The effect of TRIM5 variants on the susceptibility to HIV-1 infection and disease progression in the Polish population

BACKGROUD

Tripartite motif containing 5α protein is a factor contributing to intracellular defense mechanisms against human immunodeficiency virus-1 (HIV-1) infection. The studies of TRIM5 variants effects on the risk of HIV-1 infection and the clinical course of disease provided inconclusive results in different ethnic groups. The aim of this study was to investigate the influence of TRIM5 variants on susceptibility to HIV-1 infection and clinical parameters among Polish HIV-1-infected patients.

MATERIALS & METHODS

In our study, we investigated 301 HIV-1-infected patients and 186 age-matched seronegative controls. Seven variants of the TRIM5 gene (rs7127617, rs3824949, rs3740996, rs11601507, rs10838525, rs11038628, and rs28381981) were genotyped using both sequencing and polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) techniques.

RESULTS AND CONCLUSIONS

The frequencies of rs7127617 TT genotype and T allele occurrence were lower in HIV-1-infected subjects compared to controls (0.14 vs. 0.26 for T/T genotype and 0.45 vs. 0.54 for T allele), suggesting their possible protective effect (p = 0.005 and p = 0.007, respectively). Heterozygosity and presence of the T allele at rs3740996 were enriched in controls compared to HIV-1-infected group (0.19 vs. 0.12 for C/T genotype and 0.11 vs. 0.07 for T allele; p = 0.03 and p = 0.02, respectively). Moreover, rs3824949 CC genotype carriers had a lower viral load than patients bearing rs3824949 GG/CG genotypes (4.0 vs. 4.6 log copies/mL; p = 0.049); however, none of the variants affected CD4+ cell count. In conclusion, our data confirm the role of TRIM5 variants in the HIV-1 transmission and the clinical course of HIV-1 infection. The presence of rs7127617 TT genotype and T allele seems to protect against HIV-1 transmission in examined population.

The Direction of the Antibacterial Effect of Rutin Hydrate and Amikacin

The aim of the presented study was to examine the in vitro antimicrobial activity of rutin hydrate (RH) alone and in combination with amikacin against 12 reference strains of Gram-positive and Gram-negative bacteria. The antibacterial activity assay was evaluated in the concentration range of 2-2048 µg/mL. A serial microdilution method was used to determine the minimal inhibitory concentration (MIC) of the examined compound against reference strains. RH showed varying potential against the tested strains with MICs ranging from 128 to 1024 µg/mL. In order to examine the combinatory profile of RH and amikacin, the fractional inhibitory concentrations (FICs) were determined. The RH-amikacin combination was more active against Gram-negative bacteria where four synergism and two additive interactions were noted. For four out of six Gram-positive isolates, an indifferent effect of RH and amikacin was demonstrated, and for two strains, the tested combination had an additive effect. The results of this study showed that RH possesses antimicrobial potential in vitro towards the tested reference isolates. Moreover, it shows a promising combined effect with amikacin against Gram-negative bacteria.

From Alpha to Delta-Genetic Epidemiology of SARS-CoV-2 (hCoV-19) in Southern Poland

In Poland, the first case of SARS-CoV-2 infection was confirmed in March 2020. Since then, many circulating virus lineages fueled rapid pandemic waves which inflicted a severe burden on the Polish healthcare system. Some of these lineages were associated with increased transmissibility and immune escape. Mutations in the viral spike protein, which is responsible for host cell recognition and serves as the primary target for neutralizing antibodies, are of particular importance. We investigated the molecular epidemiology of the SARS-CoV-2 clades circulating in Southern Poland from February 2021 to August 2021. The 921 whole-genome sequences were used for variant identification, spike mutation, and phylogenetic analyses. The Pango B.1.1.7 was the dominant variant (n = 730, 89.68%) from March 2021 to July 2021. In July 2021, the B.1.1.7 was displaced by the B.1.617.2 lineage with 66.66% in July 2021 and 92.3% in August 2021 frequencies, respectively. Moreover, our results were compared with the sequencing available on the GISAID platform for other regions of Poland, the Czech Republic, and Slovakia. The analysis showed that the dominant variant in the analyzed period was B.1.1.7 in all countries and Southern Poland (Silesia). Interestingly, B.1.1.7 was replaced by B.1.617.2 earlier in Southern Poland than in the rest of the country. Moreover, in the Czech Republic and Slovakia, AY lineages were predominant at that time, contrary to the Silesia region.

