Eliana Carolina Vespero

Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms

BackgroundKlebsiella pneumoniae is an important opportunistic pathogen associated with nosocomial and community-acquired infections. A wide repertoire of virulence and antimicrobial resistance genes is present in K. pneumoniae genomes, which can constitute extra challenges in the treatment of infections caused by some strains. K. pneumoniae Kp13 is a multidrug-resistant strain responsible for causing a large nosocomial outbreak in a teaching hospital located in Southern Brazil. Kp13 produces K. pneumoniae carbapenemase (KPC-2) but is unrelated to isolates belonging to ST 258 and ST 11, the main clusters associated with the worldwide dissemination of KPC-producing K. pneumoniae. In this report, we perform a genomic comparison between Kp13 and each of the following three K. pneumoniae genomes: MGH 78578, NTUH-K2044 and 342.ResultsWe have completely determined the genome of K. pneumoniae Kp13, which comprises one chromosome (5.3 Mbp) and six plasmids (0.43 Mbp). Several virulence and resistance determinants were identified in strain Kp13. Specifically, we detected genes coding for six beta-lactamases (SHV-12, OXA-9, TEM-1, CTX-M-2, SHV-110 and KPC-2), eight adhesin-related gene clusters, including regions coding for types 1 (fim) and 3 (mrk) fimbrial adhesins. The rmtG plasmidial 16S rRNA methyltransferase gene was also detected, as well as efflux pumps belonging to five different families. Mutations upstream the OmpK35 porin-encoding gene were evidenced, possibly affecting its expression. SNPs analysis relative to the compared strains revealed 141 mutations falling within CDSs related to drug resistance which could also influence the Kp13 lifestyle. Finally, the genetic apparatus for synthesis of the yersiniabactin siderophore was identified within a plasticity region. Chromosomal architectural analysis allowed for the detection of 13 regions of difference in Kp13 relative to the compared strains.ConclusionsOur results indicate that the plasticity occurring at many hierarchical levels (from whole genomic segments to individual nucleotide bases) may play a role on the lifestyle of K. pneumoniae Kp13 and underlie the importance of whole-genome sequencing to study bacterial pathogens. The general chromosomal structure was somewhat conserved among the compared bacteria, and recombination events with consequent gain/loss of genomic segments appears to be driving the evolution of these strains.

First Report of NDM-1-Producing Acinetobacter baumannii Sequence Type 25 in Brazil

ABSTRACT New Delhi metallo-β-lactamase 1 (NDM-1) was first identified in Brazil in Enterobacter hormaechei and Providencia rettgeri in 2013. Here, we describe the first case of NDM-1-producing Acinetobacter baumannii sequence type 25 isolated from the urinary tract of a 71-year-old man who died of multiple complications, including A. baumannii infection. The NDM-1 gene was detected by quantitative PCR, and its sequence confirmed its presence in an ∼100-kb plasmid.

Pyrosequencing-based analysis reveals a novel capsular gene cluster in a KPC-producing Klebsiella pneumoniae clinical isolate identified in Brazil

