Comprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine

The Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8832 coding genes, a core genome of 5452 genes, the accessory genome of 2128 genes, and a unique genome of 1252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside. Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.

Complete genome sequence of Paenibacillus konkukensis sp. nov. SK3146 as a potential probiotic strain

Paenibacillus konkukensis sp. nov., SK3146 is a novel strain isolated from a pig feed. Here, we present complete genome sequence of SK3146. The genome consists of a single circular genome measuring 7,968,964 bp in size with an average guanine + cytosine (G+C) content of 53.4%. Genomic annotation revealed that the strain encodes 151 proteins related to hydrolases (EC3), which was higher than those in Bacillus subtilis and Escherichia coli. Diverse kinds of hydrolases including galactosidase, glucosidase, cellulase, lipase, xylanase, and protease were found in the genome of SK3146, coupled with one bacteriocin encoding gene. The complete genome sequence of P. konkukensis SK3146 indicates the immense probiotic potential of the strain with nutrient digestibility and antimicrobial activity functions.

Mutation of the cyclic di-GMP phosphodiesterase gene in Burkholderia lata SK875 attenuates virulence and enhances biofilm formation

Burkholderia sp. is a gram-negative bacterium that commonly exists in the environment, and can cause diseases in plants, animals, and humans. Here, a transposon mutant library of a Burkholderia lata isolate from a pig with swine respiratory disease in Korea was screened for strains showing attenuated virulence in Caenorhabditis elegans. One such mutant was obtained, and the Tn5 insertion junction was mapped to rpfR, a gene encoding a cyclic di-GMP phosphodiesterase that functions as a receptor. Mutation of rpfR caused a reduction in growth on CPG agar and swimming motility as well as a rough colony morphology on Congo red agar. TLC analysis showed reduced AHL secretion, which was in agreement with the results from plate-based and bioluminescence assays. The mutant strain produced significantly more biofilm detected by crystal violet staining than the parent strain. SEM of the mutant strain clearly showed that the overproduced biofilm contained a filamentous structure. These results suggest that the cyclic di-GMP phosphodiesterase RpfR plays an important role in quorum sensing modulation of the bacterial virulence and biofilm formation.

Microbiological Evaluation of Pork and Chicken By-Products in South Korea

In this study, we aimed to evaluate the microbiological risk of pork and chicken by-products by enumerating indicator bacteria (total aerobic bacteria, coliforms, and Escherichia coli) and identifying pathogens such as Campylobacter and Salmonella. The antibiotic resistance of pathogenic isolates was determined, and molecular subtyping was performed using automated repetitive sequence-based PCR (rep-PCR). Pork and chicken by-products were collected from 10 processing plants. The mean numbers of total aerobic bacteria, coliforms, and E. coli from 95 pork by-product samples and 64 chicken by-product samples were 5.1, 3.6, and 2.4 log CFU/g and 4.5, 3.0, and 1.8 log CFU/g, respectively. The numbers of indicator bacteria in the gastrointestinal tract (small intestine, large intestine, and gizzard) were significantly higher than those in other organs. Salmonella and Campylobacter species were detected in 3 and 5 of 95 pork by-product samples and in 6 and 3 of 64 chicken by-product samples, respectively. Four of 9 Salmonella isolates examined were resistant to eight antibiotics, and each of these resistant strains produced an extended-spectrum β-lactamase. Most Campylobacter isolates were resistant to tetracycline (7 of 8 strains) and quinolones (7 of 8 strains). The similarity in rep-PCR patterns among Salmonella isolates was more closely associated with serotype than with the processing plant and type of meat. Conversely, the rep-PCR patterns of Campylobacter isolates were specific to the processing plant. Our findings could help agencies develop regulations for protection from foodborne bacterial infections arising from animal by-products.