The Array of Antibacterial Action of Protocatechuic Acid Ethyl Ester and Erythromycin on Staphylococcal Strains

The spread of antibiotic resistance among bacteria has become one of the major health problems worldwide. Methicillin-resistant staphylococcal strains are especially dangerous because they are often resistant to other antibiotics. The increasing insensitivity to macrolides, lincosamides and streptogramin B antibiotics of methicillin-resistant staphylococcal isolates has limited the use of these drugs in therapy. The combination of natural compounds and antibiotics can be considered as an alternative tool to fight multi-drug-resistant pathogen infections. The aim of the presented study was to examine the antibacterial activity of protocatechuic acid ethyl ester–erythromycin combination towards Staphylococcus aureus and Staphylococcus epidermidis strains with various resistance profiles to methicillin and macrolides, lincosamides and streptogramin B (MLS_B) antibiotics. The in-vitro antibacterial potential of the above combination was investigated by minimum inhibitory concentration assays and checkerboard testing. The observed effects were strain dependent, with 8 of 12 tested staphylococcal strains showing an indifferent effect on the natural compound and erythromycin; for 2 strains, the tested combination had an additive effect, while for another 2, the effect was synergistic. Interestingly, the multi-drug-resistant strains were more sensitive to the cooperative action of the protocatechuic acid ethyl ester and the antibiotic.

Does Virus-Receptor Interplay Influence Human Coronaviruses Infection Outcome?

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is the third (following SARS-CoV and Middle East Respiratory Syndrome-CoV) zoonotic coronavirus that has crossed the species barrier in the 21st century, resulting in the development of serious human infection. The punishing effect of the recent outbreak of pandemic disease termed COVID-19 (coronavirus disease-19) caused by SARS-CoV-2 impelled us to gather the facts about the nature of coronaviruses. First, we introduce the basic information about coronavirus taxonomy, structure, and replication process to create the basis for more advanced consideration. In the following part of this review, we focused on interactions between the virus and the receptor on the host cell, as this stage is the critical process determining the species and tissue tropism, as well as clinical course of infection. We also illuminate the molecular basis of the strategy used by coronaviruses to cross the species barrier. We give special attention to the cellular receptor's interaction with S protein of different CoVs (dipeptidyl peptidase IV and angiotensin-converting enzyme 2), as well as the cellular proteases involved in proteolysis of this protein. These factors determine the virus entry and replication; thus, even fine quantitative or qualitative differences in their expression may crucially affect outcomes of infection. Understanding virus biology and characterization of the host factors involved in coronavirus transmission and pathogenesis may offer novel options for development of efficient therapeutic and preventive strategies.

Application of Erythromycin and/or Raoultella sp. Strain MC3 Alters the Metabolic Activity of Soil Microbial Communities as Revealed by the Community Level Physiological Profiling Approach

Erythromycin (EM), a macrolide antibiotic, by influencing the biodiversity of microorganisms, might change the catabolic activity of the entire soil microbial community. Hence, the goal of this study was to determine the metabolic biodiversity in soil treated with EM (1 and 10 mg/kg soil) using the community-level physiological profiling (CLPP) method during a 90-day experiment. In addition, the effect of soil inoculation with antibiotic-resistant Raoultella sp. strain MC3 on CLPP was evaluated. The resistance and resilience concept as well as multifactorial analysis of data was exploited to interpret the outcomes obtained. EM negatively affected the metabolic microbial activity, as indicated by the values of the CLPP indices, i.e., microbial activity expressed as the average well-color development (AWCD), substrate richness (R), the Shannon-Wiener (H) and evenness (E) indices and the AWCD values for the six groups of carbon substrate present in EcoPlates until 15 days. The introduction of strain MC3 into soil increased the degradative activity of soil microorganisms in comparison with non-inoculated control. In contrast, at the consecutive sampling days, an increase in the values of the CLPP parameters was observed, especially for EM-10 + MC3-treated soil. Considering the average values of the resistance index for all of the measurement days, the resistance of the CLPP indices and the AWCD values for carbon substrate groups were categorized as follows: E > H > R > AWCD and polymers > amino acids > carbohydrates > miscellaneous > amines > carboxylic acids. The obtained results suggest a low level of resistance of soil microorganisms to EM and/or strain MC3 at the beginning of the exposure time, but the microbial community exhibited the ability to recover its initial decrease in catabolic activity over the experimental period. Despite the short-term effects, the balance of the soil ecosystem may be disturbed.

