RESUMEN

Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has become a major concern worldwide due to multidrug resistance and the ability to spread locally and globally. Infections caused by KPC-KP are great challenge in the healthcare systems because these are associated with longer hospitalization and high mortality. The emergence of colistin resistance has significantly reduced already limited treatment options. This study describes the molecular background of colistin-resistant KPC-KP isolates in the largest hospital in southern Croatia. Thirty-four non-duplicate colistin-resistant KPC-KP isolates were collected during routine work from April 2019 to January 2020 and from February to May 2021. Antimicrobial susceptibility was determined using disk diffusion, broth microdilution, and the gradient strip method. Carbapenemase was detected with an immunochromatographic test. Identification of blaKPC and mcr genes or mutations in pmrA, pmrB, mgrB, phoP, and phoQ genes were performed by polymerase chain reaction (PCR) and positive products were sequenced. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for epidemiological analysis. All isolates were multidrug-resistant, with colistin minimum inhibitory concentrations (MICs) from 4 to >16 mg/L, and all harbored blaKPC-2 and had a single point mutation in the mgrB gene resulting in a premature stop codon, with the exception of one isolate with four point mutations corresponding to stop codons. All isolates were negative for mcr genes. PFGE analysis identified a single genetic cluster, and MLST revealed that all isolates belonged to sequence type 101 (ST101). These results show emergence of the high-risk ST101/KPC-2 clone of K. pneumoniae in Croatia as well as appearance of colistin resistance due to mutations in the mgrB gene. Molecular analysis of epidemiology and possible resistance mechanisms are important to develop further strategies to combat such threats.(AU)

Asunto(s)

Humanos , Colistina , Klebsiella pneumoniae , Resistencia a Medicamentos , Microbiología , Técnicas Microbiológicas , Croacia

RESUMEN

Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-KP) has become a major concern worldwide due to multidrug resistance and the ability to spread locally and globally. Infections caused by KPC-KP are great challenge in the healthcare systems because these are associated with longer hospitalization and high mortality. The emergence of colistin resistance has significantly reduced already limited treatment options. This study describes the molecular background of colistin-resistant KPC-KP isolates in the largest hospital in southern Croatia. Thirty-four non-duplicate colistin-resistant KPC-KP isolates were collected during routine work from April 2019 to January 2020 and from February to May 2021. Antimicrobial susceptibility was determined using disk diffusion, broth microdilution, and the gradient strip method. Carbapenemase was detected with an immunochromatographic test. Identification of blaKPC and mcr genes or mutations in pmrA, pmrB, mgrB, phoP, and phoQ genes were performed by polymerase chain reaction (PCR) and positive products were sequenced. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used for epidemiological analysis. All isolates were multidrug-resistant, with colistin minimum inhibitory concentrations (MICs) from 4 to >16 mg/L, and all harbored blaKPC-2 and had a single point mutation in the mgrB gene resulting in a premature stop codon, with the exception of one isolate with four point mutations corresponding to stop codons. All isolates were negative for mcr genes. PFGE analysis identified a single genetic cluster, and MLST revealed that all isolates belonged to sequence type 101 (ST101). These results show emergence of the high-risk ST101/KPC-2 clone of K. pneumoniae in Croatia as well as appearance of colistin resistance due to mutations in the mgrB gene. Molecular analysis of epidemiology and possible resistance mechanisms are important to develop further strategies to combat such threats.

Asunto(s)

Colistina , Infecciones por Klebsiella , Humanos , Colistina/farmacología , Klebsiella pneumoniae , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Tipificación de Secuencias Multilocus , Croacia/epidemiología , Infecciones por Klebsiella/epidemiología , Infecciones por Klebsiella/microbiología , Proteínas Bacterianas/genética , beta-Lactamasas/genética , Hospitales , Pruebas de Sensibilidad Microbiana , Células Clonales

RESUMEN

BACKGROUND: Klebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS). MATERIALS AND METHODS: We selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015-2016) as well as Belgian livestock animals (n = 2) (2017-2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness. RESULTS: Hospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01). Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates. CONCLUSION: The study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.

