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1.
Mymensingh Med J ; 30(2): 329-336, 2021 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-33830110

RESUMEN

The occurrence of antimicrobial resistance in Salmonella enterica serovars (both typhoidal and non-typhoidal Salmonellae) is a major public health problem especially in developing countries, which have been associated with treatment failures. Therefore, the study was undertaken to determine the current antimicrobial resistance pattern and extended spectrum ß-lactamase (ESBL) production among clinical isolates of Salmonella spp. during 2019-2020 in Mymensingh, Bangladesh. In this cross sectional study, 36 Salmonella enterica isolates were obtained from blood and stool culture of suspected 200 enteric fever and 100 gastroenteritis patients attending at Mymensingh Medical College Hospital, Mymensingh, Bangladesh. Isolated Salmonella species were identified by biochemical tests and Polymerase Chain Reaction (PCR). Disk diffusion test was performed by modified Kirby Bauer method. Minimum Inhibitory Concentration (MIC) of ceftriaxone was detected by agar dilution method. Double disk synergy test was used as a screening test for ESBL production. PCR was done for detection of blaTEM, blaSHV and blaCTX-MU genes. The isolates showed 25% resistance to Ceftriaxone and 58.3% to Azithromycin. The highest sensitivity rates were 88.9% to Meropenem and 83.3% to Amikacin. Whereas 6(16.7%) isolates were Multi Drug Resistant (MDR). Eight (8) isolates were confirmed as ESBL producer by DDST. The marked increase in MIC was observed between 8->512µg/ml to ceftriaxone. blaTEM, blaSHV and blaCTX-MU genes were detected in 3, 5 and 8 isolates respectively. In conclusion, the current study observed, higher level of resistance to ceftriaxone and azithromycin. At the same times 22.2% isolates showed ESBL production, which is a cause for concern as it may lead to treatment failure. On the other hand the study also showed the re-emergence of chloramphenicol and Sulfamethoxazole-Trimethoprim sensitivity.


Asunto(s)
Antibacterianos , beta-Lactamasas , Antibacterianos/farmacología , Bangladesh , Estudios Transversales , Farmacorresistencia Bacteriana/genética , Humanos , Pruebas de Sensibilidad Microbiana , Salmonella/genética , beta-Lactamasas/genética
2.
Int J Food Microbiol ; 344: 109109, 2021 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-33677191

RESUMEN

The objective of the present study was to characterize Salmonella enterica serovar Infantis isolated from chicken meat determining their clonal relationships with S. Infantis isolated from children with diarrhea. Fifteen meat-recovered S. Infantis were analyzed. Susceptibility levels to 14 antibacterial agents, the presence of ESBL and that of inducible plasmid-mediated AmpC (i-pAmpC) were determined by phenotypical methods. The presence of ESBL and pAmpC was confirmed by PCR, and detected ESBL-encoding genes were sequenced and their transferability tested by conjugation. The presence of gyrA mutations as well as Class 1 integrons was determined by PCR. Clonal relationships were established by REP-PCR and RAPD. In addition, 25 clinical isolates of S. Infantis were included in clonality studies. All meat-recovered S. Infantis were MDR, showing resistance to ampicillin, nitrofurans and quinolones, while none was resistant to azithromycin, ceftazidime or imipenem. ESBL (blaCTX-M-65) and i-pAmpC (blaDHA) were detected in 2 and 5 isolates respectively (in one case concomitantly), with blaCTX-M-65 being transferable through conjugation. In addition, 1 isolate presented a blaSHV gene. All isolates presented D87Y at GyrA, nalidixic acid active efflux pump and a Class 1 integron of ~1000 bp (aadA1). Clonal analysis showed that all isolates were related. Further they were identical to MDR blaCTX-M-65-producing S. Infantis isolates causing children diarrhea in Lima. The dissemination of MDR blaCTX-M-65-producing S. Infantis between marketed meat and children highlights a public health problem which needs be controlled at livestock level.


Asunto(s)
Proteínas Bacterianas/genética , Carne/microbiología , Intoxicación Alimentaria por Salmonella/transmisión , Salmonelosis Animal/transmisión , Salmonella enterica/genética , beta-Lactamasas/genética , Animales , Antibacterianos/farmacología , Proteínas Bacterianas/metabolismo , Pollos/microbiología , Niño , Humanos , Integrones/genética , Plásmidos/genética , Técnica del ADN Polimorfo Amplificado Aleatorio , Intoxicación Alimentaria por Salmonella/microbiología , Salmonelosis Animal/microbiología , Salmonella enterica/efectos de los fármacos , Salmonella enterica/aislamiento & purificación , Serogrupo , beta-Lactamasas/metabolismo
3.
Nat Commun ; 12(1): 1852, 2021 03 25.
Artículo en Inglés | MEDLINE | ID: mdl-33767175

RESUMEN

TEM-1 ß-lactamase degrades ß-lactam antibiotics with a strong preference for penicillins. Sequence reconstruction studies indicate that it evolved from ancestral enzymes that degraded a variety of ß-lactam antibiotics with moderate efficiency. This generalist to specialist conversion involved more than 100 mutational changes, but conserved fold and catalytic residues, suggesting a role for dynamics in enzyme evolution. Here, we develop a conformational dynamics computational approach to rationally mold a protein flexibility profile on the basis of a hinge-shift mechanism. By deliberately weighting and altering the conformational dynamics of a putative Precambrian ß-lactamase, we engineer enzyme specificity that mimics the modern TEM-1 ß-lactamase with only 21 amino acid replacements. Our conformational dynamics design thus re-enacts the evolutionary process and provides a rational allosteric approach for manipulating function while conserving the enzyme active site.