The Antibacterial Effect of Silver Nanoparticles on Staphylococcus epidermidis Strains with Different Biofilm-Forming Ability

Among many infectious diseases, infections caused by pathogens of Staphylococcus species exert a substantial influence upon human health, mainly due to their continuous presence on human skin and mucous membranes. For that reason, an intensive search for new, effective anistaphyloccocal agents can currently be observed worldwide. In recent years, there has been growing interest in nanoparticles, as compounds with potential antibacterial effect. The antibacterial activity of silver containing substances has been well recognized, but thoughtful studies focused on the effect of silver nanoparticles on bacterial biofilm are scarce. The aim of this study was to assess the influence of silver nanoparticles (AgNPs) with particle sizes in the range between 10 and 100 nm, and a concentration range from 1 to 10 µg/mL, upon Staphylococcus epidermidis strains with different biofilm-forming abilities (BFAs). The studies revealed the highest level of antimicrobial activity for AgNPs in relation to S. epidermidis strains with BFA, and what is more, the observed effect was proportional to the increasing particles’ size, and strains not forming biofilm were more susceptible to silver nanoparticles with the smallest examined size, which was 10 nm.

Phenolic Compounds Diminish Antibiotic Resistance of Staphylococcus Aureus Clinical Strains

There is a growing body of evidence that flavonoids show antibacterial activity against both Gram-positive and Gram-negative bacteria. The mechanisms of action of phenolic compounds on bacterial cell have been partially attributed to damage to the bacterial membrane, inhibition of virulence factors such as enzymes and toxins, and suppression of bacterial biofilm formation. What is more, some natural polyphenols, aside from direct antibacterial activity, exert a synergistic effect when combined with common chemotherapeutics. Many studies have proved that in synergy with antibiotics plant flavonoids pose a promising alternative for therapeutic strategies against drug resistant bacteria. In this review most recent reports on antimicrobial action of polyphenols on Staphylococcus aureus strains are described, highlighting where proven, the mechanisms of action and the structure–activity relationships. Since many reports in this field are, to some extent, conflicting, a unified in vitro and in vivo susceptibility testing algorithms should be introduced to ensure the selection of effective antibacterial polyphenolic compounds with low cytotoxicity and minimal side effects.

Vancomycin and/or Multidrug-Resistant Citrobacter Freundii Altered the Metabolic Pattern of Soil Microbial Community

Despite many studies, our knowledge on the impact of antibiotics and antibiotic-resistant bacteria on the metabolic activity of soil microbial communities is still limited. To ascertain this impact, the community level physiological profiles (CLPPs) and the activity of selected enzymes (dehydrogenase, urease, and phosphatases) in soils treated with vancomycin (VA) and/or multidrug resistant Citrobacter freundii were determined during a 90-day experiment. A multivariate analysis and the resistance (RS)/resilience (RL) concept were used to assess the potential of native microorganisms to maintain their catabolic activity under exposure of VA and/or a high level of C. freundii. In addition, the dissipation rate of VA was evaluated in non-sterile (nsS) and sterile (sS) soils. The results revealed a negative impact of VA on the metabolic activity of soil microorganisms on days 1, 15, and 30 as was showed by a decrease in the values of the CLPP indices (10-69%) and the enzyme activities (6-32%) for treated soils as compared to the control. These observations suggested a low initial resistance of soil microorganisms to VA and/or C. freundii but they were resilient in the long term. Considering the mean values of the RS index, the resistance of measured parameters was categorized in the following order: alkaline phosphatase (0.919) > acid phosphatase (0.899) > dehydrogenase (0.853) > the evenness index (0.840) > urease (0.833) > the Shannon-Wiener index (0.735) > substrate richness (0.485) > the AWCD (0.301). The dissipation process of VA was relatively fast and independent of the concentration used. The DT50 values for VA applied at both concentrations were about 16 days. In addition, the dissipation of VA in nsS was three times faster compared to the dissipation of antibiotic in sS. In conclusion, both CLPP and enzyme activities assays appeared to be useful tool for the determination of disturbances within soil microbial communities and used together may be helpful to understand the changes in their catabolic features. The entry of large quantities of VA and/or C. freundii into soil may temporarily change microbial activity thus pose a potential risk for soil functioning.