RESUMEN

We determined the longitudinal persistence of ceftiofur-resistant Escherichia coli from a chicken breeding farm in China. A total of 150 samples were collected from 5 breeding periods in a flock of layer hens, and the prevalence of ceftiofur-resistant E. coli fluctuated across the 5 chicken breeding stages: eggs, 3.33%; growing period, 100%; early laying period, 36.7%; peak laying period, 66.7% and late laying period, 80%. The most prevalent ceftiofur resistance genes were blaCTX-M-55, blaCMY and blaNDM, and ST101 was the most prevalent and persistent sequence type across the breeding periods. Our results indicated that this breeder flock was heavily contaminated by ST101 ceftiofur-resistant E. coli and that its presence should be intensively monitored on chicken farms.

RESUMEN

Background: The worldwide emergence and diffusion of extended-spectrum ß-lactamase-K. pneumoniae (ESBL-KP) is of particular concern. Although ESBL-KP can inhabit the human gut asymptomatically, colonization with ESBL-KP is associated with an increased risk of ESBL-KP infection and mortality. In this study, we investigated the prevalence and characteristics of ESBL-KP in fecal samples from healthy persons in 12 villages in Shandong Province, China. Methods: Screening for ESBL-KP in fecal samples was performed by selective cultivation. The bacterial species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Minimum inhibitory concentrations (MICs) of 16 antibiotics were determined by the agar dilution method. Plasmid replicons, antimicrobial resistance genes and Sequence types (STs) of the isolates were determined by whole-genome sequencing (WGS). Genetic relatedness of ESBL-KP isolates was determined by the single nucleotide polymorphisms (SNP). The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by ESBL-KP isolates. Conjugation assays was used to verify the transferability of bla CTX - M. Results: ESBL-KP prevalence rates increased from 12.0% in 2015 to 27.5% in 2017. The experimental results showed that 97% of isolates had multi-drug resistance. Multiple ESBL resistance genotypes were commonly detected in the isolates. STs among the ESBL-KP isolates were diverse. All 69 bla CTX-M-3-positive isolates were located on plasmids, and these genes could be transferred with plasmids between different strains. Phylogenetic analysis showed the possibility of transmission among some isolates. Conclusion: This study obtained the drug resistance patterns, the drug resistance phenotype and molecular characteristics of fecal-derived ESBL-KP in rural communities in Shandong Province, China. We report a rapid increase in occurrence of ESBL-KP among fecal samples collected from healthy rural residents of Shandong Province from 2015 to 2017. The carriage rate of multidrug-resistant bacteria in healthy residents is increasing. Thus, a need for further monitoring and possible interventions of ESBL-KP in this region is warranted.

Asunto(s)

Farmacorresistencia Bacteriana , Infecciones por Klebsiella , Klebsiella pneumoniae , Humanos , beta-Lactamasas/genética , Genómica , Infecciones por Klebsiella/epidemiología , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/genética , Filogenia , Población Rural

RESUMEN

Aim: We investigated the prevalence of carbapenemase-producing Enterobacteriaceae (CPE) in chicken meat in Western Algeria in 2017. Results: From February to July 2017, samples of chicken meat from three poultry farms in Western Algeria were screened for the presence of CPE. Strains were characterized with regard to antibiotic resistance, ß-lactamase content, Plasmid-mediated quinolone resistance, sulfonamide resistance genes, clonality (repetitive sequence-based profiles and multilocus sequence typing) and virulence traits. Of 181 samples analyzed, 29 (16.0%) carbapenemase-producing Klebsiella pneumoniae were detected. Twenty-three OXA-48-producers (79.3%) and six (20.7%) New Delhi metallo (NDM)-1-producers were observed. Clonality analysis showed three distinct lineages and clonal expansions of the OXA-48-producing K. pneumoniae ST48 and the NDM-1-producing K. pneumoniae ST101. These isolates harbored fimH, ureA, mrkD, entB, uge, and wabG. Neither capsular serotype genes nor hypermucoviscous phenotype were detected. Plasmid analysis confirmed that all these isolates harbored the transferable IncL and IncFIIK plasmids. Conclusions: This study reports the spread of OXA-48 and NDM-1-producing K. pneumoniae ST48 and ST101 in chicken meat in Western Algeria and demonstrates that food represents a reservoir of the carbapenemases encoding genes.