Asunto(s)
beta-Lactamasas/genética , beta-Lactamasas/metabolismo , Secuencia de Aminoácidos/genética , Dominio Catalítico/genética , Biología Computacional , Escherichia coli/efectos de los fármacos , Escherichia coli/enzimología , Evolución Molecular , Simulación de Dinámica Molecular , Penicilinas/metabolismo , Conformación Proteica , Especificidad por Sustrato
4.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33739918

RESUMEN

Introduction. Carbapenem resistance in Acinetobacter baumannii (A. baumannii) is an emerging global threat.Gap statement. The adaptation strategies of A. baumannii for this emergence as a nosocomial pathogen has been less studied.Aim. This prospective study analysed a sustained outbreak of carbapenem resistant Acinetobacter baumannii (CRAB) in the intensive care unit (ICU) with reference to antimicrobial resistance and virulence in the colonizing and pathogenic isolates under carbapenem stress.Results. The CRAB isolates from initial and sustained outbreak were found harbouring multiple carbapenemase genes. These genes included bla OXA-23 ,bla IMP, bla VIM and bla NDM. From NICU environment three phenotypically carbapenem susceptible isolates were found carrying bla OXA-23, bla IMP, bla VIM genes. Prior imipenem therapy was one of the risk factors (P=0.0016). The outbreak was polyclonal. Under imipenem stress, outbreak isolates showed no loss of carbapenemase genes against stress free conditions (23.7±1.33 days). Biofilm formation increased with imipenem concentration, with outbreak isolates producing highest biomass. While the pathogens showed a slow growth rate on imipenem exposure, the colonisers grew rapidly (P <0.0001).Methods. Sustained outbreak of CRAB was identified in the ICU (July 2015 to December 2017). Risk factors for acquisition of CRAB was studied. A. baumannii isolates were also collected from the environments of ICU and neonatal ICU (NICU) and blood cultures of septic neonates. Isolates were characterized based on antimicrobial susceptibility, genetic profile, integrons carriage and clonality. Biofilm formation and growth kinetics were studied under varying carbapenem stress.Conclusion. Intense carbapenem exposure in the ICU facilitates persistence of CRAB by several adaptations causing sustained outbreaks.


Asunto(s)
Infecciones por Acinetobacter/microbiología , Acinetobacter baumannii/fisiología , Adaptación Fisiológica , Carbapenémicos/farmacología , Infección Hospitalaria/microbiología , Brotes de Enfermedades , Farmacorresistencia Bacteriana Múltiple/fisiología , Infecciones por Acinetobacter/tratamiento farmacológico , Infecciones por Acinetobacter/epidemiología , Acinetobacter baumannii/efectos de los fármacos , Acinetobacter baumannii/patogenicidad , Adulto , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Biopelículas/efectos de los fármacos , Biopelículas/crecimiento & desarrollo , Carbapenémicos/uso terapéutico , Infección Hospitalaria/tratamiento farmacológico , Infección Hospitalaria/epidemiología , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Microbiología Ambiental , Femenino , Genes Bacterianos , Humanos , Imipenem/farmacología , Imipenem/uso terapéutico , Integrones/genética , Unidades de Cuidados Intensivos , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Estudios Prospectivos , Factores de Riesgo , Virulencia , beta-Lactamasas/genética , beta-Lactamasas/metabolismo
5.
Rev Soc Bras Med Trop ; 54: e0864, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33759932

RESUMEN

Proteus mirabilis is one of the main pathogens causing urinary tract infections and sepsis. To our knowledge, this is the first report of a P. mirabilis hosting bla GES. The presence of these genes was determined using PCR and sequencing. We identified the presence of bla GES-1 in all three isolates. In addition, we identified the bla KPC-2 and bla NDM-1 genes in the two strains. These data emphasize the importance of monitoring and surveillance of all enterobacteria. The circulation of P. mirabilis strains carrying bla GES-1 constitutes a new scenario of resistance in this species and should be an epidemiological alert for global health.


Asunto(s)
Proteus mirabilis , beta-Lactamasas , Antibacterianos , Enterobacteriaceae , Pruebas de Sensibilidad Microbiana , Proteus mirabilis/genética , beta-Lactamasas/genética
6.
Microbiome ; 9(1): 40, 2021 02 08.
Artículo en Inglés | MEDLINE | ID: mdl-33557954

RESUMEN

BACKGROUND: The spread of antibiotic resistance has become one of the most urgent threats to global health, which is estimated to cause 700,000 deaths each year globally. Its surrogates, antibiotic resistance genes (ARGs), are highly transmittable between food, water, animal, and human to mitigate the efficacy of antibiotics. Accurately identifying ARGs is thus an indispensable step to understanding the ecology, and transmission of ARGs between environmental and human-associated reservoirs. Unfortunately, the previous computational methods for identifying ARGs are mostly based on sequence alignment, which cannot identify novel ARGs, and their applications are limited by currently incomplete knowledge about ARGs. RESULTS: Here, we propose an end-to-end Hierarchical Multi-task Deep learning framework for ARG annotation (HMD-ARG). Taking raw sequence encoding as input, HMD-ARG can identify, without querying against existing sequence databases, multiple ARG properties simultaneously, including if the input protein sequence is an ARG, and if so, what antibiotic family it is resistant to, what resistant mechanism the ARG takes, and if the ARG is an intrinsic one or acquired one. In addition, if the predicted antibiotic family is beta-lactamase, HMD-ARG further predicts the subclass of beta-lactamase that the ARG is resistant to. Comprehensive experiments, including cross-fold validation, third-party dataset validation in human gut microbiota, wet-experimental functional validation, and structural investigation of predicted conserved sites, demonstrate not only the superior performance of our method over the state-of-art methods, but also the effectiveness and robustness of the proposed method. CONCLUSIONS: We propose a hierarchical multi-task method, HMD-ARG, which is based on deep learning and can provide detailed annotations of ARGs from three important aspects: resistant antibiotic class, resistant mechanism, and gene mobility. We believe that HMD-ARG can serve as a powerful tool to identify antibiotic resistance genes and, therefore mitigate their global threat. Our method and the constructed database are available at http://www.cbrc.kaust.edu.sa/HMDARG/ . Video abstract (MP4 50984 kb).


