Synergism between remdesivir and ribavirin leads to SARS-CoV-2 extinction in cell culture

BACKGROUND AND PURPOSE

There is a need for effective anti-COVID-19 treatments, mainly for individuals at risk of severe disease such as the elderly and the immunosuppressed. Drug repositioning has proved effective in identifying drugs that can find a new application for the control of coronavirus disease, in particular COVID-19. The purpose of the present study was to find synergistic antiviral combinations for COVID-19 based on lethal mutagenesis.

EXPERIMENTAL APPROACH

The effect of combinations of remdesivir and ribavirin on the infectivity of SARS-CoV-2 in cell culture has been tested. Viral populations were monitored by ultra-deep sequencing, and the decrease of infectivity as a result of the treatment was measured.

KEY RESULTS

Remdesivir and ribavirin exerted a synergistic inhibitory activity against SARS-CoV-2, quantified both by CompuSyn (Chou-Talalay method) and Synergy Finder (ZIP-score model). In serial passage experiments, virus extinction was readily achieved with remdesivir-ribavirin combinations at concentrations well below their cytotoxic 50 value, but not with the drugs used individually. Deep sequencing of treated viral populations showed that remdesivir, ribavirin, and their combinations evoked significant increases of the number of viral mutations and haplotypes, as well as modification of diversity indices that characterize viral quasi-species.

CONCLUSION AND IMPLICATIONS

SARS-CoV-2 extinction can be achieved by synergistic combination treatments based on lethal mutagenesis. In addition, the results offer prospects of triple drug treatments for effective SARS-CoV-2 suppression.

SARS-CoV-2 mutant spectra as variant of concern nurseries: endless variation?

Introduction

SARS-CoV-2 isolates of a given clade may contain low frequency genomes that encode amino acids or deletions which are typical of a different clade.

Methods

Here we use high resolution ultra-deep sequencing to analyze SARS-CoV-2 mutant spectra.

Results

In 6 out of 11 SARS-CoV-2 isolates from COVID-19 patients, the mutant spectrum of the spike (S)-coding region included two or more amino acids or deletions, that correspond to discordant viral clades. A similar observation is reported for laboratory populations of SARS-CoV-2 USA-WA1/2020, following a cell culture infection in the presence of remdesivir, ribavirin or their combinations. Moreover, some of the clade-discordant genome residues are found in the same haplotype within an amplicon.

Discussion

We evaluate possible interpretations of these findings, and reviewed precedents for rapid selection of genomes with multiple mutations in RNA viruses. These considerations suggest that intra-host evolution may be sufficient to generate minority sequences which are closely related to sequences typical of other clades. The results provide a model for the origin of variants of concern during epidemic spread─in particular Omicron lineages─that does not require prolonged infection, involvement of immunocompromised individuals, or participation of intermediate, non-human hosts.

Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps

Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.

SARS-CoV-2 Mutant Spectra at Different Depth Levels Reveal an Overwhelming Abundance of Low Frequency Mutations

Populations of RNA viruses are composed of complex and dynamic mixtures of variant genomes that are termed mutant spectra or mutant clouds. This applies also to SARS-CoV-2, and mutations that are detected at low frequency in an infected individual can be dominant (represented in the consensus sequence) in subsequent variants of interest or variants of concern. Here we briefly review the main conclusions of our work on mutant spectrum characterization of hepatitis C virus (HCV) and SARS-CoV-2 at the nucleotide and amino acid levels and address the following two new questions derived from previous results: (i) how is the SARS-CoV-2 mutant and deletion spectrum composition in diagnostic samples, when examined at progressively lower cut-off mutant frequency values in ultra-deep sequencing; (ii) how the frequency distribution of minority amino acid substitutions in SARS-CoV-2 compares with that of HCV sampled also from infected patients. The main conclusions are the following: (i) the number of different mutations found at low frequency in SARS-CoV-2 mutant spectra increases dramatically (50- to 100-fold) as the cut-off frequency for mutation detection is lowered from 0.5% to 0.1%, and (ii) that, contrary to HCV, SARS-CoV-2 mutant spectra exhibit a deficit of intermediate frequency amino acid substitutions. The possible origin and implications of mutant spectrum differences among RNA viruses are discussed.

Vaccine breakthrough infections with SARS-CoV-2 Alpha mirror mutations in Delta Plus, Iota, and Omicron

Replication of SARS-CoV-2 in the human population is defined by distributions of mutants that are present at different frequencies within the infected host and can be detected by ultra-deep sequencing techniques. In this study, we examined the SARS-CoV-2 mutant spectra of amplicons from the spike-coding (S-coding) region of 5 nasopharyngeal isolates derived from patients with vaccine breakthrough. Interestingly, all patients became infected with the Alpha variant, but amino acid substitutions that correspond to the Delta Plus, Iota, and Omicron variants were present in the mutant spectra of the resident virus. Deep sequencing analysis of SARS-CoV-2 from patients with vaccine breakthrough revealed a rich reservoir of mutant types and may also identify tolerated substitutions that can be represented in epidemiologically dominant variants.