Asunto(s)

Antibacterianos/farmacología , Klebsiella pneumoniae/genética , Aves de Corral/microbiología , beta-Lactamasas/genética , Argelia/epidemiología , Animales , Pollos/microbiología , Farmacorresistencia Bacteriana Múltiple/genética

RESUMEN

Carbapenemase-producing and colistin resistant Klebsiella pneumoniae has become a worldwide healthcare problem. This study describes molecular characterization of carbapenemase-producing and colistin resistant clinical K. pneumoniae isolates.A total of 93 non-replicate carbapenem and colistin resistant K. pneumoniae were recovered from clinical specimens in a university hospital during 2017-2019. Detection of blaOXA-48, blaKPC, blaNDM-1, blaIMP, blaVIM-1 and mcr-1, -2, -3, -4, -5, -6, -7, and -8 genes was performed by PCR. The bacterial isolates were assigned to clonal lineages by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST).All isolates harbored blaOXA-48 and only two isolates harbored blaOXA-48, and blaNDM-1 genes together. In colistin resistant K. pneumoniae, mcr-1 was detected in two (2.1%) isolates. Ninety three isolates of K. pneumoniae were categorized into three clusters and five pulsotypes. MLST revealed two different sequence types, ST101 (89/93) and ST147 (4/93).In our study ST101 was found to be a significantly dominant clone carrying blaOXA-48 and among our strains a low frequency of mcr-1 gene was determined. The emergence of colistin resistance was observed in K. pneumoniae ST101 isolates. ST101 may become a global threat in the dissemination of carbapenem and colistin resistance.

Asunto(s)

Antibacterianos/farmacología , Proteínas Bacterianas/biosíntesis , Carbapenémicos/farmacología , Colistina/farmacología , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/genética , beta-Lactamasas/biosíntesis , Proteínas Bacterianas/genética , Farmacorresistencia Bacteriana Múltiple , Electroforesis en Gel de Campo Pulsado , Genes Bacterianos , Humanos , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/enzimología , Klebsiella pneumoniae/aislamiento & purificación , Pruebas de Sensibilidad Microbiana , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Turquía/epidemiología , beta-Lactamasas/genética

RESUMEN

Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.

RESUMEN

BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is an urgent public health issue in Italy. This pattern of resistance is due mainly to dissemination of carbapenemase genes. Molecular characterization of carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains was performed over a three-year period. In-depth analysis was performed on a subset of emerging CR-KP ST101 and ST307 clones. METHODS: A prospective study was performed on 691 patients with CR-KP bloodstream infections hospitalized in 19 hospitals located in three large provinces in Southern Italy. Carbapenemase genes were identified via genotyping methods. Multi-locus sequence typing (MLST) and Whole Genome Sequencing (WGS) were carried out on ST101 and ST307 isolates. RESULTS: Among the CR-KP isolates, blaKPC was found in 95.6%, blaVIM was found in 3.5%, blaNDM was found in 0.1% and blaOXA-48 was found in 0.1%. The blaKPC-3 variant was identified in all 104 characterized KPC-KP isolates. MLST of 231 representative isolates revealed ST512 in 45.5%, ST101 in 20.3% and ST307 in 18.2% of the isolates. cgMLST of ST307 and ST101 isolates revealed presence of more than one beta-lactam resistance gene. Amino acid substitution in the chromosomal colistin-resistance gene pmrB was found in two ST101 isolates. CONCLUSIONS: ST512 is widespread in Southern Italy, but ST101 and ST307 are emerging since they were found in a significant proportion of cases. Aggressive infection control measures and a continuous monitoring of these high-risk clones are necessary to avoid rapid spread of CR-KP, especially in hospital settings.