Asunto(s)
Aprendizaje Profundo , Farmacorresistencia Microbiana/genética , Genes Bacterianos/genética , Animales , Humanos , beta-Lactamasas/genética
7.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33587030

RESUMEN

Introduction. Carbapenem-resistant Enterobacteriaceae (CRE) have been responsible for nosocomial outbreaks worldwide and have become endemic in several countries.Hypothesis/Gap Statement. To better understand the epidemiological trends and characteristics of CRE in the Henan province.Aim. We assessed the molecular epidemiological characteristics of 305 CRE strains isolated from patients in 19 secondary or tertiary hospitals in ten areas of the Henan province in China.Methodology. A total of 305 CRE isolates were subjected to multiple tests, including in vitro antimicrobial susceptibility testing, PCR for carbapenemase genes bla KPC, bla NDM, bla IMP, bla VIM, bla OXA-48-like. Tigecycline-resistant genes ramR, oqxR, acrR, tetA, rpsJ, tetX, tetM, tetL were analysed in five tigecycline non-susceptible carbapenem-resistant Klebsiella pneumoniae isolates (TNSCRKP). Additionally, multilocus sequence typing (MLST) was performed for carbapenem-resistant K. pneumoniae (CRKP).Results. The most common CRE species were K. pneumoniae (234, 77 %), Escherichia coli (36, 12 %) and Enterobacter cloacae (13, 4 %). All strains exhibited multi-drug resistance. Overall, 97 % (295/305) and 97 % (297/305) of the isolates were susceptible to polymyxin B and tigecycline, respectively. A total of 89 % (271/305) of the CRE isolates were carbapenemase gene-positive, including 70 % bla KPC, 13 % bla NDM, 6 % bla IMP, and 1 % combined bla KPC/bla NDM genes. K. pneumoniae carbapenemase (KPC) was the predominant carbapenemase in K. pneumoniae (87 %), whereas NDM and IMP were frequent in E. coli (53 %) and E. cloacae (69 %), respectively. Mutations in the ramR, tetA, and rpsJ genes were detected in five TNSCRKP. Moreover, 15 unique sequence types were detected, with ST11 (74 %), ST15 (9 %) and ST2237 (5 %) being dominant among K. pneumoniae strains.Conclusion. A high proportion of CRE strains were carbapenemase-positive, and five carbapenem-resistant K. pneumonia isolates were tigecycline non-susceptible, indicating a need for the ongoing surveillance of CRE and effective measures for the prevention of CRE infections.


Asunto(s)
Antibacterianos/farmacología , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Infecciones por Enterobacteriaceae/microbiología , Tigeciclina/farmacología , Proteínas Bacterianas/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/clasificación , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , China/epidemiología , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Enterobacteriaceae/epidemiología , Genotipo , Humanos , Pruebas de Sensibilidad Microbiana , Mutación , beta-Lactamasas/genética
8.
BMC Infect Dis ; 21(1): 235, 2021 Feb 28.
Artículo en Inglés | MEDLINE | ID: mdl-33639886

RESUMEN

BACKGROUND: This study aimed to determine the epidemiological, microbiological, and molecular characteristics of an outbreak of carbapenem-resistant Leclercia adecarboxylata in three hospitals associated with the unintended use of contaminated total parental nutrition (TPN). METHODS: For 10 days, 25 patients who received intravenous TPN from the same batch of a formula developed sepsis and had blood cultures positive for L. adecarboxylata. Antimicrobial susceptibility and carbapenemase production were performed in 31 isolates, including one from an unopened bottle of TPN. Carbapenemase-encoding genes, extended-spectrum ß-lactamase-encoding genes were screened by PCR, and plasmid profiles were determined. Horizontal transfer of carbapenem resistance was performed by solid mating. Clonal diversity was performed by pulsed-field gel electrophoresis. The resistome was explored by whole-genome sequencing on two selected strains, and comparative genomics was performed using Roary. RESULTS: All 31 isolates were resistant to aztreonam, cephalosporins, carbapenems, trimethoprim/sulfamethoxazole, and susceptible to gentamicin, tetracycline, and colistin. Lower susceptibility to levofloxacin (51.6%) and ciprofloxacin (22.6%) was observed. All the isolates were carbapenemase producers and positive for blaNDM-1, blaTEM-1B, and blaSHV-12 genes. One main lineage was detected (clone A, 83.9%; A1, 12.9%; A2, 3.2%). The blaNDM-1 gene is embedded in a Tn125-like element. Genome analysis showed genes encoding resistance for aminoglycosides, quinolones, trimethoprim, colistin, phenicols, and sulphonamides and the presence of IncFII (Yp), IncHI2, and IncHI2A incompatibility groups. Comparative genomics showed a major phylogenetic relationship among L. adecarboxylata I1 and USDA-ARS-USMARC-60222 genomes, followed by our two selected strains. CONCLUSION: We present epidemiological, microbiological, and molecular evidence of an outbreak of carbapenem-resistant L. adecarboxylata in three hospitals in western Mexico associated with the use of contaminated TPN.