Synthesis and Antimicrobial Activity of Sulfur Derivatives of Quinolinium Salts

A novel method for cleavage of the dithiine ring in 5,12-(dimethyl)-thioqinantrenium bis-chloride 1 "via" reaction with sodium hydrosulfide leads to 1-methyl-3-mercaptoquinoline-4(1H)-thione 2. Further transformation of thiol and thione functions of compound 2 leads to a series of sulfide and disulfide derivatives of quinolinium salts 4 and 6. 1-Methyl-4-chloro-3-benzylthioquinoline chloride 8 was obtained by N-alkylating 4-chloro-3-benzylthioquinoline using dimethyl sulfate. Antimicrobial activity of the obtained compounds was investigated using six Gram-positive and six Gram-negative bacterial strains, as well as Candida albicans yeast. Greater activity was demonstrated towards Gram-positive strains. MIC values for compounds and with benzylthio 4d and benzoylthio 4f substituents in 3-quinoline position were found to be in the 0.5-1 μg/mL range, at a level similar to that of ciprofloxacin (reference). Compounds 4d and 4f also demonstrated interesting antifungal properties (MIC = 1).

HIV-1 Infection in Persons Homozygous for CCR5-Δ32 Allele: The Next Case and the Review

CC-chemokine receptor 5 serves as the coreceptor for the HIV-1 R5 strains, which are responsible for the majority of HIV transmissions. A deletion of 32 nucleotides in the gene encoding this receptor (termed CCR5-Δ32) leads to the suppression of CC-chemokine receptor 5 presentation at the cell surface, thus impeding process of HIV entry into the cell. Individuals homozygous for the CCR5-Δ32 allele are resistant to infection with HIV-1 R5 strains, and are extremely rare among HIV-1-infected individuals. We have described a case of person homozygous for CCR5-Δ32, who was infected with subtype B HIV-1. Based on examination of proviral V3 sequences obtained from the first clinical blood sample within less than five months after seroconversion, the CXC-chemokine receptor 4-using strains (X4 or R5/X4) were detected. Data on HIV-1-infected patients homozygous for the CCR5-Δ32 allele, course of HIV-1 infection in these cases, and the infecting viral strains from current and all former reports on HIV-1 infection in CCR5-Δ32 homozygotes were gathered and compared. Identification of HIV-1-infected persons homozygous for CCR5-Δ32 supports the evidence that the lack of functional CC-chemokine receptor 5 at the cell surface does not confer absolute protection against HIV-1 infection, which should be considered when designing future HIV pre-exposure prophylaxis schemes basing on CC-chemokine receptor 5 blocking drugs.

Prevalence of Transmitted Drug-Resistance Mutations and Polymorphisms in HIV-1 Reverse Transcriptase, Protease, and gp41 Sequences Among Recent Seroconverters in Southern Poland

Background

Monitoring of drug resistance-related mutations among patients with recent HIV-1 infection offers an opportunity to describe current patterns of transmitted drug resistance (TDR) mutations.

Material/Methods

Of 298 individuals newly diagnosed from March 2008 to February 2014 in southern Poland, 47 were deemed to have recent HIV-1 infection by the limiting antigen avidity immunoassay. Proviral DNA was amplified and sequenced in the reverse transcriptase, protease, and gp41 coding regions. Mutations were interpreted according to the Stanford Database algorithm and/or the International Antiviral Society USA guidelines. TDR mutations were defined according to the WHO surveillance list.

Results

Among 47 patients with recent HIV-1 infection only 1 (2%) had evidence of TDR mutation. No major resistance mutations were found, but the frequency of strains with ≥1 accessory resistance-associated mutations was high, at 98%. Accessory mutations were present in 11% of reverse transcriptase, 96% of protease, and 27% of gp41 sequences. Mean number of accessory resistance mutations in the reverse transcriptase and protease sequences was higher in viruses with no compensatory mutations in the gp41 HR2 domain than in strains with such mutations (p=0.031).