Asunto(s)

Proteínas Bacterianas/genética , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , beta-Lactamasas/genética , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Niño , Preescolar , Farmacorresistencia Bacteriana Múltiple/genética , Electroforesis en Gel de Campo Pulsado , Femenino , Humanos , Lactante , Recién Nacido , Italia/epidemiología , Klebsiella pneumoniae/enzimología , Masculino , Persona de Mediana Edad , Epidemiología Molecular , Tipificación de Secuencias Multilocus , Estudios Prospectivos , Reacción en Cadena en Tiempo Real de la Polimerasa , Serogrupo , Secuenciación Completa del Genoma , Adulto Joven

RESUMEN

Klebsiella pneumoniae is a major cause of severe healthcare-associated infections and often shows MDR phenotypes. Carbapenem resistance is frequent, and colistin represents a key molecule to treat infections caused by such isolates. Here we evaluated the antimicrobial resistance (AMR) mechanisms and the genomic epidemiology of clinical K. pneumoniae isolates from Serbia. Consecutive non-replicate K. pneumoniae clinical isolates (n = 2,298) were collected from seven hospitals located in five Serbian cities and tested for carbapenem resistance by disk diffusion. Isolates resistant to at least one carbapenem (n = 426) were further tested for colistin resistance with Etest or Vitek2. Broth microdilution (BMD) was performed to confirm the colistin resistance phenotype, and colistin-resistant isolates (N = 45, 10.6%) were characterized by Vitek2 and whole genome sequencing. Three different clonal groups (CGs) were observed: CG101 (ST101, N = 38), CG258 (ST437, N = 4; ST340, N = 1; ST258, N = 1) and CG17 (ST336, N = 1). mcr genes, encoding for acquired colistin resistance, were not observed, while all the genomes presented mutations previously associated with colistin resistance. In particular, all strains had a mutated MgrB, with MgrBC28S being the prevalent mutation and associated with ST101. Isolates belonging to ST101 harbored the carbapenemase OXA-48, which is generally encoded by an IncL/M plasmid that was no detected in our isolates. MinION sequencing was performed on a representative ST101 strain, and the obtained long reads were assembled together with the Illumina high quality reads to decipher the bla OXA- 48 genetic background. The bla OXA- 48 gene was located in a novel IncFIA-IncR hybrid plasmid, also containing the extended spectrum ß-lactamase-encoding gene bla CTX-M-15 and several other AMR genes. Non-ST101 isolates presented different MgrB alterations (C28S, C28Y, K2∗, K3∗, Q30∗, adenine deletion leading to frameshift and premature termination, IS5-mediated inactivation) and expressed different carbapenemases: OXA-48 (ST437 and ST336), NDM-1 (ST437 and ST340) and KPC-2 (ST258). Our study reports the clonal expansion of the newly emerging ST101 clone in Serbia. This high-risk clone appears adept at acquiring resistance, and efforts should be made to contain the spread of such clone.

RESUMEN

Klebsiella pneumoniae (KP) is an important pathogen involved in serious nosocomial infections all over the world. Here, we describe the first report on a blood-stream infection caused by an OXA-48/NDM-1 ST101-KP, in Italy. The patient was an Italian woman, transferred from Cairo Hospital to a Neurosurgery ward in Cuneo (IT). The detection described here enhances the need for an effective National infection control strategy in Italy.

Asunto(s)

Infecciones por Klebsiella , Klebsiella pneumoniae , Enfermedad Relacionada con los Viajes , beta-Lactamasas , Antibacterianos , Proteínas Bacterianas , Egipto , Femenino , Humanos , Control de Infecciones , Italia , Infecciones por Klebsiella/sangre , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/clasificación , Klebsiella pneumoniae/genética , Tipificación de Secuencias Multilocus , beta-Lactamasas/genética

RESUMEN

Escherichia coli EC121 is a multidrug-resistant (MDR) strain isolated from a bloodstream infection of an inpatient with persistent gastroenteritis and T-zone lymphoma that died due to septic shock. Despite causing an extraintestinal infection, previous studies showed that it did not have the usual characteristics of an extraintestinal pathogenic E. coli. Instead, it belonged to phylogenetic group B1 and harbored few known virulence genes. To evaluate the pathogenic potential of strain EC121, an extensive genome sequencing and in vitro characterization of various pathogenicity-associated properties were performed. The genomic analysis showed that strain EC121 harbors more than 50 complete virulence genetic clusters. It also displays the capacity to adhere to a variety of epithelial cell lineages and invade T24 bladder cells, as well as the ability to form biofilms on abiotic surfaces, and survive the bactericidal serum complement activity. Additionally, EC121 was shown to be virulent in the Galleria mellonella model. Furthermore, EC121 is an MDR strain harboring 14 antimicrobial resistance genes, including blaCTX-M-2. Completing the scenario, it belongs to serotype O154:H25 and to sequence type 101-B1, which has been epidemiologically linked to extraintestinal infections as well as to antimicrobial resistance spread. This study with E. coli strain EC121 shows that clinical isolates considered opportunistic might be true pathogens that go underestimated.

