A novel subgenotype C6 Enterovirus A71 originating from the recombination between subgenotypes C4 and C2 strains in mainland China

Recombination plays important roles in the genetic diversity and evolution of Enterovirus A71 (EV-A71). The phylogenetics of EV-A71 in mainland China found that one strain DL71 formed a new subgenotype C6 with unknown origin. This study investigated the detailed genetic characteristics of the new variant. DL71 formed a distinct cluster within genotype C based on the genome and individual genes (5′UTR, VP4, VP1, 2A, 2B, 2C, 3D, and 3′UTR). The average genetic distances of the genome and individual genes (VP3, 2A, 2B, 2C, 3A, 3C, and 3D) between DL71 and reference strains were greater than 0.1. Nine recombination events involving smaller fragments along DL71 genome were detected. The strains Fuyang-0805a (C4) and Tainan/5746/98 (C2) were identified as the parental strains of DL71. In the non-recombination regions, DL71 had higher identities with Fuyang-0805a than Tainan/5746/98, and located in the cluster with C4 strains. However, in the recombination regions, DL71 had higher identities with Tainan/5746/98 than Fuyang-0805a, and located in the cluster with C2 strains. Thus, DL71 was a novel multiple inter-subgenotype recombinant derived from the dominant subgenotype C4 and the sporadic subgenotype C2 strains. Monitoring the emergence of new variants by the whole-genome sequencing remains essential for preventing disease outbreaks and developing new vaccines.

Investigations upon the Improvement of Dermatophyte Identification Using an Online Mass Spectrometry Application

Online MALDI-TOF mass spectrometry applications, such as MSI-2, have been shown to help identify dermatophytes, but recurrent errors are still observed between phylogenetically close species. The objective of this study was to assess different approaches to reduce the occurrence of such errors by adding new reference spectra to the MSI-2 application. Nine libraries were set up, comprising an increasing number of spectra obtained from reference strains that were submitted to various culture durations on two distinct culture media: Sabouraud gentamicin chloramphenicol medium and IDFP Conidia medium. The final library included spectra from 111 strains of 20 species obtained from cultures on both media collected every three days after the appearance of the colony. The performance of each library was then analyzed using a cross-validation approach. The spectra acquisitions were carried out using a Microflex Bruker spectrometer. Diversifying the references and adding spectra from various culture media and culture durations improved identification performance. The percentage of correct identification at the species level rose from 63.4 to 91.7% when combining all approaches. Nevertheless, residual confusion between close species, such as Trichophyton rubrum, Trichophyton violaceum and Trichophyton soudanense, remained. To distinguish between these species, mass spectrometry identification should take into account basic morphological and/or clinico-epidemiological features.

Sitafloxacin Expresses Potent Anti-Mycobacterium abscessus Activity

Therapeutic options for treating Mycobacterium abscessus infections are extremely limited; quinolones are important. The in vitro anti-M. abscessus activities of nine quinolones, emphasizing sitafloxacin, were investigated. Antimicrobial susceptibility testing was performed on 10 non-tuberculous mycobacterium reference strains and 194 clinical, M. abscessus isolates. The activity of sitafloxacin against intracellular M. abscessus residing within macrophages was also evaluated. A checkerboard assay was conducted to determine synergy between sitafloxacin and 10 clinically important antibiotics. Among the nine quinolones tested, sitafloxacin exhibited the greatest anti-M. abscessus activity with MIC50 and MIC90 of 1 and 2 mg/L, respectively. Sitafloxacin exerted a bacteriostatic effect on M. abscessus and inhibited the intracellular growth of M. abscessus at concentrations equivalent to clarithromycin. No antagonism between sitafloxacin and 10 clinically important anti-M. abscessus antibiotics was evident. In summary, sitafloxacin exhibited a significant advantage relative to other quinolones in inhibiting the growth of M. abscessus in vitro, suggesting the potential inclusion of sitafloxacin in new strategies to treat M. abscessus infections.

Pathogens in exacerbations of chronic rhinosinusitis differ in sensitivity to silver nanoparticles

Introduction: The significance of the microbiome in chronic rhinosinusitis (CRS) is not clear. Antimicrobials are recommended in acute exacerbations of the disease (AECRS). Increasing rates of antibiotic resistance stimulate research on alternative therapeutic options including silver nanoparticles (AgNPs), sometimes referred to as “colloidal silver”. However, there are concerns regarding the safety of silver administration and the emergence of silver resistance. In this cross-sectional observational study, we assessed the sensitivity of sinonasal pathogens to AgNPs and compared it with the toxicity of AgNPs for nasal epithelial cells. Method: Negatively charged AgNPs (13±5 nm) were obtained with the use of tannic acid. Minimal inhibitory concentrations (MIC) of the AgNPs were determined for pathogens isolated from patients with AECRS. Cytotoxicity was tested on human nasal epithelial cells line in vitro. Results: 48 clinical isolates and 4 reference strains were included in the study (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, Klebsiella oxytoca, Acinetobacter baumanii, Serratia marcescens, Enterobacter cloacae). The MIC values differed between isolates, even within the same species. All of the strains were sensitive to AgNPs in concentrations nontoxic to human cells during 24 hours exposition. However, 48h exposition to AgNPs increased toxicity to human cells, narrowing their therapeutic window and enabling 19% of pathogens to resist the AgNPs biocidal action. Conclusions: AgNPs can potentially be used in intranasal drugs to treat most episodes of AECRS. Sensitivity testing may be necessary before application. Results of sensitivity testing for reference strains cannot be extrapolated to other strains of the same species.