Asunto(s)
Brotes de Enfermedades , Infecciones por Enterobacteriaceae/etiología , Enterobacteriaceae/metabolismo , Nutrición Parenteral Total/efectos adversos , beta-Lactamasas/metabolismo , Antibacterianos/farmacología , Bacteriemia/epidemiología , Bacteriemia/etiología , Bacteriemia/microbiología , Enterobacteriaceae Resistentes a los Carbapenémicos/efectos de los fármacos , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/aislamiento & purificación , Enterobacteriaceae Resistentes a los Carbapenémicos/metabolismo , Niño , Enterobacteriaceae/efectos de los fármacos , Enterobacteriaceae/genética , Enterobacteriaceae/aislamiento & purificación , Infecciones por Enterobacteriaceae/epidemiología , Infecciones por Enterobacteriaceae/microbiología , Genoma Bacteriano/genética , Hospitales , Humanos , México/epidemiología , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Filogenia , beta-Lactamasas/genética
9.
Mikrobiyol Bul ; 55(1): 1-16, 2021 Jan.
Artículo en Turco | MEDLINE | ID: mdl-33590977

RESUMEN

Antibiotic resistance is one of the most important public health problem and one of the most critical steps in preventing resistance is the monitorization of the resistance. Local, regional and global monitoring enables the spread of antibiotic resistance to be understood more clearly. In this study, it was aimed to evaluate the results of the pilot study for the establishment of molecular-based carbapenem surveillance system in Escherichia coli and Klebsiella pneumoniae isolates and to investigate the carbapenemase epidemiology in Turkey. Hospitals (n= 28) from 26 different statistical level II regions from Turkey were included in the study. The hospitals participated in the study submitted ten carbapenem susceptible and ten carbapenem resistant E.coli and K.pneumoniae isolates to our laboratory that were isolated in two different periiods of six-month either between 1 March-31 August or 1 April-30 September 2019. A total of 509 isolates were collected from 26 of the 28 participating hospitals in the study. Isolates were identified by matrix assisted laser desorptionization-time of flight mass spectrophotometry (MALDI TOF MS) (Bruker Daltonics, Germany) method and antibiotic susceptibility tests for imipenem, meropenem and colistin were studied by broth microdilution. Moreover, susceptibilities to amikacin, amoxicillin-clavulanic acid, ampicillin, aztreonam, cefepime, cefotaxime, ceftazidime, ciprofloxacin, ertapenem, gentamicin, piperacillin-tazobactam, tobramycin and trimethoprim-sulfamethoxazole were determined by disc diffusion method. The resistance genes were investigated in isolates which were found to be phenotypically resistant to carbapenem and colistin, in house method was used to investigate carbapenemase genes and a commercial colistin resistant real-time PCR kit (Biospeedy, Turkey) was used for colistin resistance genes. In total, 493 of the 509 isolates collected from hospitals were identified as E.coli (25.7%, n= 127) and K.pneumoniae (74.3%, n= 366) and included in the study. It was determined that 31% of the isolates evaluated were from community-acquired infections and 69% were either from healthcare-associated infections or from colonization sites. Among the tested isolates, 248 (50.3%) were susceptible to carbapenems and 245 (49.7%) were resistant. The types of carbapenemases in carbapenemase-producing were OXA-48 (52.2%), KPC (16.1%), NDM-1 (15%), OXA-48 + NDM-1 (12.6%), KPC + NDM-1 (2.8%) and VIM (0.5%) and OXA-48+VIM (0.5%). Resistance to colistin was detected in 23.3% of the isolates but mcr1-8 genes were not detected. It was found that all colistin resistant isolates are resistant to at least one of the carbapenems. The importance of a molecular-based antimicrobial resistance surveillance system in our country was demonstrated with this pilot study. It is thought that continuous monitoring of these epidemiological features will contribute to the management of infections due to carbapenemase-producing organisms.


Asunto(s)
Proteínas Bacterianas , Infecciones por Klebsiella , Klebsiella pneumoniae , beta-Lactamasas , Antibacterianos/farmacología , Proteínas Bacterianas/genética , Escherichia coli/enzimología , Escherichia coli/genética , Humanos , Infecciones por Klebsiella/epidemiología , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/genética , Pruebas de Sensibilidad Microbiana , Proyectos Piloto , Turquia/epidemiología , beta-Lactamasas/genética
10.
Environ Pollut ; 274: 116593, 2021 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-33548670

RESUMEN

Extended-spectrum ß-lactam antibiotics are critically important antibiotics for humans, but their use in food-animals poses a potential threat for public health. This paper addressed the occurrence of high-risk ß-lactamase genes (bla genes) in intensive dairy farms, and assessed the effects of different waste treatment technologies at dairies on the propagation and dissemination of bla genes. Results showed that ESBL genes (blaTEM-1, blaOXA-1), ampC ß-lactamase genes (blaampC) and carbapenemase genes (blaGES-1, blaNDM) were prevalent in dairy cow waste, and even prevailed through each processing stage of solid manure and dairy wastewater. Significant levels of bla genes were present in the final lagoon (from 104 to 106 copies/mL, representing from 10% to 151%, of raw influent levels), raising the possibility of dissemination to the receiving environment. This concern was validated by the investigation on farmland that had long-term undergone wastewater irrigation, where causing an increase in bla gene levels in soils (approximately 1-3 orders of magnitude). More troublesomely, considerable levels of certain bla genes were still observed in the bedding material (up to 105 and 107 copies/g), which would directly threaten the dairy cow health. Otherwise, correlation analysis showed that both bacterial community and environmental factors played important roles in the bla genes abundances in dairy farms. This study demonstrated the prevalence of high-risk bla genes in dairy farms, and also underscored that dairy waste was a non-ignored great source of multidrug resistance for their surroundings.