Control of the haemodynamic response to surgical stimuli in semi-closed circuit or closed circuit anaesthesia using a multifunctional anaesthesia system

This study compared the ability of the Zeus multifunctional anaesthesia system to control haemodynamic response to surgical stimulation in semi-closed (SCA) or closed circuit anaesthesia (CCA) modes. Fifty patients undergoing gynaecological surgery were randomly assigned to SCA or CCA. Anaesthesia was induced with 2 mg propofol and 0.9 mg/kg rocuronium, intravenously, and maintained using sevoflurane (minimum alveolar concentration [MAC], 1.0) using 2 l/min oxygen plus 2 l/min nitrous oxide (SCA 4 l/min group) or 50% oxygen plus 50% nitrous oxide (CCA group). An increase in mean arterial pressure (MAP) > 20% above baseline in response to surgical stimulation provoked a stepwise increase in sevoflurane (1.3 MAC and then 1.6 MAC), followed by fentanyl 1 pg/kg intravenously (rescue drug). The time required for MAP to return to within 10% of baseline was significantly shorter in the CCA group (6.4 +/- 3.6 min) compared with the SCA 4 l/min group (10.2 +/- 6.0 min). The percentage of patients requiring fentanyl was significantly greater in the SCA 4 l/min group than in the CCA group. In conclusion, CCA controlled acute haemodynamic responses to surgical stimuli more successfully and rapidly than SCA 4 l/min, using a multifunctional anaesthesia machine.

Dissemination of transferable CTX-M-type extended-spectrum beta-lactamase-producing Escherichia coli in Korea

AIMS

Among 365 Escherichia coli isolated in 2003, 31 cefotaxime-resistant isolates were obtained from clinical specimens taken from adults hospitalized in Busan, Korea. Six extended-spectrum beta-lactamase (ESBL)-producing isolates were investigated further to determine the mechanism of resistance.

METHODS AND RESULTS

These isolates were analysed by antibiotic susceptibility testing, pI determination, plasmid profiles, transconjugation test, PCR-restriction fragment length polymorphism (RFLP), enterobacterial repetitive consensus (ERIC)-PCR and DNA sequencing. All six of these isolates were found to contain the CTX-M-type ESBL genes. Five clinical isolates and their transconjugants produced CTX-M-3. One clinical isolate (K17391) and its transconjugant (trcK17391) produced CTX-M-15. Five clinical isolates also produced another TEM-1. One clinical isolate (K12776) also contained another TEM-52. CTX-M-3 ESBL gene was responsible for the resistance to piperacillin, cephalothin, cefotaxime, cefepime and aztreonam. CTX-M-15 or TEM-52 was especially responsible for the resistance to ceftazidime.

CONCLUSIONS

These results appear to represent the in vivo evolution of CTX-M-type beta-lactamase genes (bla(CTX-M-3) --> bla(CTX-M-15)) under the selective pressure of antimicrobial therapy (especially ceftazidime). PCR-RFLP is a reliable method to discriminate CTX-M-15 gene from CTX-M-3 gene. ERIC-PCR analysis revealed that dissemination of CTX-M-3 was not due to a clonal outbreak of a resistant strain but to the intra-species spread of resistance to piperacillin, cephalothin, cefotaxime, cefepime and aztreonam in Korea.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first report of the occurrence of CTX-M-1 cluster ESBLs in Korea. A more comprehensive survey of these ESBL types from Korea is urgently needed because of the in vivo evolution of CTX-M-15 from CTX-M-3. The emergence of these CTX-M-type ESBLs suggests that diagnostic laboratories should screen for ESBLs with ceftazidime as well as cefotaxime; they should still perform clavulanate synergy tests on resistant isolates.