Conclusions

Despite the low prevalence of strains with TDR mutations, the frequency of accessory mutations was considerable, which may reflect the history of drug pressure among transmitters or natural viral genetic diversity, and may be relevant for future clinical outcomes. The accumulation of the accessory resistance mutations within the pol gene may restrict the occurrence of compensatory mutations related to enfuvirtide resistance or vice versa.

An Analysis of the Effects of Vancomycin and/or Vancomycin-Resistant Citrobacter freundii Exposure on the Microbial Community Structure in Soil

The occurrence of antibiotics and antibiotic resistance genes in the environment has become a subject of growing concern. The extensive use of vancomycin and other pharmaceuticals may alter the biodiversity of soil microbial communities and select antibiotic-resistant bacteria. Therefore, the purpose of the study was to evaluate the impact of vancomycin and/or vancomycin-resistant Citrobacter freundii on soil microbial communities using the denaturing gradient gel electrophoresis (DGGE) and the phospholipid fatty acid (PLFA) approaches. The experiment had a completely randomized block design with the following treatments: control soil (C), soil with vancomycin (1 mg/kg soil-VA1), soil with vancomycin (10 mg/kg soil-VA10), soil with C. freundii (Cit), soil with vancomycin (1 mg/kg soil) and C. freundii (VA1+Cit), and soil with vancomycin (10 mg/kg soil) and C. freundii (VA10+Cit). A bacterial strain resistant to vancomycin was isolated from raw sewage collected from the municipal sewage treatment plant. The obtained results indicated that the antibiotic and/or the bacterial strain exerted a selective pressure that resulted in qualitative and quantitative changes in the population of soil microorganisms. However, a multivariate analysis showed that the genetic and structural diversity of the soil microbial community was primarily affected by the incubation time and to a lesser extent by the antibiotic and introduced bacteria. DGGE analysis clearly showed that certain species within the bacterial community were sensitive to vancomycin as was evidenced by a decrease in the values of S (richness) and H (Shannon-Wiener) indices. Moreover, a PLFA method-based analysis revealed alterations in the structure of the soil microbial community as indicated by changes in the biomass of the PLFA biomarkers specific for Gram-positive and Gram-negative bacteria as well as fungi. The changes observed in the community of soil microorganisms may decrease the rate of microbial-mediated processes, which can lead to a disturbance in the ecological balance of the soil ecosystem.

Catechin Hydrate Augments the Antibacterial Action of Selected Antibiotics against Staphylococcus aureus Clinical Strains

Synergistic effects between commonly used antibiotics and natural substances may be an alternative to conventional antibacterial therapies. The objective of the presented study was to assess the in vitro antibacterial activity of catechin hydrate (CH) and evaluate the interactions of CH with selected antibiotics using Staphylococcus aureus clinical and reference strains. CH displayed diverse activity towards examined S. aureus strains, with minimal inhibitory concentrations (MICs) ranging from 256 to 2048 µg/mL. The interaction between CH and antibiotics was assessed by an E-test. The most significant synergistic effects were noticed for CH in combination with clindamycin and erythromycin. For cefoxitin and vancomycin a decrease of MIC values in the presence of CH was also observed, but it did not reach statistical significance. The obtained results demonstrate that CH shows antimicrobial activity against Staphylococcus aureus clinical strains. What is more, we proved a synergistic effect of CH with erythromycin and clindamycin.

Antibacterial Activity of Protocatechuic Acid Ethyl Ester on Staphylococcus aureus Clinical Strains Alone and in Combination with Antistaphylococcal Drugs

The aim of the presented study was to examine in vitro the antibacterial activity of protocatechuic acid ethyl ester (ethyl 3,4-dihydroxybenzoate, EDHB) against Staphylococcus aureus clinical isolates alone and in the combination with four selected antibiotics. The EDHB antimicrobial activity was tested against twenty S. aureus strains isolated from the clinical samples, and three reference strains. The phenotypes and genotypes of resistance to methicillin for the tested strains were defined as well as the phenotypic resistance to macrolides, lincosamides and streptogramin B (MLS_B). EDHB displayed diverse activity against examined S. aureus strains with the minimal inhibitory concentration (MIC) within the range from 64 to 1024 µg/mL. Addition of ¼ MIC of EDHB into the Mueller-Hinton Agar (MHA) resulted in augmented antibacterial effect in the presence of clindamycin. In the case of cefoxitin no synergistic effect with EDHB was noted. For erythromycin and vancomycin the decrease of mean MICs in the presence of EDHB was observed but did not reach statistical significance. The results of the present study showed that in vitro EDHB possesses antibacterial activity against S. aureus clinical strains and triggers a synergistic antimicrobial effect with clindamycin and to the lesser extent with erythromycin and vancomycin.