Online Advanced Bacterial Identification Software, an Original Tool for Phenotypic Bacterial Identification

The objective of the study is to present and validate an original online Advanced Bacterial Identification Software, ABIS, by comparison to a commercially available, standardized identification system, API strips and apiweb™ bioMerieux software. Methods and results: presentation of ABIS online software, phenotypic bacterial identification of 16 reference strains and 123 wild isolates by ABIS and apiweb TM bioMerieux software and comparative analysis of results. Closed results were obtained (same taxa) for reference and wild strains of Enterobacteriaceae, Pasteurellaceae, Bacillaceae, Lactobacillaceae, Staphylococcaceae, Streptococcaceae, and other. Conclusions: Apiweb™ confirmed the results of ABIS, overall, average identification percent for ABIS being 91.8% and 90.4% for apiweb TM. ABIS online is a powerful tool for microbiology lab and the Encyclopedia connection provides essential information about the ecological significance, pathology and other features of the identified strains.

The Effects of Sub-inhibitory Antibiotic Concentrations on Pseudomonas aeruginosa: Reduced Susceptibility Due to Mutations

Pseudomonas aeruginosa chronically infects in the lungs of people with cystic fibrosis and other forms of lung disease. Infections are treated with antibiotics, but over time, the bacteria acquire mutations that reduce their antibiotic susceptibility. The effects of inhibitory amounts of antibiotics in selecting for antibiotic-resistant mutants have been well studied. However, the concentrations of antibiotics that reach infecting bacteria can be sub-inhibitory and but may nonetheless promote emergence of antibiotic-resistant bacteria. Therefore, the aim of this research was to investigate the effects of sub-inhibitory concentrations of antibiotics on the antibiotic susceptibility of P. aeruginosa. Two P. aeruginosa reference strains, PAO1 and PA14, and six isolates from individuals with cystic fibrosis were studied. The bacteria were passaged in the presence of antibiotics (ceftazidime, ciprofloxacin, meropenem or tobramycin) at sub-inhibitory amounts. Fifteen populations of bacteria (up to five per strain) were exposed to each of the four antibiotics. Antibiotic susceptibility was determined following 10 passages on agar supplemented with antibiotic and compared with susceptibility prior to antibiotic exposure. Antibiotic exposure resulted in susceptibility being significantly (>2-fold) reduced for 13 of the 60 populations. Seven samples had reduced susceptibility to ciprofloxacin, three to tobramycin, two to ceftazidime and one to meropenem. Whole-genome sequencing revealed the mutations arising following antibiotic exposure. Mutants with reduced antibiotic susceptibility had mutations in genes known to affect antibiotic resistance, including regulators of efflux pumps (mexR, mexS, mexZ and nalC) and the fusA1 gene that is associated with aminoglycoside resistance. Genes not previously associated with resistance, including gacS, sigX and crfX and two genes with no known function, were also mutated in some isolates with reduced antibiotic susceptibility. Our results show that exposure to sub-inhibitory amounts of antibiotics can select for mutations that reduce the susceptibility of P. aeruginosa to antibiotics and that the profile of mutations is different from that arising during selection with inhibitory antibiotic concentrations. It is likely that exposure to sub-inhibitory amounts of antibiotics during infection contributes to P. aeruginosa becoming antibiotic-resistant.

Molecular detection of Campylobacter species from human and cattle faecal samples in Kilosa District, Tanzania

A growing number of Campylobacter species other than C. jejuni and C. coli have been considered as emerging human and animal pathogens but their contribution to human gastroenteritis is poorly documented. This study aimed at detecting Campylobacter species from human and cattle faecal samples in Kilosa District, Tanzania using molecular techniques without culture. Seventy (70) faecal samples were collected from five diarrheic and 65 non-diarrheic human patients attending Kilosa District Hospital in Tanzania from July to October 2019. During the same period, 30 faecal samples were also collected from healthy cattle in the same district. Genus and species identification of Campylobacter was conducted on the samples using molecular techniques [the polymerase chain reaction (PCR) and 16S rRNA sequencing]. Phylogenetic analysis was carried out by comparison of the 16S rRNA gene sequences to reference strains by the Neighbor-Joining method in MEGA X. Campylobacter species detection rate by PCR was 65.7% (46/70) and 20% (6/30) in humans and cattle, respectively. There were five human diarrheic cases, four of which were positive for Campylobacter and of these, two were children ≤15 years of age. In humans, 16S rRNA sequencing revealed that C. concisus was the most predominant species occurring at a frequency of 37.8% (14/37), followed by uncultured Campylobacter spp. 24.3% (9/37) and C. hominis 21.6% (8/37). The least represented species were C. jejuni and C. lanienae, all occurring at 2.7% (1/37). In cattle, five (100%) sequenced PCR products matched with C. lanienae. Phylogenetic analysis revealed that with the exception of C. lanienae, 16S rRNA sequences of Campylobacter species were closely related to the reference strains used (Percent identity: 90.51-96.56%). Based on our findings, we recommend that molecular techniques, mainly PCR be adopted for the direct detection of Campylobacter species during laboratory screening and surveillance studies.