Asunto(s)
Antibacterianos , beta-Lactamasas , Animales , Bovinos , China , Granjas , Femenino , Humanos , Aguas Residuales , beta-Lactamasas/genética
12.
BMC Infect Dis ; 21(1): 142, 2021 Feb 04.
Artículo en Inglés | MEDLINE | ID: mdl-33541274

RESUMEN

BACKGROUND: Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) have continually grown as a global public health threat, with significant mortality rates observed across the world. We examined the clinical data from patients with CPE infections and their outcomes, concentrating on Klebsiella pneumoniae isolates. We analysed the clinical information, performed antimicrobial susceptibility testing, and conducted molecular epidemiological and genomic analyses on the isolates to identify patterns in the data. METHODS: The clinical characteristics of 33 hospitalised patients with confirmed CPE, including patient-related factors associated with the development of CPE infections, were examined. Patients were divided according to whether they were "colonised" or "infected" with CPE and by the timing and frequency of their rectal swab collections, from which 45 swabs were randomly selected for analysis. CPE isolates were purified, and antimicrobial susceptibility tests performed. Whole genome sequences of these isolates were determined and analysed to compute bacterial multilocus sequence types and plasmid replicon types, infer phylogenetic relationships, and identify antimicrobial resistance and virulence genes. RESULTS: Altogether, 88.9% (40/45) of the CPE isolates were K. pneumoniae. The most abundant carbapenemase gene family in the K. pneumoniae isolates (33/39) was blaOXA-232, with blaNDM-1 additionally identified in 19 of them. All CPE isolates carrying either blaOXA-232 or blaNDM-1 were resistant to meropenem, but only 40 from 45 were susceptible to colistin. Among the CPE-infected patients (n = 18) and CPE-colonised patients who developed CPE infections during the study (n = 3), all but one received standard colistin-based combination therapy. Phylogenetic analysis revealed the polyclonal spread of carbapenemase-producing K. pneumoniae (CPKP) within the patient population, with the following two major subclades identified: ST16 (n = 15) and ST231 (n = 14). CPKP-ST231 had the highest virulence score of 4 and was associated with primary bacteraemia. The siderophores yersiniabactin and aerobactin, considered to be important virulence factors, were only identified in the CPKP-ST231 genomes. CONCLUSIONS: This study has revealed the genomic features of colonising CPE isolates, focusing on antimicrobial resistance and virulence determinants. This type of multi-layered analysis can be further exploited in Thailand and elsewhere to modify the regimes used for empirical antibiotic treatment and improve the management strategies for CPE infections in hospitalised patients.


Asunto(s)
Proteínas Bacterianas/aislamiento & purificación , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Enterobacteriaceae/genética , Klebsiella pneumoniae/aislamiento & purificación , Tipificación de Secuencias Multilocus , Secuenciación Completa del Genoma , beta-Lactamasas/aislamiento & purificación , Anciano , Anciano de 80 o más Años , Antibacterianos/farmacología , Colistina/farmacología , Femenino , Humanos , Masculino , Pruebas de Sensibilidad Microbiana , Persona de Mediana Edad , Epidemiología Molecular , Filogenia , Plásmidos , Tailandia/epidemiología , Factores de Virulencia , beta-Lactamasas/genética
13.
Sci Total Environ ; 771: 144828, 2021 Jun 01.
Artículo en Inglés | MEDLINE | ID: mdl-33545481

RESUMEN

Overuse of antibiotics in animal husbandry has led to an increase of antibiotic resistance microorganisms as well as antibiotic-resistance genes (ARGs). Duck farming in China is practiced on a large and diverse scale and the overuse of antibiotics in this field is gaining attention recently. We evaluated the diversity of ARGs from five duck farms using a functional metagenomic approach and constructed five libraries. A total of seventy-six resistant determinants were identified, of which sixty-one were gene variants or novel genes. The novel genes contained five ß-lactamase-encoding genes designated as blaDWA1, blaDWA2, blaDWA3, blaDWA4 and blaDWB1, respectively, and two genes conferring resistance to fosfomycin designated as fosA-like1 and fosA-like2. Three of the five ß-lactamase-encoding genes were further identified as extended-spectrum ß-lactamases (ESBL) that can hydrolyze both penicillins and cephalosporins. Besides, two of the five ß-lactamase-encoding genes were associated with mobile genetic elements, indicating a high potential for transfer of the genes to other bacterial hosts. The two novel fosA-like genes were able to increase the MICs of the test Escherichia coli strain from 2 µg/mL to as high as 256 µg/mL(up to 128-fold increase). Our study provides a reference for ARGs prevalence in duck farm wastes and implies that they are an important resistome reservoir, especially for novel ARGs with high spread potential.