Prevalence of tick-borne encephalitis virus in a highly urbanized and low risk area in Southern Poland

The knowledge of the exact distribution of tick-borne encephalitis virus (TBEV) endemic foci is crucial to plan and implement the optimal prevention of tick-borne encephalitis (TBE), including a vaccination program. In Poland, however, there is still no data on the local distribution of TBEV in many areas of the country. Silesian agglomeration area (Southern Poland) is a highly urbanized and industrialized region of the country, where TBE cases are only sporadically recorded. In this study, a total of 4350 adult Ixodes ricinus were collected between September 2010 and June 2012 at twelve locations. The screening using real-time PCR was carried out on 854 tick pools of five specimens, and the positive pools were verified by pyrosequencing. TBEV was identified in 13 pools (1.52%) at 4 sites, of which 9 pools were verified by pyrosequencing. An overall pool prevalence was estimated at 0.31% ranging from 0.19% to 1.11% for positive locations [95% CI 0.16-0.52], which is comparable with regions with high number of TBE cases reported annually.

Biofilm formation and antimicrobial susceptibility of Staphylococcus epidermidis strains from a hospital environment

The hospital environment microflora comprise a wide variety of microorganisms which are more or less pathogenic and where staphylococci are one of the most common types. The aim of the presented study was to evaluate the prevalence of the biofilm forming coagulase-negative staphylococci (CoNS) in a hospital environment as a risk factor for nosocomial infections. Among 122 isolated and tested strains of CoNS the most frequent were: S. epidermidis-32 strains, S. haemolyticus-31 strains, S. capitis subsp. capitis- 21 strains, S. hominis-11 strains, S. cohnii subsp. cohnii-nine strains. In case of CoNS, the main molecule responsible for intercellular adhesion is a polysaccharide intercellular adhesin (PIA), encoded on the ica gene operon. The analysis revealed the presence of the icaADBC operon genes in 46.88% of S. epidermidis isolates. IcaA and icaD were present in 34.38% and 28.13% of strains respectively while IcaC gene was present in 37.50% of strains. IcaB gene was found in 21.88% of S. epidermidis strains. In 15 (63%) strains all icaADBC operon genes were observed. The assessment of antibacterial drugs susceptibility demonstrated that analyzed CoNS strains were highly resistant to macrolides and lincosamides and more sensitive to rifampicin and linezolid. Our data indicates that the hospital environment can be colonized by biofilm forming coagulase-negative staphylococci and transmission of these strains can cause an increased risk of serious nosocomial infections.

Transmission of drug-resistant HIV-1 variants among individuals with recent infection in southern Poland

Transmitted drug resistance (TDR) is an important public health issue, because it may affect the outcome of antiretroviral treatment. The prevalence of human immunodeficiency virus type 1 (HIV-1) with TDR mutations defined according to the list of the World Health Organization was investigated among 53 therapy-naïve persons with confirmed recent HIV-1 infection diagnosed in Poland, in the years 2008-2010. Proviral DNA was amplified, sequenced, and screened for the TDR mutations in the pol gene fragments coding for the whole protease and the initial 256 residues of the reverse transcriptase. The frequency of sequences with at least one TDR mutation was 11.3%. In four (7.5%) sequences at least one resistance mutation related to reverse transcriptase inhibitors was identified, and in further two (3.8%) sequences one mutation related to protease inhibitors' resistance was present. The moderate rate of TDR highlights the need for a continuous surveillance and resistance testing among treatment-naïve individuals to optimize treatment effects within a country.

