Effects of the Expression of Random Sequence Clones on Growth and Transcriptome Regulation in Escherichia coli.

Comparative genomic analyses have provided evidence that new genetic functions can emerge out of random nucleotide sequences. Here, we apply a direct experimental approach to study the effects of plasmids harboring random sequence inserts under the control of an inducible promoter. Based on data from previously described experiments dealing with the growth of clones within whole libraries, we extracted specific clones that had shown either negative, neutral or positive effects on relative cell growth. We analyzed these individually with respect to growth characteristics and the impact on the transcriptome. We find that candidate clones for negative peptides lead to growth arrest by eliciting a general stress response. Overexpression of positive clones, on the other hand, does not change the exponential growth rates of hosts, and they show a growth advantage over a neutral clone when tested in direct competition experiments. Transcriptomic changes in positive clones are relatively moderate and specific to each clone. We conclude from our experiments that random sequence peptides are indeed a suitable source for the de novo evolution of genetic functions.

Gene Composition as a Potential Barrier to Large Recombinations in the Bacterial Pathogen Klebsiella pneumoniae.

Klebsiella pneumoniae (Kp) is one of the most important nosocomial pathogens worldwide, able to cause multiorgan infections and hospital outbreaks. One of the most widely disseminated lineage of Kp is the clonal group 258 (CG258), which includes the highly resistant "high-risk" sequence types ST258 and ST11. Genomic investigations revealed that very large recombination events have occurred during the emergence of Kp lineages. A striking example is provided by ST258, which has undergone a recombination event that replaced over 1 Mb of the genome with DNA from an unrelated Kp donor. Although several examples of this phenomenon have been documented in Kp and other bacterial species, the significance of these very large recombination events for the emergence of either hypervirulent or resistant clones remains unclear. Here, we present an analysis of 834 Kp genomes that provides data on the frequency of these very large recombination events (defined as those involving >100 kb), their distribution within the genome, and the dynamics of gene flow within the Kp population. We note that very large recombination events occur frequently, and in multiple lineages, and that the majority of recombinational exchanges are clustered within two overlapping genomic regions, which have been involved by recombination events with different frequencies. Our results also indicate that certain lineages are more likely to act as donors to CG258. Furthermore, comparison of gene content in CG258 and non-CG258 strains agrees with this pattern, suggesting that the success of a large recombination depends on gene composition in the exchanged genomic portion.

Recasting Human Vδ1 Lymphocytes in an Adaptive Role.

γδ T cells are unconventional lymphocytes commonly described as 'innate-like' in function, which can respond in both a T cell receptor (TCR)-independent and also major histocompatibility complex (MHC)-unrestricted TCR-dependent manner. While the relative importance of TCR recognition had remained unclear, recent studies revealed that human Vδ1 T cells display unexpected parallels with adaptive αß T cells. Vδ1 T cells undergo profound and highly focussed clonal expansion from an initially diverse and private TCR repertoire, most likely in response to specific immune challenges. Concomitantly, they differentiate from a Vδ1 T cell naïve (Tnaïve) to a Vδ1 T cell effector (Teffector) phenotype, marked by the downregulation of lymphoid homing receptors and upregulation of peripheral homing receptors and effector markers. This suggests that an adaptive paradigm applies to Vδ1 T cells, likely involving TCR-dependent but MHC-unrestricted responses to microbial and non-microbial challenges.

MAIT cell clonal expansion and TCR repertoire shaping in human volunteers challenged with Salmonella Paratyphi A.

Mucosal-associated invariant T (MAIT) cells are innate-like T cells that can detect bacteria-derived metabolites presented on MR1. Here we show, using a controlled infection of humans with live Salmonella enterica serovar Paratyphi A, that MAIT cells are activated during infection, an effect maintained even after antibiotic treatment. At the peak of infection MAIT cell T-cell receptor (TCR)ß clonotypes that are over-represented prior to infection transiently contract. Select MAIT cell TCRß clonotypes that expand after infection have stronger TCR-dependent activation than do contracted clonotypes. Our results demonstrate that host exposure to antigen may drive clonal expansion of MAIT cells with increased functional avidity, suggesting a role for specific vaccination strategies to increase the frequency and potency of MAIT cells to optimize effector function.