Comparison of the Performance of Two Galactomannan Detection Tests: Platelia Aspergillus Ag and Aspergillus Galactomannan Ag Virclia Monotest

The use of nonculture-based biomarkers such as the determination of galactomannan is sought for the diagnosis of invasive aspergillosis. To investigate the comparative yield of two tests for the detection of galactomannan in patients with or without proven or probable invasive aspergillosis. Overall, 327 samples (327 patients) were analyzed in a retrospective/prospective study performed in 3 hospitals in Madrid, comparing the determination results in serum or bronchoalveolar lavage of two techniques for galactomannan detection, namely, Platelia Aspergillus Ag (Bio-Rad) and Aspergillus galactomannan Ag Virclia Monotest (Vircell S.L.), following the manufacturer's instructions. Both techniques can automate the process, but the second technique has the advantage of individual processing and assembly of each sample without the need for the additional expense of single-dose strips in controls. In total, 288 of the 327 tests performed showed concordant results between both techniques. The agreement between both methods was к = 0.722, and the correlation between indices was ρ = 0.718. Only 39 samples showed discordant results. In those 39 cases, there were 15 patients with proven or probable invasive aspergillosis criteria. For the samples with clinical criteria as a reference, the areas under the curve of the receiver operating characteristic (ROC) curve were 0.962 for Platelia and 0.968 for VirClia. The VirClia test has been proven to be an alternative for diagnosis due to its friendlier automated format than that of the usual Platelia routine test. The VirClia test also allows individual action and, therefore, a more immediate clinical response. IMPORTANCE Invasive mycoses are increasingly present in immunosuppressed or hospitalized patients with serious illnesses, leading to high rates of morbidity and mortality. Invasive aspergillosis is an infection caused, in a percentage greater than 50%, by the genus Aspergillus. It is vitally important to make an early diagnosis that leads to the application of antifungals in the initial stage of the infection. Therefore, tools are required to help with the early diagnosis of the infection. This comparative study of two enzyme immunoassays is based on the detection of galactomannan antigen in serum and bronchoalveolar lavage samples. A new design based on chemiluminescence and presented in an automated single-dose format is compared to a conventional ELISA technique marketed for years. The results obtained from the prospective and retrospective study indicate a high correlation and degree of agreement between both techniques, as well as in their diagnostic performance.

SARS-CoV-2 Point Mutation and Deletion Spectra and Their Association with Different Disease Outcomes

Mutant spectra of RNA viruses are important to understand viral pathogenesis and response to selective pressures. There is a need to characterize the complexity of mutant spectra in coronaviruses sampled from infected patients. In particular, the possible relationship between SARS-CoV-2 mutant spectrum complexity and disease associations has not been established. In the present study, we report an ultradeep sequencing (UDS) analysis of the mutant spectrum of amplicons from the nsp12 (polymerase)- and spike (S)-coding regions of 30 nasopharyngeal isolates (diagnostic samples) of SARS-CoV-2 of the first COVID-19 pandemic wave (Madrid, Spain, April 2020) classified according to the severity of ensuing COVID-19. Low-frequency mutations and deletions, counted relative to the consensus sequence of the corresponding isolate, were overwhelmingly abundant. We show that the average number of different point mutations, mutations per haplotype, and several diversity indices was significantly higher in SARS-CoV-2 isolated from patients who developed mild disease than in those associated with moderate or severe disease (exitus). No such bias was observed with RNA deletions. Location of amino acid substitutions in the three-dimensional structures of nsp12 (polymerase) and S suggest significant structural or functional effects. Thus, patients who develop mild symptoms may be a richer source of genetic variants of SARS-CoV-2 than patients with moderate or severe COVID-19. IMPORTANCE The study shows that mutant spectra of SARS-CoV-2 from diagnostic samples differ in point mutation abundance and complexity and that significantly larger values were observed in virus from patients who developed mild COVID-19 symptoms. Mutant spectrum complexity is not a uniform trait among isolates. The nature and location of low-frequency amino acid substitutions present in mutant spectra anticipate great potential for phenotypic diversification of SARS-CoV-2.