Susceptibility of Staphylococcus aureus clinical isolates to propolis extract alone or in combination with antimicrobial drugs

The objective of this study was to assess in vitro the antimicrobial activity of ethanolic extract of Polish propolis (EEPP) against methicillin-sensitive Staphylococcus aureus (MSSA) and methicillin-resistant Staphylococcus aureus (MRSA) clinical isolates. The combined effect of EEPP and 10 selected antistaphylococcal drugs on S. aureus clinical cultures was also investigated. EEPP composition was analyzed by a High Performance Liquid Chromatography (HPLC) method. The flavonoid compounds identified in Polish Propolis included flavones, flavonones, flavonolols, flavonols and phenolic acids. EEPP displayed varying effectiveness against twelve S. aureus strains, with minimal inhibitory concentration (MIC) within the range from 0.39 to 0.78 mg/mL, determined by broth microdilution method. The average MIC was 0.54 ± 0.22 mg/mL, while calculated MIC₅₀ and MIC₉₀ were 0.39 mg/mL and 0.78 mg/mL, respectively. The minimum bactericidal concentration (MBC) of the EEPP ranged from 0.78 to 3.13 mg/mL. The in vitro combined effect of EEPP and 10 antibacterial drugs was investigated using disk diffusion method-based assay. Addition of EEPP to cefoxitin (FOX), clindamycin (DA), tetracycline (TE), tobramycin (TOB), linezolid (LIN), trimethoprim+sulfamethoxazole (SXT), penicillin (P), erythromycin (E) regimen, yielded stronger, cumulative antimicrobial effect, against all tested S. aureus strains than EEPP and chemotherapeutics alone. In the case of ciprofloxacin (CIP) and chloramphenicol (C) no synergism with EEPP was observed.

Molecular epidemiology of recent HIV-1 infections in southern Poland

The genetic diversity of human immunodeficiency virus type 1 (HIV-1) offers an opportunity to track the development of the epidemic across different populations. Viral pol gene fragments from 55 individuals of Polish origin with recent HIV-1 infection identified in 2008-2010 in four Polish cities were analyzed. Viral sequences were compared with sequences from 100 individuals (reference group) infected before 2004. Viral spread among groups with different HIV transmission categories was compared using a phylogenetic approach. The majority of sequences from individuals with recent infection were subtype B (93%) within which four transmission clusters (18% of samples) were detected. Samples from men infected through sex between men and from persons infected through injecting drugs were broadly separated (P < 0.0001), while samples from individuals infected by heterosexual contacts were dispersed uniformly within phylogenetic tree (P = 0.244) inferred from viral sequences derived from individuals infected recently and the reference group. The percentage of samples from persons infected by heterosexual contacts which clustered with samples from men infected through sex between men was not significantly higher for those with recent infection (47%), compared to the reference group (36%). In conclusion, men infected by sex between men and individuals infected through injecting drugs appear to form separate HIV transmission networks in Poland. The recent spread of HIV-1 among persons infected with subtype B by heterosexual contacts appears to be linked to both these groups.

Association between the PRNP 1368 polymorphism and the occurrence of sporadic Creutzfeldt-Jakob disease

Creutzfeldt-Jakob disease (CJD) is a rare transmissible neurodegenerative disorder. The etiology of sporadic form of CJD remains unsolved. In addition to the codon 129 polymorphism, polymorphisms in the non-coding region of PRNP are considered as important factors in sCJD development. To assess a possible association between PRNP 1368 SNP and sCJD, we compared the genotype, allele and haplotype frequencies of the 1368 SNP among 46 sCJD patients of Dutch origin with the respective frequencies in healthy controls. We detected a significant association between sCJD and 1368T/T genotype. A significant difference was also observed in 1368 alleles' distribution. In the haplotype analysis, haplotype 1368C-129G was associated with decreased risk of sCJD in Dutch population. Our findings support the hypothesis that genetic variations in the regulatory region of the PRNP gene may influence the pathogenesis of sCJD.

Association of the PRNP regulatory region polymorphisms with the occurrence of sporadic Creutzfeldt-Jakob disease

The prion protein (PrP) plays a central role in the pathogenesis of Creutzfeldt-Jakob disease and other transmissible spongiform encephalopathies (TSEs). Mutations in the coding region of the prion protein (PRNP) gene are linked to inherited forms of TSEs whereas aetiology of sporadic CJD (sCJD) remains obscure. It remains unclear whether the primary DNA sequence at non-coding region of PRNP gene influences development of the sCJD. Several recent reports showed non-coding region polymorphisms associated with sCJD but other could not support those findings. To test the hypothesis that there is a relationship between SNPs polymorphisms of PRNP non-coding regions and susceptibility to sCJD, we compared the primary structure of the regulatory region of the PRNP in 45 Dutch sCJD patients and in 135 healthy controls. We found a significant linkage of +310 C allele (OR 0.27, 95% CI 0.09-0.77; P = 0.009) and +310G/C genotype (OR 0.33, 95% CI 0.11-0.98; P = 0.048) with sCJD. No differences in frequencies of genotypes and allele of -101C/G and +258 G/A polymorphisms were found between sCJD patients and controls. We found two haplotypes protecting from sCJD (C-V in block 1 and G-C in block 2) and one susceptible haplotype for sCJD (G-G in block 2). Our findings support the hypothesis that polymorphism in the regulatory region of the PRNP gene may play an important role in the pathogenesis of sCJD.