RESUMEN

Atypical antipsychotics improve positive and negative symptoms but are not effective for treating cognitive impairments in patients with schizophrenia. We previously reported that cognitive impairments in neonatal ventral hippocampus (NVH)-lesioned rats show resistance to atypical antipsychotics risperidone and are associated with reduced calcium/calmodulin-dependent protein kinase II (CaMKII) and protein kinase C (PKC) signaling in memory-related regions. The cognitive enhancer ST101 (spiro[imi-dazo[1,2-a]pyridine-3,2-indan]-2(3H)-one) stimulates CaMKII activity in the hippocampus and medial prefrontal cortex (mPFC). We thus tested ST101 on cognitive impairments in NVH-lesioned rats. Chronic ST101 administration (0.1 and/or 0.5 mg/kg, p.o.) significantly improved deficits in prepulse inhibition (PPI), social interaction, and cognitive function in NVH-lesioned rats. ST101 administration (0.5 mg/kg, p.o.) significantly restored the decreased CaMKII autophosphorylation (Thr-286) in the mPFC and hippocampal CA1 regions of NVH-lesioned rats when assessed by immunohistochemistry. Chronic ST101 administration (0.1 mg/kg, p.o.) improved the decline in phosphorylation levels of CaMKII (Thr-286), PKCα (Ser-657), α-amino-3-hydroxy-5-methyl-4-isoxazol- propionic acid (AMPA)-type glutamate receptor subunit 1 (GluA1: Ser-831), and N-methyl-d-aspartate (NMDA) receptor subunit 1 (GluN1: Ser-896) in the mPFC and hippocampal CA1 regions. Taken together, these results suggest that ST101 improves schizophrenia-like behaviors and cognitive impairment by enhancing CaMKII/PKCα signaling in the mPFC and hippocampus in NVH-lesioned rats.

Asunto(s)

Proteína Quinasa Tipo 2 Dependiente de Calcio Calmodulina/metabolismo , Trastornos del Conocimiento/tratamiento farmacológico , Hipocampo/efectos de los fármacos , Indanos/farmacología , Proteína Quinasa C-alfa/metabolismo , Esquizofrenia/tratamiento farmacológico , Transducción de Señal/efectos de los fármacos , Compuestos de Espiro/farmacología , Animales , Animales Recién Nacidos , Antipsicóticos/farmacología , Cognición/efectos de los fármacos , Trastornos del Conocimiento/metabolismo , Femenino , Hipocampo/metabolismo , Masculino , Memoria/efectos de los fármacos , Fosforilación/efectos de los fármacos , Corteza Prefrontal/efectos de los fármacos , Corteza Prefrontal/metabolismo , Ratas , Ratas Sprague-Dawley , Receptores de N-Metil-D-Aspartato/metabolismo , Risperidona/farmacología , Esquizofrenia/metabolismo

RESUMEN

Background: This study aimed to investigate the occurrence of mcr-1 encoding plasmid-mediated colistin-resistance gene in Escherichia coli isolated from migratory birds in Thailand. Materials and Methods: A total of 178 cloacal swabs from migratory birds was sampled and isolated from 2016 to 2017 in Nan, Trang, and Bangkok, Thailand. The multiplex polymerase chain reaction was used to screen the resistance genes. After screening, a disk diffusion assay and the minimum inhibitory concentration were investigated. The draft genome sequence of isolate 2A85589 was obtained using an Illumina HiSeq X-Ten platform. The genome was assembled using SPAdes 3.0.0. Antimicrobial resistance genes were identified using ResFinder 3.1. Results: We reported E. coli ST101 of isolate 2A85589, an mcr-1-carrying resistance gene isolated from the migratory bird species Hirundo rustica in Thailand. The draft genome of 2A85589 was 4,621,016 bp in size. IncHI1A plasmid was identified using PlasmidFinder with high coverage. In silico analysis detected the presence of eight putative acquired resistance genes, namely blaTEM-1B, mcr-1, mef(A), mef(B), QnrS1, sul3, tet(A), and tet(B), which conferred resistance to ß-lactam, colistin, macrolide, quinolone, sulfonamide, and tetracycline. Conclusion: This study underlines the potential risk of the environmental contamination of mcr-1-carrying E. coli isolated from the migratory bird. The long range migration of birds can result in dissemination of mcr-1-carrying bacteria globally. Therefore, plasmid-mediated colistin is an urgent need to be addressed in both human and veterinary medicine for disease control and prevention.

