- Volume 66, Issue 9, 2017

Probiotics have been used for centuries in making fermented dairy products. The health benefits related to probiotics consumption are well recognized and they are generally regarded as safe (GRAS). Their therapeutic effects are due to the production of a variety of antimicrobial compounds, such as short-chain fatty acids, organic acids (such as lactic, acetic, formic, propionic and butyric acids), ethanol, hydrogen peroxide and bacteriocins. Ventilator-associated pneumonia (VAP) is a nosocomial infection associated with high mortality in intensive care units. VAP can result from endotracheal intubation and mechanical ventilation. These interventions increase the risk of infection as patients lose the natural barrier between the oropharynx and the trachea, which in turn facilitates the entry of pathogens through the aspiration of oropharyngeal secretions containing bacteria into the lung. In order to prevent this, probiotics have been used extensively against VAP. This review is an update containing information extracted from recent studies on the use of probiotics to treat VAP. In addition, probiotic safety, the therapeutic properties of probiotics, the probiotic strains used and the action of the probiotics mechanism are reviewed. Furthermore, the therapeutic effects of probiotic treatment procedures for VAP are compared to those of antibiotics. Finally, the influences of bacteriocin on the growth of human pathogens, and the side-effects and limitations of using probiotics for the treatment of VAP are addressed.

Purpose. To evaluate the Luminex NxTAG respiratory pathogen panel (NxTAG RPP) for the detection of respiratory viruses in clinical samples from patients with the symptoms of respiratory infection.

Methodology. The NxTAG RPP was compared to an in-house multiplex real-time PCR panel (LDT) for the detection of respiratory viruses in 314 clinical samples from patients with the symptoms of respiratory infection.

Results. Thirty-one samples were negative in both tests and 193 samples contained a single virus that was detected in both tests. Polymicrobial infections were detected in 74 samples, with 268 samples overall having concordant results in both assays, and there were a total of 51 discordant results in 44 samples. Two samples were invalid in the NxTAG RPP assay and were excluded from the final analysis. The overall agreement between the NxTAG RPP and LDT was very high, as indicated by the Kappa coefficients, which ranged from 0.85 for metapneumovirus up to 0.96 for RSV A, and the overall percentage agreement values of 96.2 % for enterovirus/rhinovirus and 100 % for influenza A, influenza B, PIV 4 and RSV B.

Conclusion. The NxTAG RPP is a sensitive and specific test for the detection of respiratory viruses and the high sample throughput and low hands-on time make the NxTAG RPP assay suitable for screening clinical samples for respiratory pathogens.

Purpose. To detect the alteration of gut bacteria in children with ALL and analyse the impact of short-term-use of antibiotics on the changes caused by ALL.

Methodology. We collected faecal samples from both children with ALL and healthy children. According to their medication history with antibiotics, we classified the samples into ALL+ATBx, ALL, CON+ATBx and CON groups. Next-generation sequencing was performed to identify the gut bacteria according to the MiSeq platform. The Shannon index, Simpson index, Chao index and Ace index were used to represent the alpha diversity of gut bacteria. The beta diversity was estimated using the principles of co-ordinate analysis and non-metric multi-dimensional scaling. The taxon composition and presence of biomarkers were then determined through bioinformatics.

Results. With regard to alpha diversity, the Shannon index and Simpson index differed significantly between the ALL and CON groups, as well as the CON+ATBx and CON groups, but not the ALL+ATBx and CON+ATBx groups. With regard to beta diversity, the ALL and CON separated clearly into clusters, as did ALL+ATBx and CON+ATBx. There were differences in composition among the four groups at different taxonomy hierarchies. More bacteria showed an obvious difference between the paired groups ALL and CON than did for the paired groups ALL+ATBx and CON+ATBx. The area under the receiver operating characteristic curves for Bacteroidales and Enterococcaceae used to predict ALL were 0.735 and 0.724, respectively.

Conclusion. ALL induced structural changes of the gut microbiota, with the alpha diversity being significantly weakened by antibiotics, but not beta diversity. Bacteroidales and Enterococcaceae can be referred to as biomarkers for ALL.