High SARS-CoV-2 viral load is associated with a worse clinical outcome of COVID-19 disease

COVID-19 severity and progression are determined by several host and virological factors that may influence the final outcome of SARS-CoV-2-infected patients. The objective of this work was to determine a possible association between viral load, obtained from nasopharyngeal swabs, and the severity of the infection in a cohort of 448 SARS-CoV-2-infected patients from a hospital in Madrid during the first outbreak of the pandemic in Spain. To perform this, we clinically classified patients as mild, moderate and severe COVID-19 according to a number of clinical parameters such as hospitalization requirement, need of oxygen therapy, admission to intensive care units and/or death. Also, Ct values were determined using SARS-CoV-2-specific oligonucleotides directed to ORF1ab. Here we report a statistically significant association between viral load and disease severity, a high viral load being associated with worse clinical prognosis, independently of several previously identified risk factors such as age, sex, hypertension, cardiovascular disease, diabetes, obesity and lung disease (asthma and chronic obstructive pulmonary disease). The data presented here reinforce viral load as a potential biomarker for predicting disease severity in SARS-CoV-2-infected patients. It is also an important parameter in viral evolution since it relates to the numbers and types of variant genomes present in a viral population, a potential determinant of disease progression.

Candida auris: a comparison between planktonic and biofilm susceptibility to antifungal drugs

Introduction. Candida auris is a pathogenic yeast that mainly affects immunosuppressed patients and those with implanted medical devices. This pathogen also displays elevated resistance to common antifungals and high survival and spreading capacities. Since no antifungal breakpoints have yet been defined for this pathogen, the data obtained here can be useful for further research concerning treatment or implementation of a prevention and disinfection protocol. Our aim was to study the antifungal resistance of C. auris to current antifungals in planktonic and sessile states. Using confocal laser scanning microscopy and viable biomass production, we demonstrated the ability of C. auris to develop a mature biofilm. We compared the minimal inhibitory concentration (MIC) and the minimal biofilm eradication concentration (MBEC) for the C. auris DSM 21092 strain plus two clinical isolates, and the results were compared with those obtained for Candida albicans and Candida parapsilosis, two species strongly linked to bloodstream infections and infections associated with biomaterials. We found that the clinical isolates of C. auris were resistant to fluconazole and sensitive to echinocandins and polyenes. The C. auris biofilms did not show susceptibility to any antifungal agent, showing MBECs that were up to 512-fold higher than the MICs. These findings highlight the importance of biofilm formation as a key factor underlying the resistance of this species to antifungals and suggest that the presence of implantable medical devices is one of the major risk factors in immunocompromised patients.

Relationship between conventional culture and flow cytometry for the diagnosis of urinary tract infection

BACKGROUND

Urine culture is the gold standard for the diagnosis of urinary tract infections (UTI). The use of flow cytometry analyzers (FCA) prior to culture allows for the quantification and recognition of cell components in urine to be automated and makes it possible to relate these data to the urine pathogens subsequently identified in cultures.

METHODS

Urine samples were assessed with the Sysmex UF-1000i analyzer. Those that met the criteria for culture (> 25 leukocytes/μL or > 385 bacteria/μL) were subjected to quantitative urine culture on chromogenic agar. Counts of red blood cells (RBC), white blood cells (WBC), epithelial cells (EC), and the kind of microorganisms identified in cultures were evaluated.

RESULTS

A total of 17,483 samples were processed by FCA. Of these, 9057 met the criteria for culture. Urine cultures were reduced by 48.2%. The most common urine pathogen was Escherichia coli (60.3%). Negative urine cultures were significantly (p < 0.001) associated with a lower WBC count than urine with E. coli, Klebsiella spp. and Proteus spp., but urine with Enterococcus spp. had a lower WBC than negative urine. Contaminated urine had a significantly (p < 0.001) lower WBC than urine with E. coli, Klebsiella spp. and Proteus spp., but no differences were found for Enterococcus spp. (p = 0.729). Negative urine cultures had significantly (p < 0.05) higher EC than all positive urine samples. Contaminated urine was associated (p < 0.001) with higher EC than cultures with E. coli and Klebsiella spp., in comparison with cultures with Enterococcus spp. (p = 0.091) and Proteus spp. (p = 0.251).

CONCLUSION

The use of the Sysmex UF-1000i flow cytometer for screening urine samples allows for a reduction in the number of urine cultures. WBC values correlate well with the main urine pathogens related to UTI. The results observed for Enterococcus spp. suggest a low impact of these pathogens as a cause of UTI.

Evaluation of a commercial multiplex PCR (Unyvero i60®) designed for the diagnosis of bone and joint infections using prosthetic-joint sonication

BACKGROUND

The development of sonication protocols over the last few years has improved the sensitivity of conventional cultures for the diagnosis of prosthetic-joint infection (PJI). However, the development of a new, specifically designed kit for the molecular diagnosis of PJI could provide a major improvement in this field.

METHODS

Prostheses retrieved from patients who underwent implant removal from May 2014 to May 2015 were sent for culture, and processed according to a previously defined protocol that included sonication. Furthermore, 180 microlitres of sonication fluid were used to carry out the multiplex PCR test (Unyvero i60 system^®). A comparison of the sensitivity, specificity, positive (PPV) and negative (NPV) predictive value, was performed. The study was approved by the Clinical Research Ethics Committee.