Frequencies of virulence genes and pulse field gel electrophoresis fingerprints in Escherichia coli isolates from canine pyometra.

Escherichia coli is the most common bacterial agent isolated from canine pyometra. The frequencies of 24 virulence genes and pulsed field gel electrophoresis (PFGE) profiles were determined for 23 E. coli isolates from cases of canine pyometra in Brazil. The frequencies of virulence genes were 91.3% fimH, 91.3% irp-2, 82.6% fyuA, 56.5% iroN, 47.8% traT, 39.1% usp, 34.8% sfaD/E, 34.8% tsh, 30.4% papC, 30.4% hlyA, 26.1% papGIII, 26.1% cnf-1, 21.7% papE/F, 21.7% iss, 17.4% iutA, 17.4% ompT, 17.4% cvaC, 17.4% hlyF, 17.4% iucD, 13.0% iucC, 13.0% astA, 4.3% papGII, 0% afaB/C and 0% papGI. The high frequency of yersiniabactin (fyuA and irp2) and salmochelin (iroN) genes suggests that iron uptake systems might be important in the pathogenesis of canine pyometra. PFGE profiles of 19 isolates were heterogeneous, confirming that E. coli isolates from canine pyometra are unlikely to be epidemic clones.

Increasing resistance in multiresistant methicillin-resistant Staphylococcus aureus clones isolated from a Chinese hospital over a 5-year period.

BACKGROUND: The aim was to study the changes in the antimicrobial resistance of methicillin-resistant Staphylococcus aureus (MRSA) clones over a 5-year period (from 2000 to 2005) at a representative hospital in Beijing, China. METHODS: A total of 100 randomly selected MRSA strains were analyzed using antimicrobial susceptibility testing, pulsed-field gel electrophoresis, spa typing, multilocus sequence typing, SCCmec typing, and PCR for the Panton-Valentine leukocidin virulence factor. RESULTS: Resistance to rifampin greatly increased from 32% (16/50) to 68% (34/50). High-level mupirocin-resistant isolates were found only in 2005, when four were identified. Intermediate susceptibly to quinupristin-dalfopristin increased from 22% (11/50) to 52% (26/50) between 2000 and 2005. The main antimicrobial resistance profiles changed from TC-GM-CI-EM-CM in 2000 to TC-GM-CI-EM-CM-RI in 2005. The main pulsed-field gel electrophoresis type changed from types C, L, and E in 2000 to types J, F, and N, respectively, in 2005. ST239-MRSA-III was the most predominant clone in 2000 and 2005, whereas ST5-MRSA-II was found only in 2005. CONCLUSIONS: There were increasing levels of antimicrobial resistance and epidemiological changes in the hospital-associated MRSA strains isolated in this facility between 2000 and 2005.

Spread of a methicillin-resistant staphylococcus aureus clone isolated from bacteremia in elderly patients in a Brazilian general hospital

A study of the genomic diversity of MRSA strains isolated from elderly patients with infection/colonization in three repeated prevalence, cross sectional studies was performed in the 1999-2000 period. In this study, 13 MRSA isolates from blood cultures and 5 from rectal and nare cultures were obtained from 18 patients (13 elderly and 5 adults). Most of the patients were being treated with two or more antimicrobials (83.3%), had insertion of invasive devices (88.9%) and were managed in ICU (Intensive Care Unit) and/or surgical units (66.7%). MIC (Minimum Inhibitory Concentration) data showed that 88.9% of the MRSA strains were resistant to high concentrations of oxacillin (MIC > 256 ìg/mL), 94.5% of the MRSA carried the mecA gene in their genome, and most (65.0%) of the isolates were indistinguishable according to their DNA finger­printing generated by PFGE (Pulsed-field gel electrophoresis). Although PFGE typing was performed with a few MRSA isolates, our results demonstrate that one MRSA clone was associated with infection/colonization in patients with an obvious connection among five out of eleven patients who stayed in the same clinic and ICU during the same period. Hospital acquired infection, a major “silent epidemy”, is associated with prolonged hospital stay and high mortality rate and its cause must be better evaluated.

