Surveillance of infections of surgical sites and lower respiratory tracts should be combined: experiences from the German surveillance module for operated patients (OP-KISS), 2018 to 2022.

BackgroundSurveillance of lower respiratory tract infections (LRTI) of operated patients conventionally focuses on intubated patients in intensive care units (ICU). Post-operative immobilisation increases the risk of LRTI not associated with ventilators. Operated patients, however, have thus far not been a primary target for LRTI surveillance.AimWe aimed to describe the applied LRTI surveillance method in the German surveillance module for operated patients (OP-KISS) and to report data between 2018 and 2022.MethodsSurveillance of LRTI can be performed voluntarily in addition to surgical site infection (SSI) surveillance in OP-KISS. We calculated LRTI rates per 100 operations for all procedures combined, as well as for individual surgical groups and procedures. Additionally, a combined post-operative infection rate (SSI and LRTI) was calculated.ResultsSurveillance of LRTI was performed in 4% of all participating OP-KISS departments and for 2% (23,239 of 1,332,438) of all procedures in the OP-KISS database. The pooled LRTI rate was 0.9 per 100 operations, with marked differences between different types of surgery (3.6 for lobectomies, 0.1 for traumatology and orthopaedics). The share of LRTI among all post-operative infections was highly variable. For lobectomies, the LRTI rate was higher than the SSI rate (3.6 vs 1.5 per 100 operations).ConclusionSurveillance of post-operative LRTI is not yet widely adopted by German hospitals. Based on the data in this study, lobectomies represent a prime target for post-operative LRTI surveillance.

Strengthening the role of hospital leadership in infection control (LEAD-IC) - a multimodal educational intervention in German acute care hospitals.

BACKGROUND: The effect of leadership support for adherence to infection control and prevention (IPC) measures has been demonstrated. To expand this support, a target group-specific educational study for chief medical officers (CMO) was implemented and its influence on IPC indicators was investigated. METHODS: A controlled cohort study was conducted between 2018 and 2019. The intervention based on an initial workshop, an e-learning course, and a final meeting. Participants' activities involving IPC management were surveyed. Consumption of alcohol hand rub (AHR) and incidence density of hospital-associated (HA) Clostridioides difficile-associated infections (CDI) were analyzed. RESULTS: Eight percent of 360 CMOs invited participated in the initial workshop; 70% of those participants registered for the online course. Overall, 43% completed the post-intervention questionnaire, in which 85% of respondents reported increased collaboration with relevant stakeholders. The pre-intervention median AHR consumption was higher in the intervention group than in the control group. Both groups showed an increase (38.6 (interquartile range (IQR) 33.6; 45.0) to 41.9 ml/patient day (PD) (IQR 35.0; 56.6) and 33.4 (IQR 28.3; 40.8) to 35.8 ml/ PD (IQR 31.6; 43.2), respectively). Pre-intervention median HA CDI cases were lower in the intervention group than in the control group. Both groups reported a decrease (0.22 (IQR 0.17; 0.33) to 0.19 cases/1000 PD (IQR 0.15; 0.26) and 0.32 (IQR 0.2; 0.48) to 0.22 cases/1000 PD (IQR 0.11; 0.33), respectively). CONCLUSION: Multimodal IPC training of CMOs is worthwhile and can lead to changes in IPC-relevant cooperation in hospitals. IPC training of hospital management should be further intensified.

Association of ward-level antibiotic consumption with healthcare-associated Clostridioides difficile infections: an ecological study in five German university hospitals, 2017-2019.