RESULTS

The analysis included 88 prostheses from 68 patients (1.29 prostheses/patient). The type of prostheses studied were knee (n=55), total hip (n=26), partial hip (n=5), and shoulder (n=2). Twenty-nine patients were diagnosed with a PJI (15 delayed, 12 acute, and 2 haematogenous infections). In 24 cases, the result of the PCR was positive, all but 1 corresponding to patients with clinical criteria of PJI. Nine resistance mechanisms were detected from 5 samples. The Unyvero i60 system^® showed slightly better results than traditional culture in terms of specificity and PPV.

CONCLUSIONS

The Unyvero i60 system^® may play a role in rapid diagnosis of PJI, due to its high specificity and PPV. However, despite these results, cultures have to be performed to detect organisms not detected by the system.

[Cryptococcal meningoencephalitis. Epidemiology and mortality risk factors in pre- and post-HAART era]

INTRODUCTION AND OBJECTIVE

Cryptococcal meningoencephalitis (CM) is an uncommon entity, but remains a major cause of morbidity and mortality in patients with AIDS.

MATERIAL AND METHODS

Review of CM cases in a university hospital. The diagnosis was determined by isolation of Cryptococcus neoformans in cerebrospinal fluid. Morbidity and mortality was assessed at 12 weeks (early mortality) and between 3 and 18 months after diagnosis (late mortality).

RESULTS

We analyzed 32 patients from 2,269 AIDS cases (1.41%). 10 patients between 1990-1996 and 22 between 1997-2014. Cryptococcal antigen in CSF was positive in all cases, with titers>1,024 in 19 patients (63%); this group had lower CD4+ counts (40 ± 33 vs. 139 ± 78 cel/μL) and greater disseminated involvement. After a first CM episode the relapse rate was 34%. Global mortality rate was 28% (9/32), much higher in the pre-HAART era.

CONCLUSIONS

CM morbidity and mortality is related to severe immunodeficiency, disseminated disease, high titers of antigen in CSF and delayed initiation of HAART.

Clinical and microbiological characteristics of patients with septic arthritis: A hospital-based study

BACKGROUND

To determine the clinical and epidemiological characteristics, etiology, underlying conditions, and outcomes of patients with primary septic arthritis and no prosthetic joints at a university hospital.

METHODS

A retrospective study was performed between 2005 and 2012. Records from the Microbiology Department were reviewed, and patients with a positive culture of synovial fluid or biopsy were selected for the study. Clinical charts were reviewed using a designed protocol.

RESULTS

41 patients were diagnosed with septic arthritis with a positive culture. Most were diagnosed with monoarticular (85.37%) and monomicrobial (92.68%) arthritis. The most commonly involved joint was the knee (34.15%). The most frequent underlying conditions were hypertension and diabetes mellitus. Staphylococcus aureus was the most common pathogen (58.54%). Two cases of chronic arthritis, both caused by Mycobacterium tuberculosis were detected. The most frequently used antibiotic combinations were cloxacillin + ciprofloxacin and vancomycin + ciprofloxacin. Surgical treatment included needle aspiration, open joint debridement, or arthroscopic techniques. Twelve cases had a poor outcome (destructive articular disease), and 3 patients died from staphylococcal sepsis.

CONCLUSIONS

In our hospital, septic arthritis is primarily acute, monoarticular, and monomicrobial; affects higher joints, is caused by S. aureus, and occurs in adult patients with underlying diseases. Outcome is good in most patients, although more than 25% of cases had articular sequels.

Prolonged incubation time does not increase sensitivity for the diagnosis of implant-related infection using samples prepared by sonication of the implants

We have designed a prospective study to evaluate the usefulness of prolonged incubation of cultures from sonicated orthopaedic implants. During the study period 124 implants from 113 patients were processed (22 osteosynthetic implants, 46 hip prostheses, 54 knee prostheses, and two shoulder prostheses). Of these, 70 patients had clinical infection; 32 had received antibiotics at least seven days before removal of the implant. A total of 54 patients had sonicated samples that produced positive cultures (including four patients without infection). All of them were positive in the first seven days of incubation. No differences were found regarding previous antibiotic treatment when analysing colony counts or days of incubation in the case of a positive result. In our experience, extending incubation of the samples to 14 days does not add more positive results for sonicated orthopaedic implants (hip and knee prosthesis and osteosynthesis implants) compared with a conventional seven-day incubation period.

Cite this article: Bone Joint J 2013;95-B:1001–6.