Purpose. Urine flow cytometry (UFC) is an automated method to quantify bacterial and white blood cell (WBC) counts. We aimed to determine whether a threshold for these parameters can be set to use UFC as a sensitive screen to predict which urine samples will subsequently grow in culture.

Methodology. Urines submitted to our microbiology laboratory at a tertiary care centre from 22 July 2015–17 February 2016 underwent UFC (Sysmex UF-1000i) analysis, regular urinalysis and urine culture. Positive urine cultures were defined as growth ≥104 c.f.u. ml−1 of organisms associated with urinary tract infections. The correlation of UFC bacterial and WBC counts with urine culture was assessed using receiver operating characteristics curves. The sensitivity (SN), specificity (SP), negative predictive values (NPVs), positive predictive values (PPVs) and false negative rate (FNR) were calculated at various thresholds in immunocompetent and immunosuppressed patients.

Results. A total of 15 046 urine specimens were submitted, of which 14 908 were analysable in the study. The average time to UFC result from receipt in the laboratory was 0.76 h (+/−1.04). The test performance at a set threshold of UFC bacteria ≥20 or WBC >5 was: SN=96.0 %, SP=39.2 %, PPV=47.0 %, NPV=94.5 % and FNR=4.0 %. This threshold eliminates 26 % of urine cultures. Immunosuppressed hosts had a lower sensitivity of 90.6 % and a higher FNR of 9.4 %.

Conclusions. UFC is a rapid and sensitive method to screen out urine samples that will subsequently be negative and to reflex urines to culture that will subsequently grow. UFC results are available within 1 h from receipt and enable the elimination of culture when the set threshold is not met.

Purpose. Streptococcus oralis and Streptococcus mitis belong to the Mitis group, which are mostly commensals in the human oral cavity. Even though S. oralis and S. mitis are oral commensals, they can be opportunistic pathogens causing infective endocarditis. A recent taxonomic re-evaluation of the Mitis group has embedded the species Streptococcus tigurinus and Streptococcus dentisani into the species S. oralis as subspecies. In this study, the distribution of virulence factors that contribute to bacterial immune evasion, colonization and adhesion was assessed in clinical strains of S. oralis (subsp. oralis, subsp. tigurinus and subsp. dentisani) and S. mitis.

Methodology. Forty clinical S. oralis (subsp. oralis, subsp. dentisani and subsp. tigurinus) and S. mitis genomes were annotated with the pipeline PanFunPro and aligned against the VFDB database for assessment of virulence factors.

Results/Key findings. Three homologues of pavA, psaA and lmb, encoding adhesion proteins, were present in all strains. Seven homologues of nanA, nanB, ply, lytA, lytB, lytC and iga, of importance regarding survival in blood and modulation of the human immune system, were variously present in the genomes. Few S. oralis subspecies specific differences were observed. iga homologues were identified in S. oralis subsp. oralis, whereas lytA homologues were identified in S. oralis subsp. oralis and subsp. tigurinus.

Conclusion. Differences in the presence of virulence factors among the three S. oralis subspecies were observed. The virulence gene profiles of the 40 S. mitis and S. oralis (subsp. oralis, subsp. dentisani and subsp. tigurinus) contribute with important new knowledge regarding these species and new subspecies.

Simkania negevensis has been implicated in respiratory diseases. This study aimed to unveil the aetiological role of this bacterium in community-acquired pneumonia (CAP) and bronchitis in Jordanian adults. Nasopharyngeal samples were collected from 98 CAP or bronchitis patients and 96 control individuals, and tested for Simkania nucleic acids using a PCR assay. The overall prevalence of the bacterial DNA in patients was markedly high and reached 57.1 %. Intriguingly, Simkania DNA was detected in 62.5 % of the nasopharyngeal swabs collected from apparently healthy controls (P>0.05). The DNA positivity in the bronchitis and CAP subgroups was 57.7 and 56.9 %, respectively, percentages that are approximately comparable to the DNA positivity assessed for the entire patient population. Simkania is most likely not a causative agent of CAP or bronchitis, despite its remarkable high prevalence. This organism, in the nasopharynx, is potentially harmless to the host and may coexist in a commensal relationship.