Genotipificación de cepas de enterobacterias procedentes de 4 centros de salud del área de Caracas / Genotyping of enterobacterias strains from 4 healthcare centers in Caracas

Las infecciones nosocomiales pueden ser producidas por microorganismos resistentes a la acción de los antimicrobianos que han sido seleccionados por la mal uso ó el uso indiscriminado de los antibióticos en el ámbito hospitalario. En los últimos años se han desarrollado nuevas técnicas moleculares de tipificación basada en la reacción en cadena de la polimerasa (PCR), que han representado un avance importante en el estudio de las enfermedades infecciosas, siendo muy útiles al permitir diferenciar serotipos estrechamente relacionados y grupos de cepas no relacionadas clonalmente, debido a su gran poder discriminatorio. En Venezuela, son pocos los estudios de eepidemiología molecular de las infecciones intrahospitalarias, y por esta razón nos propusimos genotipificar cepas de Escherichia coli y Klebsiella pneumoniae provenientes de aislados nosocomiales de cuatro centros de salud del área metropolitana (Hospital "Dr. José María Vargas", Hospital "Dr. Domingo Luciani", Centro Médico de Caracas y Policlínica Metropolitana) con la finalidad de determinar la relación clonal existente entre estas cepas. El uso de ERIC-PCR permitió relacionar parcialmente las especies de E. coli aisladas en los cuatro centros de salud, sin embargo la técnica de REP-PCR permitió discriminar entre los patrones de bandas similares, mostrando un poder de resolución mayor. El uso de ERIC-PCR y REP-PCR no permitió tipificar la mayoría de las cepas de K. pneumoniae aisladas en los cuatro centros de salud en estudio. En el Centro Médico de Caracas se identificaron dos aislados clonales provenientes de diferentes áreas del hospital, Unidad de Terapia de Adultos y Hospitalización. En la Policlínica Metropolitana se identificaron tres aislados clonales, dos en la unidad de Terapia y uno en Hospitalización. En el Hospital "Dr. Domingo Luciani" y en el Hospital "Dr. José María Vargas" no se identificaron clones. Estos resultados proporcionan un aporte a los programas de vigilancia...

Nosocomial infections can be produced by microorganisms resistand to antimicrobial agents, and they have been selected by the bad use or abuse of antibiotics in the hospital environment. Recently, new molecular typing techniques have been developed, based on polymerase chain reaction (PCR). These techniques represent an important advantage the study of infectious diseases; they are able to discriminate relate closed serovars and groups of nonrelated isolates due to its great power discriminatory. In Venezuela, there is a small number of molecular epidemiology researches. The goal of the present study is genotyping Escherichia coli and Klebsiella pneumoniae isolated of nosocomial infected patients from four healthcare centers in the metropolitan area (Hospital "Dr. José María Vargas", Hospital "Dr. Domingo Luciani", Centro Médico de Caracas, Policlínica Metropolitana) in order to investigate the clonal relationship between the isolates. ERIC-PCR allowed us to correlate E. coli isolates however REP-PCR shows greater greater resolution. The use of both ERIC-PCR and REP-PCR, did not permit us typing K. pneumoniae isolates. Two clonally related isolates from Centro Médico de Caracas were identified. Three clonally related isolates from the Policlínica Metropolitana ere identified. No clones were identified in samples from Hospital "Dr. Domingo Luciani" and the Hospital "José María Vargas". These results contribute to monitoring programs, to improve the control of the bacterial infections, helping to establish efficient procedures and reduce nosocomials infections.

Molecular epidemiology of two fowl cholera outbreaks on a free-range chicken layer farm.

Two outbreaks of fowl cholera on a multiage free-range egg farm were investigated. The outbreaks occurred in 1994 and 2002. A total of 22 strains of Pasteurella multocida were available for study, 11 from the 1994 outbreak and 11 from the 2002 outbreak. Lesions typical of acute fowl cholera were seen in the 1994 outbreak, whereas both acute and chronic fowl cholera occurred in the 2002 outbreak. The isolates were examined in an extended phenotypic typing methodology, by a P. multocida-specific polymerase chain reaction (PCR), by the Heddleston somatic serotyping scheme, and by restriction endonuclease analysis (REA) typing using the enzyme HpaII. All 22 strains had the same phenotypic properties, all were confirmed as P. multocida by PCR, all were Heddleston serovar 4, and all had the same REA pattern. The results indicate that these 2 outbreaks were caused by the same clone of P. multocida--despite the 8-year time period between the outbreaks.