OBJECTIVES: To analyse the influence of antibiotic consumption on healthcare-associated healthcare onset (HAHO) Clostridioides difficile infection (CDI) in a German university hospital setting. METHODS: Monthly ward-level antibiotic consumption measured in DDD/100 patient days (pd) and CDI surveillance data from five university hospitals in the period 2017 through 2019 were analysed. Uni- and multivariable analyses were performed with generalized estimating equation models. RESULTS: A total of 225 wards with 7347 surveillance months and 4 036 602 pd participated. With 1184 HAHO-CDI cases, there was a median incidence density of 0.17/1000 pd (IQR 0.03-0.43) across all specialties, with substantial differences among specialties. Haematology-oncology wards showed the highest median incidence density (0.67/1000 pd, IQR 0.44-1.01), followed by medical ICUs (0.45/1000 pd, IQR 0.27-0.73) and medical general wards (0.32/1000 pd, IQR 0.18-0.53). Multivariable analysis revealed carbapenem (mostly meropenem) consumption to be the only antibiotic class associated with increased HAHO-CDI incidence density. Each carbapenem DDD/100 pd administered increased the HAHO-CDI incidence density by 1.3% [incidence rate ratio (IRR) 1.013; 95% CI 1.006-1.019]. Specialty-specific analyses showed this influence only to be valid for haematological-oncological wards. Overall, factors like ward specialty (e.g. haematology-oncology ward IRR 2.961, 95% CI 2.203-3.980) or other CDI cases on ward had a stronger influence on HAHO-CDI incidence density (e.g. community-associated CDI or unknown association case in same month IRR 1.476, 95% CI 1.242-1.755) than antibiotic consumption. CONCLUSIONS: In the German university hospital setting, monthly ward-level carbapenem consumption seems to increase the HAHO-CDI incidence density predominantly on haematological-oncological wards. Furthermore, other patient-specific factors seem to be equally important to control HAHO-CDI.

Age as a risk factor for surgical site infections: German surveillance data on total hip replacement and total knee replacement procedures 2009 to 2018.

BackgroundOlder age is frequently cited as a risk factor for healthcare-associated infections in general, and surgical site infections (SSIs) specifically.AimWe aimed to investigate the correlation between age and SSI occurrence.MethodsData on total hip replacement (THR) and total knee replacement (TKR) surgeries and resulting SSIs documented in the German national surveillance network from a 10-year period from 2009 to 2018 were selected for analysis. SSI rates and adjusted odds ratios (AOR) were calculated and a multivariable analysis to determine risk factors for SSI occurrence was conducted.ResultsA total of 418,312 THR procedures resulting in 3,231 SSIs, and 286,074 TKR procedures with 1,288 SSIs were included in the analyses. For THR, SSI rates were higher in older age groups when compared with the reference age group of 61-65 years. A significantly higher risk was observed in the 76-80 years age group (AOR: 1.21, 95% CI: 1.05-1.4). An age of ≤ 50 years was associated with a significantly lower SSI risk (AOR: 0.64, 95% CI: 0.52-0.8). For TKR, a similar correlation was observed, with the exception of the youngest age group (≤ 52 years), which was shown to have an SSI risk equal to that of the knee prosthesis reference age group (78-82 years).ConclusionA strong correlation between increasing age and SSI occurrence was observed for both procedure types. The results of our analyses provide a basis to consider future targeted SSI prevention measures for different age groups.

Efficacy of universal preoperative decolonization with Polyhexanide in primary joint arthroplasty on surgical site infections. A multicenter before-and after-study.

BACKGROUND: Surgical site infections (SSI) are rare but severe complications after total joint arthroplasty (TJA). Decolonization measures prior to elective orthopedic surgeries have shown to reduce the risk of SSI with Staphylococcus aureus (S. aureus). OBJECTIVE: To determine the efficacy of universal decolonization with Polyhexanide on SSI rates with a focus on Staphylococcus aureus in patients with TJA. METHODS: Patients scheduled for elective hip or knee TJA in 5 participating certified orthopedic centers were included between 2015 and 2018 into this before and after study. Data on patients, surgeries and infections were prospectively collected. CDC-criteria were used to define and categorize Infections within 90 days after surgery. From January 2017 on, patients received decolonization sets containing Polyhexanide. Patients performed a 5 day decolonization regimen starting 4 days prior to surgery which included wipes, nasal decontamination and oral solution. RESULTS: Thirteen thousand, three hundred fifteen patients received TJA. During intervention 4437 decolonization sets were distributed among 7175 patients. Overall SSI rates increased from 0.68 /100 surgeries to 0.91/ 100 surgeries after implementation of the intervention (IRR 1.32; 95% CI 0.90-1.96). Time series analysis identified an increasing trend of SSI prior to the intervention. After implementation overall SSI rates plateaued. Regression analysis revealed surgery during intervention period to be an independent risk factor for developing a SSI (OR 1.34; 95%CI 1.18-1.53). Initial SSI rates due to S. aureus were 0.24/100 surgeries and decreased to 0.14/100 surgeries (IRR 0.57; 95% CI 0.25-1.22) after introduction of decolonization. Regression analysis revealed surgery during intervention period to be an independent protective factor for developing a SSI with S. aureus (OR 0.57, 95% CI: 0.33-0.99). Overall deep S. aureus SSI decreased significantly from 0.22/100 surgeries to 0.00/100 surgeries in patients adherent to protocol (IRR 0.00, 95% CI 0.00-.85). CONCLUSION: Universal decolonization with Polyhexanide did not reduce overall surgical site infections, but was effective in reducing Staphylococcus aureus - surgical site infections following elective joint arthroplasty. Polyhexanide could extend the list of alternatives to already established decolonization strategies. TRIAL REGISTRATION: The trial was registered at the German Registry for clinical studies www.drks.de ( DRKS00011505 ).