Asunto(s)
Antibacterianos , Patos , Animales , Antibacterianos/farmacología , China , Farmacorresistencia Microbiana/genética , Genes Bacterianos , beta-Lactamasas/genética
14.
BMC Infect Dis ; 21(1): 16, 2021 Jan 06.
Artículo en Inglés | MEDLINE | ID: mdl-33407206

RESUMEN

BACKGROUND: Epidemiological data of cephalosporin-resistant Enterobacterales in Sub-Saharan Africa is still restricted, and in particular in Mozambique. The aim of this study was to detect and characterize extended-spectrum ß-lactamase (ESBL) - and plasmid-mediated AmpC (pAmpC)-producing clinical strains of Escherichia coli at Maputo Central Hospital (MCH), a 1000-bed reference hospital in Maputo, Mozambique. METHODS: A total of 230 clinical isolates of E. coli from urine (n = 199) and blood cultures (n = 31) were collected at MCH during August-November 2015. Antimicrobial susceptibility testing was performed by the disc diffusion method and interpreted according to EUCAST guidelines. Isolates with reduced susceptibility to 3rd generation cephalosporins were examined further; phenotypically for an ESBL-/AmpC-phenotype by combined disc methods and genetically for ESBL- and pAmpC-encoding genes by PCR and partial amplicon sequencing as well as genetic relatedness by ERIC-PCR. RESULTS: A total of 75 isolates with reduced susceptibility to cefotaxime and/or ceftazidime (n = 75) from urine (n = 58/199; 29%) and blood (n = 17/31; 55%) were detected. All 75 isolates were phenotypically ESBL-positive and 25/75 (33%) of those also expressed an AmpC-phenotype. ESBL-PCR and amplicon sequencing revealed a majority of blaCTX-M (n = 58/75; 77%) dominated by blaCTX-M-15. All AmpC-phenotype positive isolates (n = 25/75; 33%) scored positive for one or more pAmpC-genes dominated by blaMOX/FOX. Multidrug resistance (resistance ≥ three antibiotic classes) was observed in all the 75 ESBL-positive isolates dominated by resistance to trimethoprim-sulfamethoxazole, ciprofloxacin and gentamicin. ERIC-PCR revealed genetic diversity among strains with minor clusters indicating intra-hospital spread. CONCLUSION: We have observed a high prevalence of MDR pAmpC- and/or ESBL-producing clinical E. coli isolates with FOX/MOX and CTX-Ms as the major ß-lactamase types, respectively. ERIC-PCR analyses revealed genetic diversity and some clusters indicating within-hospital spread. The overall findings strongly support the urgent need for accurate and rapid diagnostic services to guide antibiotic treatment and improved infection control measures.


Asunto(s)
Antibacterianos/uso terapéutico , Proteínas Bacterianas/genética , Cefotaxima/uso terapéutico , Ceftazidima/uso terapéutico , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Escherichia coli/tratamiento farmacológico , Escherichia coli/enzimología , Escherichia coli/aislamiento & purificación , Plásmidos/metabolismo , beta-Lactamasas/genética , Infección Hospitalaria/diagnóstico , Infección Hospitalaria/microbiología , Infecciones por Escherichia coli/sangre , Infecciones por Escherichia coli/epidemiología , Infecciones por Escherichia coli/orina , Humanos , Pruebas de Sensibilidad Microbiana , Mozambique/epidemiología , Fenotipo , Prevalencia
15.
Appl Environ Microbiol ; 87(6)2021 02 26.
Artículo en Inglés | MEDLINE | ID: mdl-33397699

RESUMEN

Little is known about the drivers of critically important antibacterial resistance in species with zoonotic potential present on farms (e.g., CTX-M ß-lactamase-positive Escherichia coli). We collected samples monthly between January 2017 and December 2018 on 53 dairy farms in South West England, along with data for 610 variables concerning antibacterial usage, management practices, and meteorological factors. We detected E. coli resistant to amoxicillin, ciprofloxacin, streptomycin, and tetracycline in 2,754/4,145 (66%), 263/4,145 (6%), 1,475/4,145 (36%), and 2,874/4,145 (69%), respectively, of samples from fecally contaminated on-farm and near-farm sites. E. coli positive for bla CTX-M were detected in 224/4,145 (5.4%) of samples. Multilevel, multivariable logistic regression showed antibacterial dry cow therapeutic choice (including use of cefquinome or framycetin) to be associated with higher odds of bla CTX-M positivity. Low average monthly ambient temperature was associated with lower odds of bla CTX-M E. coli positivity in samples and with lower odds of finding E. coli resistant to each of the four test antibacterials. This was in addition to the effect of temperature on total E. coli density. Furthermore, samples collected close to calves had higher odds of having E. coli resistant to each antibacterial, as well as E. coli positive for bla CTX-M Samples collected on pastureland had lower odds of having E. coli resistant to amoxicillin or tetracycline, as well as lower odds of being positive for bla CTX-M IMPORTANCE Antibacterial resistance poses a significant threat to human and animal health and global food security. Surveillance for resistance on farms is important for many reasons, including tracking impacts of interventions aimed at reducing the prevalence of resistance. In this longitudinal survey of dairy farm antibacterial resistance, we showed that local temperature-as it changes over the course of a year-was associated with the prevalence of antibacterial-resistant E. coli We also showed that prevalence of resistant E. coli was lower on pastureland and higher in environments inhabited by young animals. These findings have profound implications for routine surveillance and for surveys carried out for research. They provide important evidence that sampling at a single time point and/or single location on a farm is unlikely to be adequate to accurately determine the status of the farm regarding the presence of samples containing resistant E. coli.