Asunto(s)

Antibacterianos/farmacología , Infecciones por Escherichia coli/epidemiología , Proteínas de Escherichia coli/genética , Escherichia coli/efectos de los fármacos , Animales , Aves/microbiología , Colistina/farmacología , Farmacorresistencia Bacteriana/genética , Escherichia coli/genética , Escherichia coli/aislamiento & purificación , Infecciones por Escherichia coli/microbiología , Infecciones por Escherichia coli/veterinaria , Genes Bacterianos , Pruebas de Sensibilidad Microbiana , Plásmidos/genética , Tailandia/epidemiología

RESUMEN

The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried blaoxa-48 and blaNDM-1 genes located on different plasmids belonging to the IncM/L and IncA/C2 groups, respectively. The 13 strains had identical PFGE profiles. MLST and cgMLST showed that K. pneumoniae was dominated by CRKp ST101 and two novel STs (ST3666 and ST3367), identified after submission to the MLST database for ST assignment. All isolates shared the same virulence factors such as type 3 fimbriae, genes for yersiniabactin biosynthesis, yersiniabactin receptor, and iron ABC transporter. They carried the wzi137 variant associated with the K17 serotype. To the best of our knowledge, this is the first report of two novel STs, 3366 and 3367, NDM-OXA-48-co-producing K. pneumoniae clinical isolates, in Italy.

Asunto(s)

Antibacterianos/farmacología , Klebsiella pneumoniae/genética , beta-Lactamasas/genética , Proteínas Bacterianas/genética , Técnicas de Tipificación Bacteriana , Carbapenémicos/farmacología , Brotes de Enfermedades , Electroforesis en Gel de Campo Pulsado , Humanos , Recién Nacido , Cuidado Intensivo Neonatal , Italia , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/enzimología , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Secuenciación Completa del Genoma

RESUMEN

The global dissemination of Klebsiella pneumoniae and Klebsiella pneumoniae carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that has been identified in different parts of the world with the potential to become a global, persistent public health threat. Recent research suggests the ST101 lineage is associated with an 11% increase in mortality rate in comparison to non-ST101 infections. In this study, we generated a high-quality, near-finished genome assembly of a multidrug-resistant (MDR) isolate from Italy (isolate 4743) that is a single locus variant of ST101 (ST1685). We demonstrate that the 4743 genome contains virulence features such as an integrative conjugative element carrying the yersiniabactin siderophore (ICEKp3), the mannose-resistant Klebsiella-like (type III) fimbriae cluster (mrkABCDFHIJ), the ferric uptake system (kfuABC), the yersiniabactin receptor gene fyuA, a capsular K type K17, and an O antigen type of O1. K. pneumoniae 4743 carries the blaKPC-2 carbapenemase gene along with genes conferring resistance to aminoglycosides, beta-lactams, fluoroquinolones, fosfomycin, macrolides, lincosamides, and streptogramin B. A comparative genomics analysis of 44 ST101 genomes as well as newly sequenced isolate 4743 identified variable antimicrobial resistance (AMR) resistance profiles and incompatibility plasmid types, but similar virulence factor profiles. Using Bayesian methodologies, we estimate the common ancestor for the ST101 lineage emerged in 1990 (95% HPD: 1965 to 2007) and isolates within the lineage acquired bla KPC after the divergence from its parental clonal group and dissemination. The identification of virulence factors and antibiotic resistance genes acquired by this newly emerging clone provides insight into the reported increased mortality rates and highlights its potential success as a persistent nosocomial pathogen. With a combination of both colistin resistance, carbapenem resistance, and several known virulence factors, the ST101 genetic repertoire may be a "perfect storm" allowing for a newly emerging, high-risk, extensively antibiotic resistant clone. This high-risk clone appears adept at acquiring resistance and may perpetuate the dissemination of extensive antimicrobial resistance. Greater focus on the acquisition of virulence factors and antibiotic resistance genes is crucial for understanding the spread of antibiotic resistance.