Epidemiological and clinical characteristics of SARS-CoV-2 infections at a testing site in Berlin, Germany, March and April 2020-a cross-sectional study.

OBJECTIVE: In Berlin, the first public severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing site started 1 day after the first case in the city occurred. We describe epidemiological and clinical characteristics and aim at identifying risk factors for SARS-CoV-2 detection during the first 6 weeks of operation. METHODS: Testing followed national recommendations, but was also based on the physician's discretion. We related patient characteristics to SARS-CoV-2 test positivity for exploratory analyses using a cross-sectional, observational study design. RESULTS: Between 3 March and 13 April 2020, 5179 individuals attended the site (median age 34 years; interquartile range 26-47 years). The median time since disease onset was 4 days (interquartile range 2-7 days). Among 4333 persons tested, 333 (7.7%) were positive. Test positivity increased up to 10.3% (96/929) during the first 3 weeks and then declined, paralleling Germany's lock-down and the course of the epidemic in Berlin. Strict adherence to testing guidelines resulted in 10.4% (262/2530) test positivity, compared with 3.9% (71/1803) among individuals tested for other indications. A nightclub was a transmission hotspot; 27.7% (26/94) of one night's visitors were found positive. Smell and/or taste dysfunction indicated coronavirus disease 2019 (COVID-19) with 85.6% specificity (95% CI 82.1%-88.1%). Four per cent (14/333) of those infected were asymptomatic. Risk factors for detection of SARS-CoV-2 infection were recent contact with a positive case (second week after contact, OR 3.42; 95% CI 2.48-4.71), travel to regions of high pandemic activity (e.g. Austria, OR 4.16; 95% CI 2.48-6.99), recent onset of symptoms (second week, OR 3.61; 95% CI 1.87-6.98) and an impaired sense of smell/taste (4.08; 95% CI 2.36-7.03). CONCLUSIONS: In this young population, early-onset presentation of COVID-19 resembled flu-like symptoms, except for smell and/or taste dysfunction. Risk factors for SARS-CoV-2 detection were return from regions with high incidence and contact with confirmed SARS-CoV-2 cases, particularly when tests were administered within the first 2 weeks after contact and/or onset of symptoms.

Evolution of resistance in vitro reveals mechanisms of artemisinin activity in Toxoplasma gondii.

Artemisinins are effective against a variety of parasites and provide the first line of treatment for malaria. Laboratory studies have identified several mechanisms for artemisinin resistance in Plasmodium falciparum, including mutations in Kelch13 that are associated with delayed clearance in some clinical isolates, although other mechanisms are likely involved. To explore other potential mechanisms of resistance in parasites, we took advantage of the genetic tractability of Toxoplasma gondii, a related parasite that shows moderate sensitivity to artemisinin. Resistant populations of T. gondii were selected by culture in increasing concentrations and whole-genome sequencing identified several nonconservative point mutations that emerged in the population and were fixed over time. Genome editing using CRISPR/Cas9 was used to introduce point mutations conferring amino acid changes in a serine protease homologous to DegP and a serine/threonine protein kinase of unknown function. Single and double mutations conferred a competitive advantage over wild-type parasites in the presence of drug, despite not changing EC50 values. Additionally, the evolved resistant lines showed dramatic amplification of the mitochondria genome, including genes encoding cytochrome b and cytochrome c oxidase I. Prior studies in yeast and mammalian tumor cells implicate the mitochondrion as a target of artemisinins, and treatment of wild-type parasites with high concentrations of drug decreased mitochondrial membrane potential, a phenotype that was stably altered in the resistant parasites. These findings extend the repertoire of mutations associated with artemisinin resistance and suggest that the mitochondrion may be an important target of inhibition of resistance in T. gondii.

Incidence of healthcare-associated Clostridioides difficile infections and association with ward-level antibiotic consumption in a German university hospital: an ecological study.

