us to position this enzyme as the founder of a new group inside the Class C ß-lactamases. Consequently, its diversity might be wider than expected.
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Carbapenémicos , Pseudomonas aeruginosa , Zinc , beta-Lactamasas , Pseudomonas aeruginosa/enzimología , beta-Lactamasas/química , beta-Lactamasas/metabolismo , Carbapenémicos/farmacología , Carbapenémicos/metabolismo , Carbapenémicos/química , Zinc/metabolismo , Zinc/química , Modelos Moleculares , Dominio Catalítico , Hidrólisis , Especificidad por Sustrato , Metales/metabolismo , Metales/química , Metales/farmacología , Relación Estructura-Actividad , Meropenem/farmacología , Meropenem/química , Meropenem/metabolismo , Secuencia de Aminoácidos , Cristalografía por Rayos XRESUMEN
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.
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COVID-19 , Infecciones por Enterobacteriaceae , SARS-CoV-2 , beta-Lactamasas , Humanos , COVID-19/microbiología , Brasil , beta-Lactamasas/genética , SARS-CoV-2/genética , Infecciones por Enterobacteriaceae/microbiología , Variación Genética , Antibacterianos/farmacología , Pruebas de Sensibilidad Microbiana , Enterobacteriaceae/genética , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/aislamiento & purificación , Carbapenémicos/farmacología , Hospitales , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Klebsiella pneumoniae/efectos de los fármacosRESUMEN
Antimicrobial resistance (AMR) poses a significant threat to global public health. Notably, resistance to carbapenem and extended-spectrum ß-lactam antibiotics in Gram-negative bacteria is a major impediment to treating infections. Genes responsible for antibiotic resistance are frequently carried on plasmids, which can transfer between bacteria. Therefore, exploring strategies to prevent this transfer and the prevalence of AMR plasmids is timely and pertinent. Here, we show that certain natural product extracts and associated pure compounds can reduce the conjugation of AMR plasmids into new bacterial hosts. Using our established high-throughput fluorescence-based flow cytometry assay, we found that the natural products were more active in reducing transmission of the IncK extended-spectrum ß-lactamase-encoding plasmid pCT in Escherichia coli EC958c, compared to Klebsiella pneumoniae Ecl8 carrying the IncFII carbapenemase-encoding plasmid pKpQIL. The exception was the natural product rottlerin, also active in K. pneumoniae. In classical conjugation assays, rottlerin also reduced the conjugation frequency of the IncFII bla NDM-1 carrying plasmid pCPE16_3 from a clinical K. pneumoniae isolate. Our data indicate that the natural products tested here, in their current molecular structure, reduced conjugation by a small amount, which is unlikely to achieve a large-scale reduction in AMR in bacterial populations. However, certain natural products like rottlerin could provide a foundation for further research into compounds with effective anti-plasmid activity.
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Antibacterianos , Productos Biológicos , Escherichia coli , Klebsiella pneumoniae , Plásmidos , beta-Lactamasas , Plásmidos/genética , Antibacterianos/farmacología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Productos Biológicos/farmacología , Farmacorresistencia Bacteriana/genética , Conjugación Genética , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/genética , Pruebas de Sensibilidad Microbiana , Microbiología de Alimentos , Transferencia de Gen HorizontalRESUMEN
BACKGROUND: In this study, Escherichia coli, Klebsiella oxytoca, and Citrobacter amalonaticus carrying blaNDM-5 were isolated from a single patient. METHODS: The antibiotic susceptibility of the isolates was evaluated by using E-test and agar dilution methods, and blaNDM-5 was identified in genomic and plasmid DNA by using polymerase chain reaction and sequencing. Whole genome sequencing and de novo assembly were used for species characterization, resistance gene identification, and plasmid analysis. RESULTS: All three species had identical plasmids, which were similar to pEC463-NDM5, a plasmid harboring blaNDM-5. Transconjugation experiments confirmed the horizontal gene transfer of blaNDM-5, highlighting the need for a close monitoring of Enterobacteriaceae species harboring this gene. CONCLUSIONS: This study conclusively demonstrates the propensity for horizontal gene transfer of blaNDM-5 among Enterobacteriaceae species, underlining the importance of vigilant monitoring to combat antibiotic resistance.
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Antibacterianos , Enterobacteriaceae , Transferencia de Gen Horizontal , Pruebas de Sensibilidad Microbiana , Plásmidos , beta-Lactamasas , Humanos , beta-Lactamasas/genética , Enterobacteriaceae/genética , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/aislamiento & purificación , Antibacterianos/farmacología , Plásmidos/genética , Infecciones por Enterobacteriaceae/microbiología , Infecciones por Enterobacteriaceae/diagnóstico , Infecciones por Enterobacteriaceae/tratamiento farmacológico , Secuenciación Completa del Genoma , Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Klebsiella oxytoca/genética , Klebsiella oxytoca/aislamiento & purificación , Klebsiella oxytoca/efectos de los fármacos , Citrobacter/genética , Citrobacter/aislamiento & purificación , Citrobacter/efectos de los fármacosRESUMEN
The increasing prevalence of antibiotic resistance, driven by the production of extended-spectrum beta-lactamases (ESBLs), presents a critical challenge to current medical treatments, particularly in clinical settings. Understanding the distribution and frequency of ESBL-producing bacteria is essential for developing effective control strategies. This study investigated the antibiotic resistance and extended-spectrum beta-lactamase (ESBL) production in bacterial isolates in clinical and non-clinical (food) specimens in Tabuk, KSA. A total of 57 bacterial isolates were analysed, with E. coli and Pseudomonas sp. being the most prevalent. High resistance rates were observed, particularly against third-generation cephalosporins in clinical isolates. ESBL screening revealed a significant prevalence in clinical samples (58.3%), with E. coli showing the highest positivity. Conversely, only a low percentage of food isolates were ESBL positive. Molecular analysis confirmed the presence of various ESBL genes, with blaCTX-M being the most frequent, predominantly found in clinical isolates. This study highlights the concerning levels of antibiotic resistance and ESBL production in the region, emphasising the need for effective infection control measures and prudent antibiotic use.