The first report of porcine parvovirus 7 (PPV7) in Colombia demonstrates the presence of variants associated with modifications at the level of the VP2-capsid protein

There are a wide variety of porcine parvoviruses (PPVs) referred to as PPV1 to PPV7. The latter was discovered in 2016 and later reported in some countries in America, Asia, and Europe. PPV7 as a pathogenic agent or coinfection with other pathogens causing disease has not yet been determined. In the present study, we report the identification of PPV7 for the first time in Colombia, where it was found retrospectively since 2015 in 40% of the provinces that make up the country (13/32), and the virus was ratified for 2018 in 4/5 provinces evaluated. Additionally, partial sequencing (nucleotides 380 to 4000) was performed of four Colombian strains completely covering the VP2 and NS1 viral genes. A sequence identity greater than 99% was found when comparing them with reference strains from the USA and China. In three of the four Colombian strains, an insertion of 15 nucleotides (five amino acids) was found in the PPV7-VP2 capsid protein (540–5554 nt; 180–184 aa). Based on this insertion, the VP2 phylogenetic analysis exhibited two well-differentiated evolutionarily related groups. To evaluate the impact of this insertion on the structure of the PPV7-VP2 capsid protein, the secondary structure of two different Colombian strains was predicted, and it was determined that the insertion is located in the coil region and not involved in significant changes in the structure of the protein. The 3D structure of the PPV7-VP2 capsid protein was determined by threading and homology modeling, and it was shown that the insertion did not imply a change in the shape of the protein. Additionally, it was determined that the insertion is not involved in suppressing a potential B cell epitope, although the increase in length of the epitope could affect the interaction with molecules that allow a specific immune response.

Richardia brasiliensis Collected in Southern-Benin: Phytochemical Screening, Antimicrobial Activity and Toxicity

Aims: The aim of this study is to evaluate the antimicrobial activity of the R. brasiliensis aerial part extracts collected in southern-Benin. Methodology: The phytochemical screening was performed by a differential precipitation staining method. Aqueous and ethanolic extracts were made using conventional method with water and ethanol as solvent. The obtained extracts were used to evaluate their antimicrobial activity on Staphylococcus aureus strains isolated from skin infections and ten reference strains by the solid-medium diffusion method. The minimum inhibitory concentrations (MIC) and minimum bactericidal concentrations (MBC) were determined by the liquid macro-dilution method. The cytotoxic effect of the extracts was evaluated on Artemia salina larvae obtained by hatching. Results: The phytochemical screening showed a strong presence of tannins, flavonoids, terpenes, steroids and a medium presence of alkaloids, anthocyanins and mucilage’s. The extraction yields vary according to the solvent: water (15.5%) and ethanol (10.30%). The two extracts variously (p<0.001) inhibited the growth of Staphylococcus aureus strains isolated from skin infections and four reference strains (Staphylococcus aureus ATCC29213, Pseudomonas aeruginosa ATCC27853, Proteus mirabilis A24974, Escherichia coli ATCC25922). However, there is no difference (p > 0.05) in inhibition of strains growth between 24h and 48h. The largest diameter (21±0.75 mm) of inhibition with the reference strains was obtained with P. aeruginosa by action of the aqueous extract. Regarding Staphylococcus aureus strains isolated from skin infections, the largest diameter of inhibition is about 19.25±2.75 mm obtained with strains isolated from ulcers. The average mics of 2.81 mg/ml and 2.08 mg/ml were obtained respectively for the aqueous and ethanolic extracts in the presence of the reference strains. The LC50 determination obtained using the regression line is 0.36 mg/ml for the aqueous extract and 1.16 mg/ml for the ethanolic extract. Conclusion: The aqueous extract is more effective because of its action spectrum. This extract can be used for the development of a soap or ointment to fight against skin infections.

Morphological, ultrastructural and brightness quantitative characteristics of Helicobacter pylori electronic microscopic images

Using an original computer program, a quantitative characteristic of the structural features of the cultures of two reference strains of Helicobacter pylori, identified by transmission electron microscopy, was performed. The results obtained made it possible to establish morphological, ultrastructural and brightness differences between individual bacterial cells of the studied strains. The proposed program, compiled in accordance with the requirements of computer vision technology, makes it possible to detect differences in the structure of bacterial cells that are not detected by visual assessment, and also opens up the possibility of studying the phenotypic heterogeneity of isogenic populations of Helicobacter pylori and its pathogenic significance.