Investigation of a nosocomial outbreak of Acinetobacter baumannii producing PER-1 extended-spectrum beta-lactamase in an intensive care unit

We investigated an outbreak of Acinetobacter baumannii in an adult intensive care unit of Kosin University Gospel Hospital in Busan, Republic of Korea. The outbreak involved 10 cases of infection by A. baumannii producing PER-1 extended-spectrum beta-lactamase over a seven-month period, and was caused by a single pulsed-field gel electrophoresis clone. The epidemic isolates were characterized by slight synergy between clavulanic acid and cefepime. Isoelectric focusing of crude bacterial extracts detected two nitrocefin-positive bands with pI values of 8.0 and 5.3. Polymerase chain reaction amplification and characterization of the amplicons by restriction analysis and direct sequencing indicated that the epidemic isolates carried a bla(PER-1) determinant. The epidemic isolates were characterized by a multidrug-resistant phenotype that remained unchanged over the outbreak, including penicillins, beta-lactam/beta-lactamase inhibitor, extended-spectrum cephalosporins and monobactams. Isolation of infected patients and appropriate carbapenem therapy were successful in ending the outbreak. Our report indicates that the bla(PER-1) resistance determinant may become an emerging therapeutic problem.

Investigation of extended-spectrum beta-lactamases produced by clinical isolates of Klebsiella pneumoniae and Escherichia coli in Korea

AIMS

Isolates obtained from various regions in Korea in 2002 were identified and their susceptibility to extended-spectrum cephalosporins, monobactams and/or cephamycins was studied along with any production of extended-spectrum beta-lactamases (ESBLs).

METHODS AND RESULTS

Bacteria identified by the conventional techniques and Vitek GNI card were Klebsiella pneumoniae and Escherichia coli. Using disk diffusion and double-disk synergy tests, we found that 39.2% of strains produced ESBLs. About 52% of isolates transferred resistance to ceftazidime by conjugation. Banding patterns of PCR amplification with the designed primers showed that 837- and 259-bp fragments specific to bla(TEM) genes were amplified in 63.3% of strains. 929- and 231-bp fragments (bla(SHV)), 847- and 520-bp fragments (bla(CMY)), 597- and 858-bp fragments (bla(CTX-M)) were amplified in 61.5, 17.3 and 7.7% of strains respectively. About 51.9% of strains contained more than two types of beta-lactamase genes. Especially, one strain contained bla(TEM), bla(CMY) and bla(CTX-M) genes.

SIGNIFICANCE

Resistance mechanisms to beta-lactams, comprising mostly ESBL production, lead to the resistance against even recently developed beta-lactams in enterobacteria, which is now a serious threat to antibiotic therapy. The high prevalence of bla(CMY) genes and multidrug-resistant genes may also make therapeutic failure and lack of eradiation of these strains by extended-spectrum cephalosporins or cephamycins.

Sites of limited proteolysis in the pyruvate decarboxylase component of the pyruvate dehydrogenase multienzyme complex of Bacillus stearothermophilus and their role in catalysis

The E1 component (pyruvate decarboxylase) of the pyruvate dehydrogenase complex of Bacillus stearothermophilus is a heterotetramer (alpha2beta2) of E1alpha and E1beta polypeptide chains. The domain structure of the E1alpha and E1beta chains, and the protein-protein interactions involved in assembly, have been studied by means of limited proteolysis. It appears that there may be two conformers of E1alpha in the E1 heterotetramer, one being more susceptible to proteolysis than the other. A highly conserved region in E1alpha, part of a surface loop at the entrance to the active site, is the most susceptible to cleavage in E1 (alpha2beta2). As a result, the oxidative decarboxylation of pyruvate catalysed by E1 in the presence of dichlorophenol indophenol as an artificial electron acceptor is markedly enhanced, but the reductive acetylation of a free lipoyl domain is unchanged. The parameters of the interaction between cleaved E1 and the peripheral subunit-binding domain of the dihydrolipoyl acetyltransferase E2 component are identical to those of the wild-type E1. However, a pyruvate dehydrogenase complex assembled in vitro with cleaved E1p exhibits a markedly lower overall catalytic activity than that assembled with untreated E1. This implies that active site coupling between the E1 and E2 components has been impaired. This has important implications for the way in which a tethered lipoyl domain can interact with E1 in the assembled complex.