RESUMEN

Resistance to carbapenems in Enterobacteriaceae, including Klebsiella pneumoniae, represents a major clinical problem given the lack of effective alternative antibiotics. Bacteriophages could provide a valuable tool to control the dissemination of antibiotic resistant isolates, for the decolonization of colonized individuals and for treatment purposes. In this work, we have characterized a lytic bacteriophage, named vB_Kpn_F48, specific for K. pneumoniae isolates belonging to clonal group 101. Phage vB_Kpn_F48 was classified as a member of Myoviridae, order Caudovirales, on the basis of transmission electron microscopy analysis. Physiological characterization demonstrated that vB_Kpn_F48 showed a narrow host range, a short latent period, a low burst size and it is highly stable to both temperature and pH variations. High throughput sequencing and bioinformatics analysis revealed that the phage is characterized by a 171 Kb dsDNA genome that lacks genes undesirable for a therapeutic perspective such integrases, antibiotic resistance genes and toxin encoding genes. Phylogenetic analysis suggests that vB_Kpn_F48 is a T4-like bacteriophage which belongs to a novel genus within the Tevenvirinae subfamily, which we tentatively named "F48virus". Considering the narrow host range, the genomic features and overall physiological parameters phage vB_Kpn_F48 could be a promising candidate to be used alone or in cocktails for phage therapy applications.

Asunto(s)

Bacteriólisis , Bacteriófagos/crecimiento & desarrollo , Bacteriófagos/aislamiento & purificación , Klebsiella pneumoniae/virología , Myoviridae/crecimiento & desarrollo , Myoviridae/aislamiento & purificación , Bacteriófagos/clasificación , Bacteriófagos/genética , Biología Computacional , Secuenciación de Nucleótidos de Alto Rendimiento , Especificidad del Huésped , Concentración de Iones de Hidrógeno , Microscopía Electrónica de Transmisión , Myoviridae/clasificación , Myoviridae/genética , Filogenia , Homología de Secuencia , Temperatura , Virión/ultraestructura

RESUMEN

This study characterizes KPC-2 producing Klebsiella pneumoniae belonging to ST101. Whole genome sequencing using the Ion Torrent PGM platform with 400 bp chemistry was performed. blaKPC-2 was found on an IncFIIK plasmid associated with ISKpn6 and ISKpn7 without Tn4401. This is the first report of KPC-2 K. pneumoniae from bacteremia in India. The isolate also coded for other resistance genes such as aadA1, aadA2, armA, aac(3)-Ild, aac(6')-Ild for aminoglycoside; blaSHV-11, blaTEM-1B, blaOXA-9, for ß-lactams and aac(6')-Ild, oqxA, oqxB, qnrB1 for fluoroquinolones. It belonged to the K17 capsular type. India is endemic to New Delhi metallo-ß-lactamase and OXA48-like carbapenemases and K. pneumoniae carbapenemase (KPC) is seldom reported. With high rates of carbapenem resistance, emergence of KPC in India will challenge patient management. The isolate was susceptible to colistin. The patient had a fatal outcome.

Asunto(s)

Genotipo , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/clasificación , Klebsiella pneumoniae/enzimología , Sepsis/microbiología , beta-Lactamasas/metabolismo , Cápsulas Bacterianas/genética , Elementos Transponibles de ADN , Farmacorresistencia Bacteriana , Genes Bacterianos , Humanos , India , Klebsiella pneumoniae/genética , Klebsiella pneumoniae/aislamiento & purificación , Persona de Mediana Edad , Tipificación de Secuencias Multilocus , Plásmidos/análisis , Plásmidos/clasificación , Análisis de Secuencia de ADN , Secuenciación Completa del Genoma