Evidence of Muller's ratchet in herpes simplex virus type 1

Population bottlenecks can have major effects in the evolution of RNA viruses, but their possible influence in the evolution of DNA viruses is largely unknown. Genetic and biological variation of herpes simplex virus type 1 (HSV-1) has been studied by subjecting 23 biological clones of the virus to 10 plaque-to-plaque transfers. In contrast to large population passages, plaque transfers led to a decrease in replicative capacity of HSV-1. Two out of a total of 23 clones did not survive to the last transfer in 143 TK(-) cells. DNA from three genomic regions (DNA polymerase, glycoprotein gD and thymidine kinase) from the initial and passaged clones was sequenced. Nucleotide substitutions were detected in the TK and gD genes, but not in the DNA polymerase gene. Assuming a uniform distribution of mutations along the genome, the average rate of fixation of mutations was about five mutations per viral genome and plaque transfer. This value is comparable to the range of values calculated for RNA viruses. Four plaque-transferred populations lost neurovirulence for mice, as compared with the corresponding initial clones. LD(50) values obtained with the populations subjected to serial bottlenecks were 4- to 67-fold higher than for their parental clones. These results equate HSV-1 with RNA viruses regarding fitness decrease as a result of plaque-to-plaque transfers, and show that population bottlenecks can modify the pathogenic potential of HSV-1. Implications for the evolution of complex DNA viruses are discussed.

Construction and properties of a recombinant pseudorabies virus with tetracycline-regulated control of immediate-early gene expression

A study was carried out to determine whether altering the control of expression of the IE180 gene of pseudorabies virus (PRV), by replacing the IE180 promoter with the tetracycline-responsive promoter (Ptet), affects virus replication and virulence. This PRV-BT90 mutant virus was constructed by complementation and recombination in Hela Tet-Off cells. The virus yield produced by infection of Hela Tet-Off cells with PRV-BT90 was similar to that of the parental virus vBecker2. Viral replication of PRV-BT90 was reduced in Vero cells as reflected by a reduction of virus yield and plating efficiency compared to vBecker2. PRV-BT90 plaque formation in Hela Tet-Off cells was inhibited in the presence of doxycycline, whereas vBecker2 plaque formation was not affected. Subcutaneous infection of mice with the two viruses revealed a LD(50) higher than 10(6) TCID(50) for the PRV-BT90 mutant virus while the LD(50) was 178 TCID(50) for the vBecker2 parental virus.

Detection of lfrA and tap efflux pump genes among clinical isolates of non-pigmented rapidly growing mycobacteria

This study was performed to detect LfrA and Tap efflux pumps among clinical isolates of non-pigmented rapidly growing mycobacteria (NPRGM). Gene detection was performed using polymerase chain reaction (PCR) with specific primers designed for each gene. Susceptibility of the strains to doxycycline, tigecycline and ciprofloxacin was analysed using the broth microdilution reference technique. In total, 166 clinical isolates were included in the study. The lfrA gene was detected in four strains (2.4%), comprising two strains of Mycobacterium chelonae (6.7% of this species), one Mycobacterium fortuitum (1.1%) and one Mycobacterium mucogenicum (14.3%). The tap gene was detected in 109 strains (65.7%), comprising 3 Mycobacterium abscessus (33.3%), 12 M. chelonae (40%), 75 M. fortuitum (84.3%), 2 Mycobacterium mageritense (40%), 15 Mycobacterium peregrinum (68.2%), 1 Mycobacterium alvei and 1 Mycobacterium porcinum; no strains of M. mucogenicum were tap-positive. No differences between tap-positive and -negative strains were observed for resistance to doxycycline (Fisher's exact test, P=0.055). lfrA is rare among clinical isolates of NPRGM, whilst tap is found more commonly. No correlation was detected between the presence of the efflux pumps and resistance to quinolones or tetracyclines.

Biofilm development by potentially pathogenic non-pigmented rapidly growing mycobacteria

BACKGROUND

A study to evaluate the biofilm-development ability in three different media (Middlebrook 7H9, sterile tap water and PBS-5% glucose) was performed with 19 collection strains from 15 different species on non-pigmented rapidly growing mycobacteria (NPRGM). A microtiter plate assay was developed to evaluate the percentage of covered surface of the microtiter plate wells in different days from day 1 to day 69.

RESULTS

All strains were able to develop biofilm in all the tested media. Middlebrook 7H9 showed the fastest growth, followed by sterile tap water and PBS-5% glucose. A sigmoid growth curve was detected in all the strains both in Middlebrook 7H9 and in sterile tap water. A difference could be detected for Mycobacterium abscessus in tap water, where it showed faster growth than all the other strains.

CONCLUSION

Biofilm development seems to be a property of all the species of NPRGM and it depends on the nutrients present in the medium. The microtiter plate assay described here is a useful tool to evaluate differences in biofilm development among the different species of rapidly growing mycobacteria.