A common clone of erythromycin-resistant Streptococcus pneumoniae in Greece and the UK.

OBJECTIVE: To investigate the possible genetic relationship among erythromycin-resistant Streptococcus pneumoniae strains isolated in Greece and the UK. METHODS: During 1995-97, 140 S. pneumoniae strains were isolated from clinical specimens submitted to the microbiology departments of the two main children's hospital in Athens. All erythromycin-resistant strains were further studied with respect to the presence of genes encoding for the two major mechanisms of macrolide resistance, their serotypes, and pulsed-field gel electrophoresis (PFGE) types, in comparison to a previously characterized UK erythromycin-resistant clone. RESULTS: Eleven of the 140 isolates (7.9%) were resistant to erythromycin; nine of these were susceptible to penicillin. Serotyping allocated seven, three and one isolates to serotypes 14, 19F and serogroup 6, respectively. The mefA gene was detected in seven isolates (five serotype 14 and two serotype 19F), ermB in two (one serotype 19F and the serogroup 6 isolate), whilst in the remaining two isolates no resistance gene could be detected by polymerase chain reaction (PCR). Pulsed-field gel electrophoresis of genomic DNA showed that five Greek serotype 14 isolates belonged to the same chromosomal type as the serotype 14 erythromycin-resistant UK clone. CONCLUSIONS: The present study showed that erythromycin resistance among the S. pneumoniae isolates was mostly owing to the efflux mechanism and suggested a possible clonal spread of serotype 14 erythromycin-resistant S. pneumoniae strains between Greece and the UK.

Effect of monensin on Mayaro virus replication in monkey kidney and Aedes albopictus cells.

The effect of a cationic ionophore, monensin, on the replication of Mayaro virus in monkey kidney TC7 and Aedes albopictus cells has been studied. Treatment of these cells with 1 micromol/l monensin during infection did not affect the virus protein synthesis but inhibited severely the virus replication. Electron microscopy of the cells infected with Mayaro virus and treated with monensin revealed that the morphogenesis of Mayaro virus was impaired in TC7 but not in A. albopictus cells.

Variation in frequency of the virulence-factor gene in Escherichia coli clones colonizing the stools and urinary tracts of healthy prepubertal girls.

To provide information on virulence expression of Escherichia coli in healthy hosts, stool, periurethral, and urine samples were collected weekly from healthy 3-6-year-old girls who lived in a small rural community. Dominant and nondominant clones were defined in stool specimens, and the expression of virulence factors was determined. We found that healthy girls commonly shared dominant clones. P adhesin, hemolysin, and type I adhesin were commonly found in clones in the stool and in clones in the urinary tract. In addition, expression of virulence factors, among both dominant and nondominant clones in the stool, changed from week to week. The presence of P adhesin was a marker for the persistence of a dominant clone in the stool and was associated with an increased likelihood that a nondominant clone would be detected in the urinary tract. Type I adhesin was ubiquitous among stool strains, with orientation of the fimbrial switch being both in the "off" position and in both the "on" and "off" positions. In summary, the intestinal flora of healthy girls is complex, with frequent changes in virulence expression.

The protective immune response to heat shock protein 60 of Histoplasma capsulatum is mediated by a subset of V beta 8.1/8.2+ T cells.

Immunization with recombinant heat shock protein 60 (rHsp60) from Histoplasma capsulatum or a region of the protein designated fragment 3 (F3) confers protection from a subsequent challenge in mice. To determine the T cell repertoire involved in the response to Hsp60, T cell clones from C57BL/6 mice immunized with rHsp60 were generated and examined for Vbeta usage by flow cytometry and RT-PCR. Vbeta8.1/8.2(+) T cells were preferentially expanded; other clones bore Vbeta4, -6, or -11. When Vbeta8.1/8.2(+) cells were depleted in mice, Vbeta4(+) T cell clones were almost exclusively isolated. Measurement of cytokine production demonstrated that nine of 16 Vbeta8.1/8.2(+) clones were Th1, while only three of 13 non-Vbeta8.1/8.2(+) clones were Th1. In mice immunized with rHsp60, depletion of Vbeta8.1/8.2(+), but not Vbeta6(+) plus Vbeta7(+), T cells completely abolished the protective efficacy of Hsp60 to lethal and sublethal challenges. Examination of the TCR revealed that a subset of Vbeta8.1/2(+) clones that produced IFN-gamma and were reactive to F3 shared a common CDR3 sequence, DGGQG. Transfer of these T cell clones into TCR alpha/beta(-/-) or IFN-gamma(-/-) mice significantly improved survival, while transfer of other Vbeta8.1/8.2(+) clones that were F3 reactive but were Th2 or clones that were not reactive to F3 but were Th1 did not confer protection. These data indicate that a distinct subset of Vbeta8.1/8.2(+) T cells is crucial for the generation of a protective response to rHsp60.