OBJECTIVES: Clostridioides difficile infection (CDI) is one of the most important healthcare-associated infections. We aimed to describe the incidence density of healthcare-associated CDI (HA-CDI) in Germany's largest hospital and to identify associations with ward-level antimicrobial consumption. METHODS: We used surveillance data on CDI and antimicrobial consumption from 2014 to 2017 and analysed a potential association by means of multivariable regression analysis. RESULTS: We included 77 wards with 404998 admitted patients and 1850862 patient-days. Six hundred and seventy-one HA-CDI cases were identified, resulting in a pooled mean incidence density of 0.36/1000 patient-days (IQR = 0.34-0.39). HA-CDI incidence density on ICU and haematological-oncological wards was about three times higher than on surgical wards [incidence rate ratio (IRR) = 3.00 (95% CI = 1.96-4.60) and IRR = 2.78 (95% CI = 1.88-4.11), respectively]. Ward-level consumption of third-generation cephalosporins was the sole antimicrobial risk factor for HA-CDI. With each DDD/100 patient-days administered, a ward's HA-CDI incidence density increased by 2% [IRR = 1.02 (95% CI = 1.01-1.04)]. Other risk factors were contemporaneous community-associated CDI cases [IRR = 1.32 (95% CI = 1.07-1.63)] and CDI cases in the previous month [IRR = 1.27 (95% CI = 1.07-1.51)]. Furthermore, we found a significant decrease in HA-CDI in 2017 compared with 2014 [IRR = 0.68 (95% CI = 0.54-0.86)]. CONCLUSIONS: We confirmed that ward-level antimicrobial use influences HA-CDI and specifically identified third-generation cephalosporin consumption as a risk factor.

Impact of fluoroquinolone prophylaxis during neutropenia on bloodstream infection: Data from a surveillance program in 8755 patients receiving high-dose chemotherapy for haematologic malignancies between 2009 and 2014.

OBJECTIVES: Antibacterial chemoprophylaxis with fluoroquinolones (FQPx) has been commonly used in cancer patients with neutropenia, but its efficacy has been challenged by the emergence of fluoroquinolone resistance. METHODS: The impact of FQPx on bloodstream infections (BSI) during neutropenia after high-dose chemotherapy for haematologic malignancies was evaluated through a multicenter hospital infection surveillance system for the period 2009-2014. RESULTS: Among 8755 patients (4223 allogeneic [allo-] HSCT, 3602 autologous [auto-] HSCT, 930 high-dose chemotherapy for acute leukemia [HDC]), 5302 (61%) had received FQPx. Administration of FQPx was associated with fewer Gram-negative BSI in the overall study cohort patients (4.6% vs. 7.7%, adjusted subdistribution hazard ratio [aSHR] 0.59, 95%CI 0.50-0.70), in patients with HDC (3.7% vs. 9.2%, adjusted subdistribution hazard ratio [aSHR] 0.40, 95%CI 0.22-0.70) and auto-HSCT patients (4% vs. 9%, aSHR 0.43, 95%CI 0.33-0.56). In HDC patients, FQPx was associated with a marked reduction in all-cause mortality during neutropenia (2.3% vs. 7.8%, aSHR 0.30, 95%CI 0.15-0.58). Patients receiving FQPx had significantly more BSIs due to ESBL-positive Enterobacteriacea (0.8 vs. 0.3%, RR 2.2, 95%CI 1.17-4.26). BSIs by MRSA (n = 5) and VRE (n = 11) were rare in our cohort. CONCLUSIONS: As used in the participating centers, FQPx was associated with reduced Gram-negative BSI and improved survival among HDC patients. Among HSCT patients, the benefits were less clear. If adapted to local resistance patterns and patient characteristics, FQPx still may be useful in the management of patients with haematologic malignancies.

QTL Mapping and CRISPR/Cas9 Editing to Identify a Drug Resistance Gene in Toxoplasma gondii.