Current and future assays for identifying recent HIV infections at the population level

The precise diagnosis of recent human immunodeficiency virus (HIV) infection is crucial for estimating HIV incidence, defined as the number of new infections in a population, per person at risk, during a specified time period. Incidence assessment is considered to be a tool for surveillance, public health and research. Differentiating recent from long-term HIV infections is possible thanks to the evaluation of HIV-specific immune response development or viral markers measurement. Several methods that enable the recognition of recent HIV-1 infection with the use of a single blood specimen have been developed, and their value for use in population level studies has been demonstrated. However, they are still inadequate due to a variable window period and false recent rates among HIV clades and across populations. Application of these assays at an individual level is far more questionable because of person-to-person variability in the antibody response and the course of HIV infection, and because of the prospective regulatory approval requirements.

In this article we review the principles and the limitations of the currently available major laboratory techniques that allow detection of recent HIV infection. The assays based on the alteration of serological parameters, as well as the newest method based on an increase of HIV genetic diversity with the progress of infection, are described.

Retrospective analysis of the HIV-1 reverse transcriptase inhibitors' resistance in Silesia, Poland

Background

This study was a retrospective analysis of drug resistance mutations among HIV-1 strains prevalent in Silesia, Poland, from the origin of the epidemic to 2004. The investigations included both type and frequency of the reverse transcriptase inhibitors’ resistance mutations and estimation of the drugs’ resistance levels.

Material/Methods

Proviral DNA, obtained from peripheral blood mononuclear cells of the 101 HIV-1–infected patients, was amplified and sequenced in the pol gene fragment covering the first 256 codons of the reverse transcriptase (RT). Reverse transcriptase inhibitors resistance mutations were determined and interpreted with the HIVdb: Genotypic Resistance Interpretation Algorithm available from the Stanford University HIV Drug Resistance Database. In the examined population, 35 subjects (34.7%) received no antiretroviral treatment by the time of specimen collection.

Results

The overall frequency of the RT inhibitors resistance mutations in the studied population was 15.8%. Substitutions related to the reverse transcriptase inhibitors resistance were identified in 10 pol gene sequences (9.9%), all of them were present in the HIV-1 sequences obtained from persons receiving antiretroviral therapy.

Conclusions

Lack of drug-resistant viruses among treatment-naïve Silesian patients HIV-1-infected before the year 2004 may indicate that there was no transmission of the drug-resistant viruses in the studied population to that time.

HIV type 1 genetic diversity in Silesia, Poland: a retrospective analysis

To characterize the genetic diversity of HIV-1 strains circulating among patients with different transmission risk behaviors in Silesia, Poland, from the origin of the epidemic to the year 2004, we have sequenced and analyzed the p24 coding region of the gag gene and part of the pol gene covering the first 256 codons for the reverse transcriptase (RT). The proviral DNA was obtained from the 101 HIV-1-infected patients, 80 of whom (79.2%) were intravenous drug users (IDUs) and 21 of whom (20.8%) reported sexual transmission risk practices (STs) with 11 (10.9%) being heterosexuals and 10 (9.9%) being homosexual men, which corresponds to the population's epidemiological data. All of the investigated viral sequences were classified as HIV-1 subtype B with low genetic heterogeneity. There was an association between HIV-1 genetic diversity and the risk of virus transmission in the investigated population. The mean nucleotide distances were significantly lower among sequences derived from IDUs than among sequences obtained from STs. Additionally, strains present among IDUs, as opposed to viruses circulating among STs, were genetically more distinct from HIV-1 subtype B strains found in other populations worldwide. Our findings that HIV-1 strains circulating among IDUs were closely related to each other, but were distinct from viruses prevalent in other geographic regions, allow further tracing of the spread of these strains.