BackgroundAn important virulence factor of Klebsiella pneumoniae is the production of capsular polysaccharide (CPS), a thick mucus layer that allows for evasion of the hosts defense and creates a barrier against antibacterial peptides. CPS production is driven mostly by the expression of genes located in a locus called cps, and the resulting structure is used to distinguish between different serotypes (K types). In this study, we report the unique genetic organization of the cps cluster from K. pneumoniae Kp13, a clinical isolate recovered during a large outbreak of nosocomial infections that occurred in a Brazilian teaching hospital.ResultsA pyrosequencing-based approach showed that the cps region of Kp13 (cpsKp13) is 26.4 kbp in length and contains genes common, although not universal, to other strains, such as the rmlBADC operon that codes for L-rhamnose synthesis. cpsKp13 also presents some unique features, like the inversion of the wzy gene and a unique repertoire of glycosyltransferases. In silico comparison of cpsKp13 RFLP pattern with 102 previously published cps PCR-RFLP patterns showed that cpsKp13 is distinct from the C patterns of all other K serotypes. Furthermore, in vitro serotyping showed only a weak reaction with capsular types K9 and K34. We confirm that K9 cps shares common genes with cpsKp13 such as the rmlBADC operon, but lacks features like uge and Kp13-specific glycosyltransferases, while K34 capsules contain three of the five sugars that potentially form the Kp13 CPS.ConclusionsWe report the first description of a cps cluster from a Brazilian clinical isolate of a KPC-producing K. pneumoniae. The gathered data including K-serotyping support that Kp13’s K-antigen belongs to a novel capsular serotype. The CPS of Kp13 probably includes L-rhamnose and D-galacturonate in its structure, among other residues. Because genes involved in L-rhamnose biosynthesis are absent in humans, this pathway may represent potential targets for the development of antimicrobial agents. Studying the capsular serotypes of clinical isolates is of great importance for further development of vaccines and/or novel therapeutic agents. The distribution of K-types among multidrug-resistant isolates is unknown, but our findings may encourage scientists to perform K-antigen typing of KPC-producing strains worldwide.

Presence of virulence genes and pathogenicity islands in extraintestinal pathogenic Escherichia coli isolates from Brazil

INTRODUCTION Extraintestinal pathogenic Escherichia coli (ExPEC) is associated with various diseases such as urinary tract infections, neonatal meningitis and septicemia. There are many virulence factors (VF) encoded by genes in ExPEC, including papC, papG, ecpA, iroN, fyuA, iutA, ompTp, tsh, hlyF, hlyA and iss. These virulence genes may be present in pathogenicity islands (PAI) or plasmids. METHODOLOGY In this study, we analyzed the presence of VF encoding genes, PAI sequences and phylogenetic groups of 96 ExPEC strains isolated from the urine and blood of patients at the University Hospital of Londrina, and we compared them with 50 faecal commensal strains from healthy individuals. RESULTS The VF fyuA (65.60%) was detected in pathogenic strains and commensal strains (46%). A comparison of the distribution of ExPEC and commensal strains in the phylogenetic groups showed that more ExPEC strains belonged to group B2 whereas more of the commensal isolates belonged to group A. The distribution of the seven PAI sequences between commensal strains and ExPEC strains showed that PAI IV536 was common in both ExPEC and commensal isolates. CONCLUSIONS These results showed that the ExPEC strains that belonged to group B2 had more PAI sequences compared to those of the other groups, especially group B1, which had virulence genes but the lowest percentage of PAI sequences, which leads us to conclude that the virulence of ExPEC strains characterized as B2 is likely attributed to PAI encoded genes, whereas the virulence of ExPEC strains belonging to phylogenetic group B1 is likely due to plasmid encoded virulence genes.

Effect of a Metalloantibiotic Produced by Pseudomonas aeruginosa on Klebsiella pneumoniae Carbapenemase (KPC)-producing K. pneumoniae.

Multidrug-resistant organisms (MDRO) are a great problem in hospitals, where thousands of people are infected daily, with the occurrence of high mortality rates, especially in infections caused by Klebsiella pneumoniae carbapenemase-producing K. pneumoniae (KPC-producing Kpn). The challenge is to find new compounds that can control KPC producing-Kpn infections. The aim of this study was to evaluate the antibiotic activity of the F3d fraction produced by the Pseudomonas aeruginosa LV strain against clinical isolates of KPC-producing Kpn. The results showed that the minimum inhibitory concentration of F3d (62.5 µg mL(-1)), containing an organic metallic compound, killed planktonic cells of KPC-producing Kpn strains after 30 min of incubation. At the same concentration, this fraction also showed an inhibitory effect against biofilm of these bacteria after 24 h of incubation. Treatment with the F3d fraction caused pronounced morphological alterations in both planktonic and biofilm cells of the bacteria. The inhibitory effect of the F3d fraction seems to be more selective for the bacteria than the host cells, indicating its potential in the development of new drugs for the treatment of infections caused by KPC-producing Kpn and other MDRO.