Detection of a widespread clone of Pseudomonas aeruginosa in a pediatric cystic fibrosis clinic.

Cross-infection by Pseudomonas aeruginosa between unrelated patients with cystic fibrosis (CF) is believed to be uncommon. After detecting a genotypically identical strain of P. aeruginosa in five unrelated children with CF dying from severe lung disease, we determined its prevalence within a large CF clinic using pulsed-field gel electrophoresis and random amplified polymorphic DNA assays. The clinical status of P. aeruginosa-infected patients was also determined. Between September and December 1999, 152 patients, aged 3.9-20.7 years, provided sputum for culture. P. aeruginosa was detected in 118 children of mean (SD) age 13.5 (3.8) years. The genotyping techniques were concordant, showing that 65 (55%) infected patients carried an indistinguishable or closely related strain. No distinctive antibiogram or environmental reservoir was found. Patients with the clonal strain were more likely than those with unrelated isolates to have been hospitalized in the preceding 12 months for respiratory exacerbations. This study demonstrates extensive spread of a single, clonal strain of P. aeruginosa in a large pediatric CF clinic. Whether this strain is also more virulent than sporadic isolates remains to be determined. As transmissible strains could emerge elsewhere, other CF clinics may also need to consider molecular methods of surveillance for cross-infection.

Persistent bacteraemia caused by a single clone of Burkholderia cepacia with unusual phenotype.

We report a case of persistent bacteraemia caused by a single clone of Burkholderia cepacia with unusual characteristics. Six isolates of B. cepacia were recovered from a patient with acute myeloid leukaemia and chemotherapy-induced neutropenia within a 3-week period. All six isolates were initially incompletely identified as B. cepacia with the API 20NE system. The further use of cellular fatty acid analysis and PCR-restriction fragment length polymorphism of the 16S rDNA confirmed the identification. These isolates also displayed an identical but unusual antibiotype. The identical cellular fatty acid profiles and genomic typing generated by random amplified polymorphic DNA identified these isolates as derivatives of a single strain.

Characterization of the Brazilian endemic clone of methicillin-resistant staphylococcus aureus (MRSA) from hospitals throughout Brazil

The objective of this study was to characterize patterns of the Brazilian endemic clone of methicillin-resistant staphylococcus aureus (MRSA) from hospitals throughout Brazil. We studied 83 MRSA strains isolated from patients hospitalized in 27 public and private hospitals in 19 cities located in 14 brazilian states from september, 1995, to june, 1997. The MRSA strains were typed using antibiograms, bacteriophage typing and pulsed field gel electrophoresis (PFGE). The analysis of genomic DNA by PFGE showed that 65 isolates presented the same SFGE pattern. This pattern was presente in all of the hospitals studied indicating the presence of an endemic MRSA clone widely disseminated throughout brazilian hospitals (BEC). All isolates belonging to the BEC proved to be resistant to ciprofloxacin, erythromycin, lincomycin, trimethoprim-sulphamethoxazole, and tetracycline. Variable susceptibility to these drugs was found only in isolates belonging to clones other than the BEC. The results show that, among MRSA, the BEC is common in Brazil. The best method for mapping changes in the frequency of this clone among MRSA is pulsed field gel electrophoresis. Use of molecular mapping is an important tool for monitoring the spread of potentially dangerous microbes.

Human epidermal differentiation complex in a single 2.5 Mbp long continuum of overlapping DNA cloned in bacteria integrating physical and transcript maps.