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beta-Lactamasas , Humanos , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Pruebas de Sensibilidad Microbiana , Escherichia coli/efectos de los fármacos , Pseudomonas/efectos de los fármacos , Farmacorresistencia Bacteriana , Microbiología de AlimentosRESUMEN
Introduction: Extended-spectrum ß-lactamase (ESBL) production among Enterobacteriaceae, such as E. coli, has been increasing worldwide, which causes treatment failure for urinary tract infections. Therefore, this study aimed to determine the prevalence and risk factors for the production of ESBL in E. coli from patients with urinary tract infections (UTI) in Zanzibar. Methods: a prospective cross-sectional study was conducted from January 2018 to December 2021 in Zanzibar. Data were retrieved from a routine bacteriological laboratory culture report from urine samples of 4306 patients at the Lancet Laboratory. In addition, the patient's social demographics and clinical data were retrieved by examining the medical records in the respective hospitals. All inpatients older than fifteen years diagnosed with urinary tract infections (UTI) and requested urine culture and sensitivity were included. The Chi-square and Fischer's exact tests were used to compare antibiotic resistance. In addition, a binary logistic regression analysis was used to predict ESBL production risk factors. Results: the prevalence of E. coli-producing ESBL was 13.4% (578/4030). Infection of ESBL. E. coli was prevalent in females 52.6% (n=304) compared to male patients, 47.4% (n=274), and the majority 38.8% (n=224), were people of young age, between 16-30 years. The average age of patients was 31.5±10.2 years, with minimum age of 16 years and a maximum age of 72 years. In multivariate analysis, results shown that previously hospitalised patients aOR: 6.35, 95% Cl 3.37-11.92; p=0.001, long hospital stays aOR: 10.34, 95% Cl 3.03-22.29; p <0.001, prior use of penicillin aOR: 7.78, 95% Cl 2.99-29.11; p < 0.001, and prior use of cephalosporin drugs aOR: 4.64, 95% Cl 2.99-9.96; p=0.001, were strongly associated with the emergence of ESBL-producing E. coli in urinary tract infection patients. ESBL E. coli showed high resistance to amoxicillin 99.5% (n=575), ampicillin 97.8.% (n=570), cotrimazaxole 86.2% (n=344), ceftriaxone 73.7% (n=344), ciprofloxacin 73.2% (n=423), and ceftaxime 59.5% (n=426). There was a less resistance to ampicillin -cloxacillin 44.3% (n=256), gentamicin 22.5% (n=22.5), and norfloxacin 18.9% (n=109) respectively. Isolates were shown to be more susceptible to meropenem at 1.6% (n=9). Conclusion: the overall prevalence of ESBL-producing E. coli is 13.4%. The risk of emergence ESBL was higher in patients with previous history of hospitalisation, long hospital stay, prior use of penicillin and cephalosporin drugs. High level of antimicrobial resistance observed against most commonly used antibiotics in treatment of urinary tract infections. The clinicians should rely on microbiological diagnosis in treatment of UTIs to reduce risk of treatment failure. Further study should be carried out to assess the prevalence and resistance pattern of other uropathogens and other risk factors.
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Antibacterianos , Infecciones por Escherichia coli , Escherichia coli , Centros de Atención Terciaria , Infecciones Urinarias , beta-Lactamasas , Humanos , Infecciones Urinarias/microbiología , Infecciones Urinarias/epidemiología , Infecciones Urinarias/tratamiento farmacológico , Estudios Transversales , Femenino , Estudios Prospectivos , Masculino , Factores de Riesgo , beta-Lactamasas/metabolismo , Escherichia coli/aislamiento & purificación , Escherichia coli/efectos de los fármacos , Prevalencia , Adulto , Persona de Mediana Edad , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/tratamiento farmacológico , Infecciones por Escherichia coli/microbiología , Antibacterianos/farmacología , Adulto Joven , Tanzanía/epidemiología , Anciano , Adolescente , Farmacorresistencia Bacteriana , Pacientes Internos/estadística & datos numéricos , Pruebas de Sensibilidad MicrobianaRESUMEN
The extended-spectrum ß-lactamases (ESßLs) are bacterial enzymes capable of hydrolyzing penicillins, cephalosporins, and aztreonam. The prevalence of ESßL is increasing among clinically significant microorganisms worldwide, drastically reducing the therapeutic management of infectious diseases. The study aimed to determine the drug susceptibility of ESßL-positive clinical isolates acquired from patients hospitalized in Lodz, central Poland, and analyze the prevalence of specific genes, determining acquired resistance in these bacteria. The samples of ESßL-positive clinical isolates were gathered in 2022 from medical microbiological laboratories in the city of Lodz, central Poland. The strains were subjected to biochemical identification and antimicrobial susceptibility testing following EUCAST guidelines. The presence of studied genes (blaCTX-M, blaSHV, blaTEM, blaPER, blaVEB) was confirmed by PCR. Over 50% of studied isolates were resistant to gentamicin, cefepime, ceftazidime and ciprofloxacin. The most common ESßL gene was blaCTX-M. In most isolates, the resistance genes occurred simultaneously. The blaPER was not detected in any of the tested strains. ESßL-producing strains are largely susceptible to the currently available antibiotics. The observation of the coexistence of different genes in most clinical isolates is alarming.