Both methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) are rapidly overcoming the current array of drugs. One hundred and fifty isolates from a hospital were studied for resistance towards linezolid and vancomycin. Fifty-four (36.0 %) isolates were MRSA. Both MRSA and MSSA showed high resistance towards linezolid when using the disc diffusion method, with the figures being 48.1 and 29.2 %, respectively. The figures for the E-test were 46.3 and 27.0 %, respectively. The vancomycin resistance was remarkable in MRSA (14.8 %), but relatively low in MSSA (3.1 %). The E-test results were 13.0 and 4.16 %, respectively. The cfr gene was detected in 78 % of linezolid-resistant isolates and the vanA operon was detected in 74 % of vancomycin-resistant isolates. This level of resistance against linezolid and vancomycin is unprecedented. These results are alarming and highlight the threat of non-treatable S. aureus strains.

Two hundred and thirty-three nonduplicated clinical isolates of carbapenem-resistant Enterobacteriaceae were collected from four hospitals in Zhejiang, China. 45.1 % (105/233) strains were resistant to fosfomycin, among which plasmid-mediated fosfomycin-modifying enzymes fosA, fosA2, fosA3 and fosA5 were positive, and the other fos genes were negative. 80 % (12/15) Enterobacter cloacae isolates were positive for fosA. 100 % (73/73) Klebsiella pneumoniae isolates were positive for fosA5. A conjugation experiment indicated that fosfomycin resistance could be transferred to an Escherichia coli recipient strain successfully. Fosfomycin still exhibits partial activity in carbapenem-resistant Enterobacteriaceae, especially carbapenem-resistant Escherichia coli. To our knowledge, plasmid-mediated fosfomycin-modifying enzymes account for the dominance in the carbapenem-resistant Enterobacteriaceae. Therefore, we need to pay attention to the plasmid-mediated fosfomycin-modifying enzymes fosA and fosA5 in Enterobacter cloacae and K. pneumoniae to prevent clonal dissemination in China.

Molecular typing is an important tool for control and prevention of infection. A suitable molecular typing method for epidemiological investigation must be easy to perform, highly reproducible, inexpensive, rapid and easy to interpret. In this study, two molecular typing methods including the conventional PCR-sequencing method and high resolution melting (HRM) analysis were used for staphylococcal protein A (spa) typing of 30 Methicillin-resistant Staphylococcus aureus (MRSA) isolates recovered from clinical samples. Based on PCR-sequencing method results, 16 different spa types were identified among the 30 MRSA isolates. Among the 16 different spa types, 14 spa types separated by HRM method. Two spa types including t4718 and t2894 were not separated from each other. According to our results, spa typing based on HRM analysis method is very rapid, easy to perform and cost-effective, but this method must be standardized for different regions, spa types, and real-time machinery.

Purpose. Polymorphic variability in the tumour-suppressor protein p53 at codon 72 has a considerable impact on cervical cancer development. The present study clarified the association between p53 codon 72 genotypes and the risk of cervical disease in Greek patients. We also examined whether the presence of specific p53 genotypes in combination with HPV16 variants or E6 T350G sequence variation can modify an individual's susceptibility to cervical disease.

Methodology. The analysis of p53 genotypes was performed through PCR-RFLP. Sequence and phylogenetic tree analyses of the HPV16 E6 gene were also performed in order to identify HPV16 variants and T350G sequence variation.

Results/Key findings. The outcomes of the present analysis revealed that women who are homozygous for the arg genotype are at a 4.17-fold higher risk of developing HPV16-associated HSIL+ (OR=4.17, 95 % CI:1.48–4.9, P=0.0049). Moreover, p53 arg/arg patients infected by an HPV16 prototype strain were associated with an increased risk of more severe lesions, while a significant relationship between the p53 arg/arg genotype in patients with T350G sequence variation and the risk of high-grade squamous intraepithelial lesions (HSILs) was revealed.

Conclusion. The oncogenic potential of the virus is increased by the presence of the p53 arg/arg genotype in the Greek population in such a way that the specific protein interaction E6 (L83V)–p53 (Arg-72) can modify an individual's susceptibility to cervical disease.