Procedimientos de diagnóstico microbiológico de las micosis y estudios de sensibilidad a los antifúngicos

Fungal infections are a diagnostic and therapeutic problem of increasing concern due to the frequency and severity of disseminated infection in immunocompromised patients. Culture-based methods are characteristically slow and have poor sensitivity; hence, other methods, based on the detection of fungus-specific genetic, antigenic and metabolic components are being developed to enable early diagnosis and specific treatment. Moreover, reproducible antifungal susceptibility methods that can be adapted for use in clinical laboratories have been standardized to allow in vitro detection of resistance, which correlates with a less favorable clinical outcome. In this paper we review the main microbiological procedures available for the diagnosis of fungal infections and for antifungal susceptibility testing.

Impact of zygomycosis on microbiology workload: a survey study in Spain

This multicenter, population-based study evaluated the laboratory workload produced by zygomycetes and the number of cases of zygomycosis in Spain during 2005. Less than 8% of the patients who harbored zygomycete isolates had zygomycosis. The incidence of zygomycosis (6 cases) was 0.43 cases/1,000,000 inhabitants and 0.62 cases/100,000 hospital admissions.

Evaluación de la capacidad invasiva de las micobacterias no pigmentadas de crecimiento rápido mediante el estudio de la morfología de las microcolonias en fibroblastos

OBJECTIVE

The invasive capacity of rapidly-growing nonpigmented mycobacteria strains was evaluated by means of a fibroblast microcolony assay and related to the colony phenotype on Middlebrook 7H11 and to the clinical significance of the isolates.

METHODS

Twenty-nine strains [Mycobacterium chelonae (8), M. fortuitum (6), M. peregrinum (5), M. abscessus (5), M. mucogenicum (4) and M. septicum (1)], proceeding from a bacterial collection and clinical isolates, were evaluated. The smooth or rough phenotype of the colonies was assessed in Middlebrook 7H11 medium. Intracellular invasiveness was determined by the fibroblast-microcolony assay described by Shepard. Quantitative culture characteristics were compared with Student's t-test, and qualitative characteristics with Fisher's exact test.

RESULTS

No significant differences were found between colonies with different phenotypes or strains having a different clinical significance, except for two strains of Mycobacterium chelonae isolated from cases of catheter-related bacteremia, which showed elongated microcolonies. M. fortuitum and M. peregrinum strains showed larger microcolonies than M. chelonae, M. abscessus and M. mucogenicum, and displayed a fluffy appearance, while the latter two strains showed rounded colonies.

CONCLUSION

Very few strains of mycobacteria had invasive capacity and the majority of strains isolated from human infections do not show this characteristic; hence this trait is not essential for mycobacteria to cause infection in humans.

Genotyping and antifungal susceptibility profile of Dipodascus capitatus isolates causing disseminated infection in seven hematological patients of a tertiary hospital

Seven cases of disseminated infection due to Dipodascus capitatus are reported. Infections occurred in a hematological unit of a tertiary hospital during a period of 5 years. Five cases were refractory to antifungal therapy. Antifungal susceptibility testing of seven isolates was performed, and strains were typed by PCR fingerprinting with the core sequence of phage M13 and by random amplification of polymorphic DNA with two primers, Ap12h and W-80A. A very short range of MICs of each antifungal agent was observed. The MICs of amphotericin B ranged between 0.50 and 2 microg/ml. Strains were susceptible in vitro to flucytosine and susceptible (dose-dependent) to fluconazole and itraconazole. Voriconazole exhibited an activity in vitro comparable to that of itraconazole. Typing techniques allowed seven additional isolates of D. capitatus neither geographically nor temporally related to be classified into two different genomic patterns. The genomic type of the seven strains from the hematological unit was identical regardless of typing technique utilized. It would indicate that the seven cases of disseminated infection could be related epidemiologically.

Antimicrobial susceptibility of Haemophilus influenzae, Haemophilus parainfluenzae and Moraxella catarrhalis isolated from adult patients with respiratory tract infections in four southern European countries. The ARISE project

Over a 7-month period in 2000-2001, 1213 Haemophilus influenzae, 112 Haemophilus parainfluenzae and 142 Moraxella catarrhalis isolates were recovered from adult patients with respiratory tract infections. Patients were from four southern European countries (Spain, Italy, Portugal and Greece). The antimicrobial susceptibility of the isolates to 11 antibiotics was determined in a central laboratory. The most active drugs on the basis of MICs were levofloxacin, cefditoren, cefotaxime, cefpodoxime and amoxicillin/clavulanate. MICs > or = 2 mg/l for amoxicillin were found in 19.5, 28.6, and 75.4% of H. influenzae, H. parainfluenzae and M. catarrhalis isolates, respectively. Isolates of H. influenzae and H. parainfluenzae with reduced susceptibility or that were fully resistant to amoxicillin/clavulanate, cefuroxime and clarithromycin were detected (0.2-1.8%) as well as M. catarrhalis resistant to clarithromycin (0.7%). Regular surveys of resistance patterns for antimicrobial agents are necessary.