Scientific knowledge is intrinsically linked to available technologies and methods. This article will present two methods that allowed for the identification and verification of a drug resistance gene in the Apicomplexan parasite Toxoplasma gondii, the method of Quantitative Trait Locus (QTL) mapping using a Whole Genome Sequence (WGS) -based genetic map and the method of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 -based gene editing. The approach of QTL mapping allows one to test if there is a correlation between a genomic region(s) and a phenotype. Two datasets are required to run a QTL scan, a genetic map based on the progeny of a recombinant cross and a quantifiable phenotype assessed in each of the progeny of that cross. These datasets are then formatted to be compatible with R/qtl software that generates a QTL scan to identify significant loci correlated with the phenotype. Although this can greatly narrow the search window of possible candidates, QTLs span regions containing a number of genes from which the causal gene needs to be identified. Having WGS of the progeny was critical to identify the causal drug resistance mutation at the gene level. Once identified, the candidate mutation can be verified by genetic manipulation of drug sensitive parasites. The most facile and efficient method to genetically modify T. gondii is the CRISPR/Cas9 system. This system comprised of just 2 components both encoded on a single plasmid, a single guide RNA (gRNA) containing a 20 bp sequence complementary to the genomic target and the Cas9 endonuclease that generates a double-strand DNA break (DSB) at the target, repair of which allows for insertion or deletion of sequences around the break site. This article provides detailed protocols to use CRISPR/Cas9 based genome editing tools to verify the gene responsible for sinefungin resistance and to construct transgenic parasites.

Genetic mapping reveals that sinefungin resistance in Toxoplasma gondii is controlled by a putative amino acid transporter locus that can be used as a negative selectable marker.

Quantitative trait locus (QTL) mapping studies have been integral in identifying and understanding virulence mechanisms in the parasite Toxoplasma gondii. In this study, we interrogated a different phenotype by mapping sinefungin (SNF) resistance in the genetic cross between type 2 ME49-FUDR(r) and type 10 VAND-SNF(r). The genetic map of this cross was generated by whole-genome sequencing of the progeny and subsequent identification of single nucleotide polymorphisms (SNPs) inherited from the parents. Based on this high-density genetic map, we were able to pinpoint the sinefungin resistance phenotype to one significant locus on chromosome IX. Within this locus, a single nonsynonymous SNP (nsSNP) resulting in an early stop codon in the TGVAND_290860 gene was identified, occurring only in the sinefungin-resistant progeny. Using CRISPR/CAS9, we were able to confirm that targeted disruption of TGVAND_290860 renders parasites sinefungin resistant. Because disruption of the SNR1 gene confers resistance, we also show that it can be used as a negative selectable marker to insert either a positive drug selection cassette or a heterologous reporter. These data demonstrate the power of combining classical genetic mapping, whole-genome sequencing, and CRISPR-mediated gene disruption for combined forward and reverse genetic strategies in T. gondii.

A prospective study on surgical-site infections in thyroid operation.

BACKGROUND: To evaluate the incidence and the microbe spectrum of surgical-site infections (SSIs) in patients undergoing elective thyroid operation and to develop a risk factor-based predictive model. METHODS: This prospective study included 6,778 consecutive patients who underwent thyroid operation at a single institution between 2007 and 2012. SSI was defined according to the Centers for Disease Control and Prevention. Regression models were fitted to evaluate risk factors for SSI. A predictive nomogram was constructed from relevant variables in the multivariable analysis. Discrimination and calibration of the nomogram were assessed. RESULTS: The cumulative incidence of SSI after 30 days was 0.49%. The median time from operation to SSI was 7 days (interquartile range, 4-10.5 days). SSI was classified as superficial incisional in 30 cases (93.8%), deep incisional in 1 case (3.1%), and organ/space in 1 case (3.1%). Staphylococcus aureus was the most common isolate. In multivariable analysis, duration of operation (P = .004) and American Society of Anesthesiologists' score (P = .031) were identified as independent risk factors for SSI. These variables formed the basis of a nomogram, which was validated internally by bootstrapping and reached a predictive accuracy of 70.1%. The calibration curve showed a good agreement between predicted probability and actual observation. CONCLUSION: The cumulative incidence of SSI in thyroid operation is <0.5%. American Society of Anesthesiologists' score and the duration of operation are independent risk factors for SSI. Antibiotic prophylaxis may be considered for selected patients based on the individual risk profile.

Compensatory dendritic cell development mediated by BATF-IRF interactions.