Terminal differentiation of keratinocytes involves the sequential expression of several major proteins which can be identified in distinct cellular layers within the mammalian epidermis and are characteristic for the maturation state of the keratinocyte. Many of the corresponding genes are clustered in one specific human chromosomal region 1q21. It is rare in the genome to find in such close proximity the genes belonging to at least three structurally different families, yet sharing spatial and temporal expression specificity, as well as interdependent functional features. This DNA segment, termed the epidermal differentiation complex, contains 27 genes, 14 of which are specifically expressed during calcium-dependent terminal differentiation of keratinocytes (the majority being structural protein precursors of the cornified envelope) and the other 13 belong to the S100 family of calcium binding proteins with possible signal transduction roles in the differentiation of epidermis and other tissues. In order to provide a bacterial clone resource that will enable further studies of genomic structure, transcriptional regulation, function and evolution of the epidermal differentiation complex, as well as the identification of novel genes, we have constructed a single 2.45 Mbp long continuum of genomic DNA cloned as 45 p1 artificial chromosomes, three bacterial artificial chromosomes, and 34 cosmid clones. The map encompasses all of the 27 genes so far assigned to the epidermal differentiation complex, and integrates the physical localization of these genes at a high resolution on a complete NotI and SalI, and a partial EcoRI restriction map. This map will be the starting resource for the large-scale genomic sequencing of this region by The Sanger Center, Hinxton, U.K.

Enhancement of the Listeria monocytogenes p60-specific CD4 and CD8 T cell memory by nonpathogenic Listeria innocua.

The contact of T cells to cross-reactive antigenic determinants expressed by nonpathogenic environmental micro-organisms may contribute to the induction or maintenance of T cell memory. This hypothesis was evaluated in the model of murine Listeria monocytogenes infection. The influence of nonpathogenic L. innocua on the L. monocytogenes p60-specific T cell response was analyzed. We show that some CD4 T cell clones raised against purified p60 from L. monocytogenes cross-react with p60 purified from L. innocua. The L. monocytogenes p60-specific CD4 T cell clone 1A recognized the corresponding L. innocua p60 peptide QAAKPAPAPSTN, which differs only in the first amino acid residue. In vitro experiments revealed that after L. monocytogenes infection of APCs, MHC class I-restricted presentation of p60 occurs, while MHC class II-restricted p60 presentation is inhibited. L. innocua-infected cells presented p60 more weakly but equally well in the context of both MHC class I and MHC class II. In contrast to these in vitro experiments the infection of mice with L. monocytogenes induced a strong p60-specific CD4 and CD8 T cell response, while L. innocua infection failed to induce p60-specific T cells. L. innocua booster infection, however, expanded p60-specific memory T cells induced by previous L. monocytogenes infection. In conclusion, these findings suggest that infection with a frequently occurring environmental bacterium such as L. innocua, which is nonpathogenic and not adapted to intracellular replication, can contribute to the maintenance of memory T cells specific for a related intracellular pathogen.

Lyme arthritis synovial gamma delta T cells respond to Borrelia burgdorferi lipoproteins and lipidated hexapeptides.

Lyme arthritis synovial fluid contains a large proportion of gamma delta T cells that proliferates upon stimulation with the causative spirochete, Borrelia burgdorferi. A panel of Borrelia-reactive gamma delta T cell clones was derived from synovial fluid of two patients with Lyme arthritis. Each of six gamma delta clones from one patient used the V delta 1 TCR segment but had otherwise unique CDR3 sequences and diverse V gamma segment usage. Stimulation of the V delta 1 clones was optimal in the presence of Borrelia, dendritic cells, and exogenous IL-2, which was reflected by proliferation, TCR down-modulation, as well as induction of CD25 and Fas ligand expression. Stimulation by B. burgdorferi-pulsed dendritic cells withstood chemical fixation and was not restricted to class I or class II MHC, CD1a, CD1b, or CD1c. In contrast, anti-gamma delta antibody potently inhibited proliferation. Extraction of B. burgdorferi lipoproteins with Triton X-114 enriched for the stimulatory component. This was confirmed using lipidated vs nonlipidated hexapeptides of Borrelia outer surface proteins. These observations suggest that synovial V delta 1 T cells may mediate an innate immune response to common lipoprotein products of spirochetes.