Asunto(s)
Farmacorresistencia Bacteriana , Escherichia coli/genética , beta-Lactamasas/genética , Envejecimiento , Amoxicilina/farmacología , Animales , Antibacterianos/farmacología , Bovinos , Enfermedades de los Bovinos/microbiología , Ciprofloxacino/farmacología , Escherichia coli/efectos de los fármacos , Escherichia coli/aislamiento & purificación , Infecciones por Escherichia coli/microbiología , Granjas , Heces/microbiología , Estreptomicina/farmacología , Temperatura , Tetraciclina/farmacología
16.
Carbohydr Polym ; 255: 117484, 2021 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-33436244

RESUMEN

Wound dressing composed of chitosan, based crosslinked gelatin/ polyvinyl pyrrolidone, embedded silver nanoparticles were fabricated using solution casting method. The membrane was characterized by FTIR, SEM and TGA. Glutaraldehyde (0.5 %) was used for the crosslinking of membrane components and associated with 7-folds boosted mechanical performance, 28 % more hydrolytic stability, 3-folds thickness reduction and morphological roughness. Silver nanoparticles were characterized by UV-vis, XRD and TEM for an average size of 9.9 nm. The membrane with higher concentration of silver nanoparticles showed maximum antibacterial activity against human pathogenic bacteria; and the measured inhibition zones ranged from 1.5 to 3 cm. The activity of the particles ranged from severe to complete reduction in Penicillin, Erythromycin and Macrolide family's resistance genes expression such as ß-Lactamase, mecA and erm. This developed membrane can serve as promising and cost-effective system against severe diabetic and burn wound infections.


Asunto(s)
Antibacterianos/farmacología , Vendajes , Quitosano/química , Citrullus colocynthis/química , Gelatina/química , Povidona/química , Plata/farmacología , Bacillus subtilis/efectos de los fármacos , Bacillus subtilis/crecimiento & desarrollo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Farmacorresistencia Bacteriana Múltiple/efectos de los fármacos , Farmacorresistencia Bacteriana Múltiple/genética , Eritromicina/farmacología , Escherichia coli/efectos de los fármacos , Escherichia coli/crecimiento & desarrollo , Fibroblastos/citología , Fibroblastos/efectos de los fármacos , Regulación Bacteriana de la Expresión Génica/efectos de los fármacos , Humanos , Macrólidos/farmacología , Nanopartículas del Metal/química , Nanopartículas del Metal/ultraestructura , Metiltransferasas/genética , Metiltransferasas/metabolismo , Pruebas de Sensibilidad Microbiana , Proteínas de Unión a las Penicilinas/genética , Proteínas de Unión a las Penicilinas/metabolismo , Penicilinas/farmacología , Cultivo Primario de Células , Pseudomonas aeruginosa/efectos de los fármacos , Pseudomonas aeruginosa/crecimiento & desarrollo , Salmonella typhi/efectos de los fármacos , Salmonella typhi/crecimiento & desarrollo , Plata/química , Staphylococcus aureus/efectos de los fármacos , Staphylococcus aureus/crecimiento & desarrollo , beta-Lactamasas/genética , beta-Lactamasas/metabolismo
17.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33448924

RESUMEN

Introduction. Gram-negative bacteria are a common source of infection both in hospitals and in the community, and antimicrobial resistance is frequent among them, making antibiotic therapy difficult, especially when these isolates carry carbapenem resistance determinants.Hypothesis/Gap Statement. A simple method to detect all the commonly found carbapenemases in Germany was not available.Aim. The aim of this study was to develop a multiplex PCR for the rapid and reliable identification of the most prevalent carbapenemase-encoding genes in Gram-negative bacteria in Germany.Methodology. Data from the German Gram-negative reference laboratory revealed the most prevalent carbapenemase groups in Germany were (in order of prevalence): bla VIM, bla OXA-48, bla OXA-23, bla KPC, bla NDM, bla OXA-40, bla OXA-58, bla IMP, bla GIM, bla GES, ISAba1-bla OXA-51, bla IMI, bla FIM and bla DIM. We developed and tested two multiplex PCRs against 83 carbapenem-resistant Gram-negative clinical isolates. Primers were designed for each carbapenemase group within conserved regions of the encoding genes obtained from publicly available databases. Multiplex-1 included the carbapenemase groups bla VIM, bla OXA-48, bla OXA-23, bla KPC, bla NDM and bla OXA-40, while multiplex-2 included bla OXA-58, bla IMP, bla GIM, bla GES, ISAba1-bla OXA-51 and bla IMI.Results. In the initial evaluation, all but one of the carbapenemases encoded by 75 carbapenemase-positive isolates were detected using the two multiplex PCRs, while no false-positive results were obtained from the remaining eight isolates. After evaluation, we tested 546 carbapenem-resistant isolates using the multiplex PCRs, and all carbapenemases were detected.Conclusion. A rapid and reliable method was developed for detection and differentiation of 12 of the most prevalent carbapenemase groups found in Germany. This method allows for the rapid testing of clinical isolates prior to species identification and does not require prior phenotypical characterization, constituting a rapid and valuable tool in the management of infections in hospitals.