Comparison of Antibiotic Resistance and Virulence Factors among Escherichia coli Isolated from Conventional and Free-Range Poultry

Microbiological contamination in commercial poultry production has caused concerns for human health because of both the presence of pathogenic microorganisms and the increase in antimicrobial resistance in bacterial strains that can cause treatment failure of human infections. The aim of our study was to analyze the profile of antimicrobial resistance and virulence factors of E. coli isolates from chicken carcasses obtained from different farming systems (conventional and free-range poultry). A total of 156 E. coli strains were isolated and characterized for genes encoding virulence factors described in extraintestinal pathogenic E. coli (ExPEC). Antimicrobial susceptibility testing was performed for 15 antimicrobials, and strains were confirmed as extended spectrum of β-lactamases- (ESBLs-) producing E. coli by phenotypic and genotypic tests. The results indicated that strains from free-range poultry have fewer virulence factors than strains from conventional poultry. Strains from conventionally raised chickens had a higher frequency of antimicrobial resistance for all antibiotics tested and also exhibited genes encoding ESBL and AmpC, unlike free-range poultry isolates, which did not. Group 2 CTX-M and CIT were the most prevalent ESBL and AmpC genes, respectively. The farming systems of poultries can be related with the frequency of virulence factors and resistance to antimicrobials in bacteria.

Spread of multidrug-resistant high-risk Klebsiella pneumoniae clones in a tertiary hospital from southern Brazil

Klebsiella pneumoniae is among the most important pathogens found in hospitals. The emergence of multiple antibiotic resistant K. pneumoniae associated with its virulence factors is a worldwide concern and its early identification is crucial, especially for controlling the spread of emerging clones. This article reports a high prevalence of multiresistant K. pneumoniae in a university hospital in southern Brazil, harboring several virulence and β-lactamase encoding genes, including pandrug-resistant high-risk international clones belonging to the clonal group 258 (ST11, ST15, ST101, ST258, ST340 and ST874).

Antimicrobial activity evaluation and comparison of methods of susceptibility for Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter spp. isolates

The production of KPC (Klebsiella pneumoniae carbapenemase) is the major mechanism of resistance to carbapenem agents in enterobacterias. In this context, forty KPC-producing Enterobacter spp. clinical isolates were studied. It was evaluated the activity of antimicrobial agents: polymyxin B, tigecycline, ertapenem, imipenem and meropenem, and was performed a comparison of the methodologies used to determine the susceptibility: broth microdilution, Etest® (bioMérieux), Vitek 2® automated system (bioMérieux) and disc diffusion. It was calculated the minimum inhibitory concentration (MIC) for each antimicrobial and polymyxin B showed the lowest concentrations for broth microdilution. Errors also were calculated among the techniques, tigecycline and ertapenem were the antibiotics with the largest and the lower number of discrepancies, respectively. Moreover, Vitek 2® automated system was the method most similar compared to the broth microdilution. Therefore, is important to evaluate the performance of new methods in comparison to the reference method, broth microdilution.