Colchicine activates actin polymerization by microtubule depolymerization

Swiss 3T3 fibroblasts were treated with the microtubule-disrupting agent colchicine to study any interaction between microtubule dynamics and actin polymerization. Colchicine increased the amount of filamentous actin (F-actin), in a dose- and time-dependent manner with a significant increase at 1 h by about 130% over control level. Confocal microscopic observation showed that colchicine increased F-actin contents by stress fiber formation without inducing membrane ruffling. Colchicine did not activate phospholipase C and phospholipase D, whereas lysophosphatidic acid did, indicating that colchicine may have a different mechanism of actin polymerization regulation from LPA. A variety of microtubule-disrupting agents stimulated actin polymerization in Swiss 3T3 and Rat-2 fibroblasts as did colchicine, but the microtubule-stabilizing agent taxol inhibited actin polymerization induced by the above microtubule-disrupting agents. In addition, colchicine-induced actin polymerization was blocked by two protein phosphatase inhibitors, okadaic acid and calyculin A. These results suggest that microtubule depolymerization activates stress fiber formation by serine/threonine dephosphorylation in fibroblasts.

Isolation and characterization of guamerin, a new human leukocyte elastase inhibitor from Hirudo nipponia

A new human leukocyte elastase inhibitor was extracted and purified from a Korean native leech Hirudo nipponia. The inhibitor, called guamerin, has a molecular weight of 6,110 and shows inhibition constant (Ki) of 8.1 x 10(-14) M. It is stable at a wide range of pH from 1 to 11 and heat-stable up to 90 degrees C. The complete amino acid sequence of guamerin reveals a cysteine-rich polypeptide of 57 amino acid residues that shows no similarity to any known elastase inhibitors but has 51% sequence homology with hirustasin. Guamerin has identical spacing of 10 cysteine residues as antistasin-type serine proteinase inhibitors, but the P1 reactive site residue is Met36 instead of Arg. The neighboring sequence of the reactive site consists primarily of hydrophobic amino acid residues. Based on examinations of the target proteinases and the reactive site specificity, guamerin is a new low molecular weight protein that inhibits elastases.

[A study of psychiatric patients perceived effect and expectancy of activity therapy]

The intent of this descriptive study is to investigate the patients perceived effect and expectance of activity therapy. The subjects for this study were 56 patients from the psychiatric ward in Severance Hospital. The data were collected during the period from June 1, 1991 to January 18, 1992. The effect and expectance of the activity therapy was measured using a questionnaire developed by this study's investigators. The date were analyzed by descriptive statistics, t-test and one-way ANOVA, using the SPSS program. The results of this study can be summarized as following; 1. For motivation for the activity therapy, the response range was from 64.3% to 89.3%, that is, it showed a relatively positive response. 2. For the degree of improvement according to the nurse's method in the activity therapy, it was shown that the nurses need professional skill and meeting after activity therapy. 3. For the relevance of the nurse in the activity therapy, 90% of the subjects had a positive answer for all of the activity therapy except the painting therapy. 4. For the perceived effect of the activity therapy, the following results were obtained. 1) 92% of the subjects had a positive response to the dance therapy, that is-I am vigorous physically. 2) 90% of the subjects had a positive response to the reading therapy, that is-I acquire good ideas and instruction. 3) 98.1% of the subjects had a positive response to the recreation therapy, that is-I am joyful. 4) 88.9% of the subjects had a positive response to the writing therapy, that is-I am interested and become acquainted with other patients. 5) 86.8% of the subjects had a positive response to the occupation therapy, that is-I am happy when I work. 6) 92.6% of the subjects had a positive response to the painting therapy, that is-I can express myself in painting. 7) 87.3% of the subjects had a positive response to the music therapy, that is-I am comforted. 5. For the expectance related to the activity therapy, 97.1% of the subjects had the most positive response to the music therapy which is a pleasant comfortable time. From the above-mentioned findings, it is suggested that psychiatric nurses need to development systematic and professional group activity therapy, and know the patient premorbid hobbies, interests and occupations.