Asunto(s)
Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana/genética , Bacterias Gramnegativas , Infecciones por Bacterias Gramnegativas/microbiología , Reacción en Cadena de la Polimerasa/métodos , beta-Lactamasas/genética , Genes Bacterianos , Alemania , Bacterias Gramnegativas/enzimología , Bacterias Gramnegativas/genética , Infecciones por Bacterias Gramnegativas/epidemiología , Humanos , Prevalencia
18.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33475479

RESUMEN

Klebsiella pneumoniae causes a diversity of infections in both healthcare and community settings. This pathogen is showing an increased ability to accumulate antimicrobial resistance and virulence genes, making it a public health concern. Here we describe the whole-genome sequence characteristics of an ST15 colistin-resistant K. pneumoniae isolate obtained from a blood culture of a 79-year-old female patient admitted to a university hospital in Brazil. Kp14U04 was resistant to most clinically useful antimicrobial agents, remaining susceptible only to aminoglycosides and fosfomycin. The colistin resistance in this isolate was due to a ~1.3 kb deletion containing four genes, namely mgrB, yebO, yobH and the transcriptional regulator kdgR. The study isolate presented a variety of antimicrobial resistance genes, including the carbapenemase-encoding gene bla KPC-2, the extended-spectrum beta-lactamase (ESBL)-encoding gene bla SHV-28 and the beta-lactamase-encoding gene bla OXA-1. Additionally, Kp14U04 harboured a multiple stress resistance protein, efflux systems and regulators, heavy metal resistance and virulence genes, plasmids, prophage-related sequences and genomic islands. These features revealed the high potential of this isolate to resist antimicrobial therapy, survive in adverse environments, cause infections and overcome host defence mechanisms.


Asunto(s)
Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana Múltiple/genética , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae , Eliminación de Secuencia , beta-Lactamasas/genética , Anciano , Antibacterianos/farmacología , Brasil , Colistina/farmacología , Femenino , Genes Bacterianos , Humanos , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , Plásmidos
19.
J Med Microbiol ; 70(3)2021 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-33507142

RESUMEN

Klebsiella pneumoniae strains carrying OXA-48-like carbapenemases are increasingly prevalent across the globe. There is thus an urgent need to better understand the mechanisms that underpin the dissemination of bla OXA-48-like carbapenemases. To this end, four ertapenem-resistant K. pneumoniae isolates producing OXA-48-like carbapenemases were isolated from two patients. Genome sequencing revealed that one sequence type (ST) 17 isolate carried bla OXA-181, whilst three isolates from a single patient, two ST76 and one ST15, carried bla OXA-232. The 50514 bp bla OXA-181-harbouring plasmid, pOXA-181_YML0508, was X3-type with a conjugation frequency to Escherichia coli of 1.94×10-4 transconjugants per donor. The bla OXA-232 gene was located on a 6141 bp ColKP3-type plasmid, pOXA-232_WSD, that was identical in the ST76 and ST15 K. pneumoniae isolates. This plasmid could be transferred from K. pneumoniae to E. coli at low frequency, 8.13×10-6 transconjugants per donor. Comparative analysis revealed that the X3 plasmid acquired the bla OXA-48-like gene via IS3000-mediated co-integration of the ColKP3-type plasmid. Our study highlights how plasmid integration and rearrangements can contribute to the spread of bla OXA-48-like genes, which provides important clues for clinical prevention of the dissemination of K. pneumoniae strains carrying bla OXA-48-like carbapenemases.


Asunto(s)
Proteínas Bacterianas/genética , Enterobacteriaceae Resistentes a los Carbapenémicos/genética , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , beta-Lactamasas/genética , Anciano de 80 o más Años , China , Genes Bacterianos , Humanos , Klebsiella pneumoniae/genética , Masculino , Persona de Mediana Edad , Plásmidos
20.
Sci Total Environ ; 763: 144119, 2021 Apr 01.
Artículo en Inglés | MEDLINE | ID: mdl-33418471

RESUMEN

It is important that environmental parameters that may affect the prevalence of AmpC beta-lactamase genes are investigated to devise frameworks for their surveillance, management and prevention. The aim of this study was thus to determine which environmental parameters are associated with the prevalence of clinically relevant AmpC beta-lactamase genes in aquatic systems. River water was sampled from seven sites in the Crocodile West River, South Africa. Physical-chemical parameters, metal levels and beta-lactam levels were measured. Environmental DNA was extracted from the water samples and six AmpC beta-lactamase gene groups (ACC, ACT/MIR, BIL/LAT/CMY, DHA, FOX, MOX/CMY) were quantified using quantitative PCR. Additionally, 16S rRNA gene metabarcoding analyses were performed on eDNA for each site and metabolic pathways were predicted using PICRUST2. Network analysis was performed to establish co-occurrences of AmpC genes with environmental factors. Quantification results indicated that AmpC gene copy numbers were significantly high (Kruskal Wallis H Test, p < 0.05) at Sites 1-3 of the Crocodile West River. In contrast, no significant changes regarding environmental factors were observed across the seven sites. Results of network analysis indicated that the AmpC gene groups had limited associations with all the environmental parameters, except for some key bacterial families, specifically Pseudomonadaceae, Aeromonadaceae and Enterobacteriaceae. A significant positive correlation between population density and AmpC genes suggested that in more densely populated areas more faecal pollution will be prevalent which is associated with high AmpC gene levels. Areas such as these are also likely to be linked with more antibiotic use which supports the notion that pre-selection of AmpC genes occurs before entering the aquatic environment. Moreover, it was demonstrated that prevalent selectors of AmpC genes do not ensure that continuous selection occurs in an aquatic environment. This information could be vital in future detection and management of AmpC genes in aquatic systems.


Asunto(s)
Proteínas Bacterianas , beta-Lactamasas , Antibacterianos , Proteínas Bacterianas/genética , Humanos , Pruebas de Sensibilidad Microbiana , Plásmidos , Prevalencia , ARN Ribosómico 16S/genética , Sudáfrica , beta-Lactamasas/genética
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