Characterisation of penciclovir resistant acyclovir sensitive herpes simplex virus type 2 isolated from an AIDS patient

A heterogeneous herpes simplex virus type 2 (HSV-2) population was characterised from an AIDS patient with relapsing genital ulcer. The isolate had an unusual antiviral spectrum, showing resistance to penciclovir and susceptibility to acyclovir. Two viral populations were plaque purified, one resistant and the other susceptible to both antiviral drugs. The resistant clone was deficient in thymidine kinase (TK) activity and a nucleotide substitution, thymine for cytosine, at position 153 was identified in its TK gene. This mutation resulted in an amino acid change, arginine to tryptophan, in the ATP binding site. In the deficient mutant, a loss of virulence was observed in mice.

Blastoschizomyces capitatus infection in patients with leukemia: report of 26 cases

Twenty-six cases of Blastoschizomyces capitatus infection were diagnosed in 25 patients at 7 tertiary care hematology units in Spain over a 10-year period. Most patients (92%) had acute leukemia and developed infection during a period of severe and prolonged neutropenia. Two patients had esophagitis, and the rest had invasive infection. Fungemia (20 cases) was a common finding, with frequent visceral dissemination. The 30-day mortality associated with this infection was 52%, compared with 57% among patients with systemic infection. In a univariate analysis, the following 3 variables had a positive impact on 30-day survival: removal of the central venous catheter within 5 days after the onset of infection (P=.02), a good performance status (P=.003), and receipt of systemic prophylactic or empirical antifungal therapy before infection onset (P=.006). Outcome for neutropenic patients with B. capitatus infection is still poor. Rapid removal of the central venous catheter and novel antifungal therapies are recommended for treatment of this rare infection.

Recomendaciones para el diagnóstico micológico y estudios de sensibilidad a los antifúngicos

The guidelines presented herein, which are based on the indications established by various studies and expert opinions, analyze several issues related to laboratory diagnosis of invasive fungal infections in immunosuppressed patients.

Immunological properties of a DNA plasmid encoding a chimeric protein of herpes simplex virus type 2 glycoprotein B and glycoprotein D

A DNA plasmid containing a chimeric sequence encoding both herpes simplex virus type 2 (HSV-2) glycoprotein B (gB) and glycoprotein D (gD) external domains (pcgDB) was used to immunize BALB/c mice against genital HSV-2 infection. To determine the efficacy of this vaccine, groups of mice immunized with the pcgDB plasmid were compared with animals immunized with plasmids corresponding to the individual proteins (pcgBt or pcgDt), administered separately or in combination (pcgBt + pcgDt). We studied the response of the different mouse groups to viral challenge by analyzing clinical disease (vaginitis), serum antibody levels, as well as lymphoproliferative responses and cytokine production by spleen cells. Increased IFN-gamma levels correlated with prolonged survival in mice immunized with the plasmid pcgDB, relative to mice immunized with plasmids coding for the individual proteins alone or in combination. Our results show that immunization with the plasmid encoding the chimeric protein is advantageous over separate proteins. These findings may have important implications for the development of multivalent DNA vaccines against HSV and other complex pathogens.

Antimicrobial resistance among clinical isolates of Streptococcus pneumoniae isolated in four southern European countries (ARISE project) from adult patients: results from the cefditoren surveillance program

From four southern European countries (Spain, Italy, Portugal, and Greece) 877 Streptococcus pneumoniae isolates were recovered from adult patients with respiratory tract infections between September 2000 and March 2001. The antimicrobial susceptibility to 11 antibiotics was determined in a central laboratory. Penicillin resistance was high in Greece (47.1%) and Spain (25.1%) but much lower in Portugal (7.9%) and Italy (4.8%). On the other hand, erythromycin resistance was high in Italy (38.5%) and Spain (36.2%) with no statistical difference with Greece (29.4%) but reaching significance (p <0.01) with Portugal (15.7%). Resistance to levofloxacin was low (1.5%) but present in Spanish and Italian isolates. Cefditoren, a new cephem antibiotic tested, was the most potent compound (MIC90 = 0.5 microg/ml) followed by levofloxacin and cefotaxime (MIC90 = 1 microg/ml). Given the high rates of penicillin and macrolide resistance reported, there is an evident need for new drugs and continued antimicrobial surveillance of S. pneumoniae.

A comparison between disk diffusion and microdilution for susceptibility testing of Mycobacterium fortuitum complex

We evaluated a disk diffusion method using Mueller-Hinton agar for susceptibility testing of Mycobacterium fortuitum complex organisms. Ninety-five strains were tested both by broth microdilution and disk diffusion. Global results showed good correlation for all antimicrobials except for clarithromycin and erythromycin. However, when the results were analyzed according to species, correlation was poor except for a few antimicrobials. The analysis of the resistant/susceptible results was good for all the antimicrobials tested except azithromycin and erythromycin. In conclusion, the disk diffusion technique could be useful as a screening technique for some antibiotics, but the results must be confirmed by using an accepted reference technique.