The AP1 transcription factor Batf3 is required for homeostatic development of CD8α(+) classical dendritic cells that prime CD8 T-cell responses against intracellular pathogens. Here we identify an alternative, Batf3-independent pathway in mice for CD8α(+) dendritic cell development operating during infection with intracellular pathogens and mediated by the cytokines interleukin (IL)-12 and interferon-γ. This alternative pathway results from molecular compensation for Batf3 provided by the related AP1 factors Batf, which also functions in T and B cells, and Batf2 induced by cytokines in response to infection. Reciprocally, physiological compensation between Batf and Batf3 also occurs in T cells for expression of IL-10 and CTLA4. Compensation among BATF factors is based on the shared capacity of their leucine zipper domains to interact with non-AP1 factors such as IRF4 and IRF8 to mediate cooperative gene activation. Conceivably, manipulating this alternative pathway of dendritic cell development could be of value in augmenting immune responses to vaccines.

Phosphorylation of immunity-related GTPases by a Toxoplasma gondii-secreted kinase promotes macrophage survival and virulence.

Macrophages are specialized to detect and destroy intracellular microbes and yet a number of pathogens have evolved to exploit this hostile niche. Here we demonstrate that the obligate intracellular parasite Toxoplasma gondii disarms macrophage innate clearance mechanisms by secreting a serine threonine kinase called ROP18, which binds to and phosphorylates immunity-related GTPases (IRGs). Substrate profiling of ROP18 revealed a preference for a conserved motif within switch region I of the GTPase domain, a modification predicted to disrupt IRG function. Consistent with this, expression of ROP18 was both necessary and sufficient to block recruitment of Irgb6, which was in turn required for parasite destruction. ROP18 phosphorylation of IRGs prevented clearance within inflammatory monocytes and IFN-γ-activated macrophages, conferring parasite survival in vivo and promoting virulence. IRGs are implicated in clearance of a variety of intracellular pathogens, suggesting that other virulence factors may similarly thwart this innate cellular defense mechanism.

Antibiotics: MRSA prevention measures in German hospitals: results of a survey among hospitals, performed as part of the MRSA-KISS module.

BACKGROUND: In this study, we investigated the measures currently being taken in German hospitals to prevent infection with methicillin-resistant strains of Staphylococcus aureus (MRSA). To this end, we circulated a questionnaire among hospitals participating in the MRSA-KISS module. "KISS" in the name of this project stands for "hospital infection surveillance system" (in German, Krankenhaus-Infektions-Surveillance-System). METHODS: The questionnaire was sent to all MRSA-KISS participants. A study doctor visited a representative sample of hospitals to validate the responses. The study doctor checked the questionnaire responses with a systematic on-site interview of the contact person in each hospital, then evaluated the information contained in them by recording all of the MRSA patients who were present in the hospital on the day of the visit in a point-prevalence study (PPS). RESULTS: All 134 participants filled out the questionnaire. The screening of patients at risk on admission is an established part of the clinical routine in all of the surveyed hospitals, as are MRSA decolonization procedures. These preventive measures have been recommended for routine use in Germany by the Robert Koch Institute (RKI, the German counterpart of the Centers for Disease Control and Prevention). The surveyed hospitals also used further preventive strategies, including, for example, an alerting system for the identification, upon hospital admission, of patients with a known history of MRSA positivity (72%); pre-admission screening of all patients (13%); universal screening on admission in some hospital wards (19%); and the prophylactic isolation of patients suspected of having MRSA with pending microbiological test results (21%). 35 hospitals were visited for validation. Most of the responses in each hospital were internally consistent and adequately reflected the real situation on site. Less consistency was seen in responses regarding the detection of MRSA by clinical testing and the measures that were taken after MRSA was detected. CONCLUSION: The surveyed hospitals are, in fact, implementing many of the RKI's recommendations, as well as other preventive measures against MRSA.

The transcription of bradyzoite genes in Toxoplasma gondii is controlled by autonomous promoter elements.

Experimental evidence suggests that apicomplexan parasites possess bipartite promoters with basal and regulated cis-elements similar to other eukaryotes. Using a dual luciferase model adapted for recombinational cloning and use in Toxoplasma gondii, we show that genomic regions flanking 16 parasite genes, which encompass examples of constitutive and tachyzoite- and bradyzoite-specific genes, are able to reproduce the appropriate developmental stage expression in a transient luciferase assay. Mapping of cis-acting elements in several bradyzoite promoters led to the identification of short sequence spans that are involved in control of bradyzoite gene expression in multiple strains and under different bradyzoite induction conditions. Promoters that regulate the heat shock protein BAG1 and a novel bradyzoite-specific NTPase during bradyzoite development were fine mapped to a 6-8 bp resolution and these minimal cis-elements were capable of converting a constitutive promoter to one that is induced by bradyzoite conditions. Gel-shift experiments show that mapped cis-elements are bound by parasite protein factors with the appropriate functional sequence specificity. These studies are the first to identify the minimal sequence elements that are required and sufficient for bradyzoite gene expression and to show that bradyzoite promoters are maintained in a 'poised' chromatin state throughout the intermediate host life cycle in low passage strains. Together, these data demonstrate that conventional eukaryotic promoter mechanisms work with epigenetic processes to regulate developmental gene expression during tissue cyst formation.