Prevalence and antimicrobial susceptibility profile of Streptococcus agalactiae in pregnant women seen at the University Hospital of Londrina, Paraná, Brazil

1 Mestranda do Programa de Pós-Graduação em Microbiologia da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Departamento de Microbiologia do Centro de Ciências Biológicas da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 2 Doutoranda em Microbiologia pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Departamento de Microbiologia do Centro de Ciências Biológicas da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 3 Doutorado em Doenças Infecciosas e Parasitárias pela Universidade de São Paulo, São Paulo, Brasil. Professor associado do Laboratório de Análises Clínicas, Setor de Microbiologia do Hospital Universitário da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 4 Mestrado em Microbiologia pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Departamento de Patologia, Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 5 Doutorado em Microbiologia pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Professor adjunto do Departamento de Patologia, Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 6 Doutorado em Microbiologia pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Departamento de Patologia, Análises Clínicas e Toxicológicas, Centro de Ciências da Saúde, Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 7 Doutorado em Educação pela Universidade Estadual Paulista Júlio de Mesquita Filho, Marília, São Paulo, Brasil. Departamento de Enfermagem, Centro de Ciências da Saúde da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 8 Doutorado em Microbiologia pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Professor adjunto do Departamento de Enfermagem do Centro de Ciências da Saúde da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 9 Doutorado em Ciências da Saúde pela Universidade Estadual de Londrina, Londrina, Paraná, Brasil. Departamento de Clínica Médica do Centro de Ciências da Saúde da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 10 Doutorado em Imunologia Básica e Aplicada pela Universidade de São Paulo, Ribeirão Preto, São Paulo, Brasil. Departamento de Microbiologia do Centro de Ciências Biológicas da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. 11 Doutorado em Biologia Celular e Molecular pela Fundação Oswaldo Cruz, Curitiba, Paraná, Brasil. Departamento de Microbiologia do Centro de Ciências Biológicas da Universidade Estadual de Londrina, Londrina, Paraná, Brasil. E-mail: ogatta@uel.br DOI: 10.5433/1679-0367.2018v39n1p77 Um estudo retrospectivo foi realizado com gestantes atendidas no Hospital Universitário de Londrina, Paraná, Brasil para determinar a prevalência de colonização vaginal-retal por estreptococos do Grupo B (EGB) e o perfil de sensibilidade de EGB aos antimicrobianos utilizados para a antibioticoterapia profilática intraparto. Swabs vaginais-retais foram coletados de 2.901 mulheres entre a 35a e 37a semana de gestação. Destes, 527 (18,2%) apresentaram cultura positiva para EGB, e 0,4%, 10,2% e 10% dos ARTIGOS / ARTICLES C ÊN C AS IO LÓ G IC AS E D A AÚ D E A retrospective study of pregnant women seen at the University Hospital of Londrina, Paraná, Brazil was performed to determine the prevalence of Group B Streptococcus (GBS) vaginal-rectal colonization, and the GBS susceptibility for antimicrobials used in intrapartum antibiotic prophylaxis. A vaginal-rectal swab was collected from 2,901 women between 35 and 37 weeks of gestation. Of these, 527 (18.2%) had a positive culture for GBS, and 0.4%, 10.2% and 10% of the isolates were resistant to penicillin, erythromycin and clindamycin, respectively. These results highlight the importance of continuous surveillance of GBS colonization in pregnant women for preventing GBS infections in neonates. Resumo

Análise do Perfil de Resistência Aos Beta-Lactâmicos em Escherichia Coli Isolada de Carcaças de Frango de Granja e Caipira

Vanessa Lumi Koga, Gabriela Regina Rodrigues, Paula Signolfi Cyoia, Gerson Nakazato, Eliana Carolina Vespero, Benito Guimaraes de Brito, Kelly Cristina Tagliari de Brito, Renata Katsuko Takayama Kobayashi. Analise do Perfil de Resistencia Aos Beta-Lactâmicos em Escherichia coli Isolada de Carcacas de Frango de Granja e “Caipira”. In: Anais do 12o Congresso Latinoamericano de Microbiologia e Higiene de Alimentos MICROAL 2014 [= Blucher Food Science Proceedings, num.1, vol.1]. Sao Paulo: Editora Blucher, 2014. DOI 10.5151/foodsci-microal-317 Analise do Perfil de Resistencia Aos Beta-Lactâmicos em Escherichia coli Isolada de Carcacas de Frango de Granja e “Caipira”