Nosocomial enterococcal endocarditis: a serious hazard for hospitalized patients with enterococcal bacteraemia

OBJECTIVES

Enterococci are a major leading cause of infectious endocarditis and also a common cause of hospital-acquired bacteraemia, which is not believed to represent a serious hazard for the endocarditis. The incidence and risk factors for infectious endocarditis in patients with hospital-acquired enterococcal bacteraemia is determined.

METHODS

Prospective analysis of 116 patients with enterococcal bacteraemia admitted to medical or surgical wards of a tertiary-care, university affiliated hospital during a period of 5 years. Echocardiography was performed when indicated by clinical criteria.

RESULTS

Seventy-five (61.4%) episodes were hospital-acquired and 47 (38.5%) were community-acquired. Most patients had one or more underlying chronic diseases and major abdominal (58.6%) or genitourinary (38.6%) surgery. Seventeen patients (14.6%) developed enterococcal endocarditis. By univariate analysis the risk factors associated with endocarditis were community-acquired infection (P 0.012); monomicrobial bacteraemia (P 0.006); three or more positive blood cultures (P < 0.001); underlying valvulopathy (P < 0.001); presence of a prosthetic valve (P < 0.001) and age (P 0.012). Six patients (8%) developed nosocomial endocarditis. In this group of patients, three or more positive blood cultures (P < 0.01), bacteraemia as a result of Enterococcus faecalis (P 0.007); underlying valvulopathy (P < 0.001) and presence of a prosthetic valve (P < 0.001) were associated with endocarditis. By logistic regression, the presence of underlying valvulopathy and three or more positive blood cultures were associated with endocarditis (OR 21.0; CI 95% 1.65-26.9; P 0.019).

CONCLUSIONS

The risk of developing infectious endocarditis in patients with hospital-acquired enterococcal bacteraemia is significant. Patients with underlying valvulopathy and three or more positive blood cultures with E. faecalis are prone to nosocomial enterococcal endocarditis.

Mycobacterium tuberculosis bacteremia in a university hospital

SETTING

Patients with blood cultures positive for Mycobacterium tuberculosis between 1988 and 1999.

OBJECTIVE

To study the clinical and microbiological characteristics of patients with tuberculous bacteremia, including data about evolution and management.

DESIGN

Retrospective review of the clinical charts and microbiological records of patients with culture-proven tuberculous bacteremia between 1988-1999.

RESULTS

During the study period, 19 patients with culture-proven M. tuberculosis bacteremia were detected (1.42 isolates/patient, 4.7% of all patients with blood cultures for mycobacteria). Four patients were non-infected with the human immunodeficiency virus and 15 were HIV-infected. In four patients blood was the only positive sample. Five patients were diagnosed simultaneously with tuberculosis and HIV infection. Only 13 had a temperature higher than 37.5 degrees C. Most patients had symptoms or signs of respiratory tract involvement, and 11 patients died (10 from tuberculosis). The average time for detection of positive blood cultures was 33.25 days for lysis-centrifugation cultures and 26.46 days for BACTEC cultures. The incidence of M. tuberculosis bacteremia remained stable during the study period.

CONCLUSIONS

Although blood cultures are useful for definitive diagnosis of disseminated tuberculosis, the long incubation times made them of limited usefulness in the clinical management of patients. Mortality remains high in these patients.

Tuberculous infection in student nurses in Madrid, Spain

To determine the incidence of tuberculous infection in student nurses we performed a 3-year study in our hospital. Before training was initiated, 18.75% of males and 5.7% of females were Mantoux-positive (P = 0.09). During the following two years, 9.2% of the previously Mantoux-negative students became positive. No differences were found between males and females. We conclude that student nurses must be considered at risk for tuberculous infection in our hospital, and that stricter isolation procedures for tuberculous patients must be implemented.

In vitro activity of gemifloxacin (SB-265805) compared with 14 other antimicrobials against intestinal pathogens

We studied the in vitro activity of gemifloxacin (SB-265805) and 14 comparator antimicrobials against 288 recent isolates of enteropathogenic bacteria (106 Salmonella: spp., 32 Hafnia alvei, 22 Yersinia enterocolitica, 21 Shigella: spp., 16 Aeromonas: spp. and 91 Campylobacter jejuni). Gemifloxacin, the other fluoroquinolones and cefotaxime were very active against all microorganisms tested except for C. jejuni. Seventy-seven per cent of isolates of C. jejuni were inhibited by erythromycin < or =0.5 mg/L. Only one strain of C. jejuni was highly resistant to this antimicrobial agent. Of the compounds tested, gentamicin was the most active in vitro. The in vitro activity of the other antibiotics tested was variable. A quinolone could be a good choice for treating gastrointestinal infections when antimicrobial therapy is indicated. For C. jejuni, another antibiotic such as erythromycin should be considered.