Risk factors for the development of nosocomial pneumonia and mortality on intensive care units: application of competing risks models.

INTRODUCTION: Pneumonia is a very common nosocomial infection in intensive care units (ICUs). Many studies have investigated risk factors for the development of infection and its consequences. However, the evaluation in most of theses studies disregards the fact that there are additional competing events, such as discharge or death. METHODS: A prospective cohort study was conducted over 18 months in five intensive care units at one university hospital. All patients that were admitted for at least 2 days were included, and surveillance of nosocomial pneumonia was conducted. Various potential risk factors (baseline- and time-dependent) were evaluated in two competing risks models: the acquisition of nosocomial pneumonia and discharge (dead or alive; model 1) and for the risk of death in the ICU and discharge alive (model 2). RESULTS: Patients from 1,876 admissions were included. A total of 158 patients developed nosocomial pneumonia. The main risk factors for nosocomial pneumonia in the multivariate analysis in model 1 were: elective surgery (cause-specific hazard ratio = 1.95; 95% CI 1.33 to 2.85) or emergency surgery (1.59; 95% CI 1.10 to 2.28) prior to ICU admission, usage of a nasogastric tube (3.04; 95% CI 1.25 to 7.37) and mechanical ventilation (5.90; 95% CI 2.47 to 14.09). Nosocomial pneumonia prolonged the length of ICU stay but was not directly associated with a fatal outcome (p = 0.55). CONCLUSION: More studies using competing risk models, which provide more accurate data compared to naive survival curves or logistic models, should be carried out to verify the impact of risk factors and patient characteristics for the acquisition of nosocomial infections and infection-associated mortality.

The transcriptome of Toxoplasma gondii.

BACKGROUND: Toxoplasma gondii gives rise to toxoplasmosis, among the most prevalent parasitic diseases of animals and man. Transformation of the tachzyoite stage into the latent bradyzoite-cyst form underlies chronic disease and leads to a lifetime risk of recrudescence in individuals whose immune system becomes compromised. Given the importance of tissue cyst formation, there has been intensive focus on the development of methods to study bradyzoite differentiation, although the molecular basis for the developmental switch is still largely unknown. RESULTS: We have used serial analysis of gene expression (SAGE) to define the Toxoplasma gondii transcriptome of the intermediate-host life cycle that leads to the formation of the bradyzoite/tissue cyst. A broad view of gene expression is provided by >4-fold coverage from nine distinct libraries (approximately 300,000 SAGE tags) representing key developmental transitions in primary parasite populations and in laboratory strains representing the three canonical genotypes. SAGE tags, and their corresponding mRNAs, were analyzed with respect to abundance, uniqueness, and antisense/sense polarity and chromosome distribution and developmental specificity. CONCLUSION: This study demonstrates that phenotypic transitions during parasite development were marked by unique stage-specific mRNAs that accounted for 18% of the total SAGE tags and varied from 1-5% of the tags in each developmental stage. We have also found that Toxoplasma mRNA pools have a unique parasite-specific composition with 1 in 5 transcripts encoding Apicomplexa-specific genes functioning in parasite invasion and transmission. Developmentally co-regulated genes were dispersed across all Toxoplasma chromosomes, as were tags representing each abundance class, and a variety of biochemical pathways indicating that trans-acting mechanisms likely control gene expression in this parasite. We observed distinct similarities in the specificity and expression levels of mRNAs in primary populations (Day-6 post-sporozoite infection) that occur prior to the onset of bradyzoite development that were uniquely shared with the virulent Type I-RH laboratory strain suggesting that development of RH may be arrested. By contrast, strains from Type II-Me49B7 and Type III-VEGmsj contain SAGE tags corresponding to bradyzoite genes, which suggests that priming of developmental expression likely plays a role in the greater capacity of these strains to complete bradyzoite development.