RESUMEN

OBJECTIVES: This study investigated the prevalence of extended-spectrum ß-lactamase-producing Klebsiella pneumoniae (ESBL-KP) strains in the National Bone Marrow Transplant Center of Tunis between 2002 and 2011 as well as their associated antimicrobial resistance patterns and molecular features. METHODS: Antimicrobial susceptibility was determined by the disk diffusion method according to CA-SFM guidelines. All of the strains were screened for ß-lactamase genes, plasmid-encoded AmpC genes and integrons. Carbapenemase genes were analysed by PCR and sequencing for strains showing reduced susceptibility to ertapenem. Genetic relatedness was determined by pulsed-field gel electrophoresis (PFGE) and multilocus sequencing typing (MLST). RESULTS: A total of 128 non-repetitive ESBL-KP strains (23.4%) responsible for infection or colonisation were recovered among 548 K. pneumoniae strains. The isolates were also multidrug-resistant. Molecular analysis revealed the prevalence of blaSHV-type (92.2%), followed by blaOXA-1 (81.3%) and blaCTX-M-1 group (73.4%). Four ertapenem-resistant ESBL-KP strains (3.1%) carried the blaOXA-48 gene associated with the blaCTX-M-15 gene. Class 1 integrons were the most prevalent among the isolates (85.2%). High diversity was demonstrated by PFGE with limited clonal dissemination of 1 major (n=13 strains) and 11 minor clusters (each comprising 2-3 strains). MLST of representative strains also showed high diversity with two main epidemic clones: ST15, associated with the major cluster; and ST101, associated with five minor clusters (n=11 strains). CONCLUSIONS: This study provides relevant information on the epidemiology of ESBL-KP strains in oncohaematology patients, of which 18.8% belonged to the specific CTX-M-15 K. pneumoniae clones ST15 and ST101.

Asunto(s)

Huésped Inmunocomprometido , Infecciones por Klebsiella/epidemiología , Klebsiella pneumoniae/genética , Antibacterianos/farmacología , ADN Bacteriano/genética , Farmacorresistencia Bacteriana Múltiple , Humanos , Infecciones por Klebsiella/microbiología , Klebsiella pneumoniae/efectos de los fármacos , Klebsiella pneumoniae/enzimología , Pruebas de Sensibilidad Microbiana , Tipificación de Secuencias Multilocus , Estudios Retrospectivos , Túnez/epidemiología , beta-Lactamasas/genética

RESUMEN

INTRODUCTION: The worldwide dissemination of the acquired carbapenemases in Gram-negative bacteria is a strongly expressed demand for the emergence of post antibiotic era. The aim of this study was to test the production of carbapenemase by Klebsiella pneumoniae strains isolated from hospitalized cancer patients and to investigate the genetic relationship of carbapenemase producing carbapenem resistant K. pneumoniae using multilocus sequence typing (MLST). METHODOLOGY: Antibiotic susceptibility testing and phenotypic testing for extended spectrum b-lactamases (ESBL) and carbapenemases production were performed. PCR amplification of ESBL and carbapenemase genes was performed. MLST was done to detect the genetic relatedness of the isolates. RESULTS: Our data showed all strains were sensitive to colistin. Carba NP test was positive in thirty-one carbapenem resistant K. pneumoniae isolates and 26 out of 34 K. pneumoniae isolates were metallo-beta-lactamases (MBL) positive. All carbapenemase-positive isolates were ESBL CTX-M-1-like positive. blaOXA-48 gene was detected in 25 isolates (80.65%) and 21 isolates (67.75%) produced blaNDM-1 like enzyme. VIM and KPC genes were not identified in this study. Association of blaOXA-48 like and blaNDM-1 like was found in 15 (48.39%) isolates, while the coproduction of OXA-48-like and IMP-1 was revealed in only one K. pneumoniae isolate. MLST revealed ten distinct sequence types (STs). CONCLUSION: Here we have documented the coexistence of NDM-type and OXA-48-like, and the coproduction of OXA-48-like and IMP in carbapenem resistant K. pneumoniae in patients with cancer. The dominant clone of the OXA-48-like-producing K. pneumoniae isolates from Egypt was ST101 epidemic clone belonging to clonal complex 101, an association that has been reported worldwide. The second most frequent ST was ST383.ST11 was assigned to OXA-48-producing K. pneumoniae.