Prevalences and characteristics of cultivable nasal bacteria isolated from preclinical medical students

Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities

Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at the Prince Mohammed Bin Abdulaziz Hospital Riyadh. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.

Effects of preoperative Staphylococcus aureus screening and targeted decolonization bundle protocols in cardiac surgery: a nine-year review of a regional cardiovascular center in China

Background

Nosocomial infection (NI) prolongs hospital stay and heightens mortality among patients who underwent cardiac surgery. We constructed a retrospective study to explore the prevalence of Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (SA/MRSA) nasal colonization, as well as the effects of SA/MRSA decolonization bundle measures on SA/MRSA-related infection among Chinese cardiac patients.

Methods

After reviewing the medical records, we divided cardiovascular surgery patients treated at our central campus into two groups: the baseline group (treated between January 2012 and December 2013) and the intervention group (treated between May 2014 and December 2020). Intervention measures consisted of preoperative nasal screening and targeted decolonization bundle therapy. The medical records of patients at our southern campus (treated between January 2017 and December 2020) were collected as an additional control group, since we did not implement SA intervention measures at this location. The incidences of SA/MRSA-related NI were then compared between the groups.

Results

There were 794 patients in the baseline group and 2,826 in the intervention group. A total of 131 (4.6%) patients had SA nasal colonization, and among them, 33 patients (1.2%) were MRSA colonized. SA/MRSA was cleared in approximately 95% of the carriers. The total level of SA-related infection was significantly lower in the intervention group compared to the baseline group [0.354% vs. 1.133%, respectively; P=0.021; risk ratio (RR): 0.312; 95% confidence interval (CI): 0.127-0.766]. The incidence of MRSA-related infection followed the same trend (0.212% vs. 0.756%, respectively; P=0.030; RR: 0.281; 95% CI: 0.091-0.860). When compared to the southern campus, SA intervention measures at the central campus resulted in a significant reduction in total SA-related infection (1.132% vs. 0.284%, respectively; P=0.035; RR: 0.251; 95% CI: 0.077-0.820).

Conclusions

The prevalence of SA/MRSA colonization is relatively low among Chinese patients who received cardiovascular surgery. Targeted decolonization bundle therapy was associated with cleared colonization and reduced incidence of SA/MRSA-related infection.

Characterization of Bacterial Differences Induced by Cleft-Palate-Related Spatial Heterogeneity

Background: Cleft palate (CP) patients have a higher prevalence of oral and respiratory tract bacterial infections than the general population. Nevertheless, characteristics of bacterial differences induced by CP-related anatomical heterogeneity are unknown. Methods: In this study, we systematically described the characteristics of bacteria in the oral and nasal niches in healthy children, CP children, healthy adolescents, CP adolescents, and postoperative adolescents by 454-pyrosequencing technology (V3−V6) to determine bacterial differences induced by CP. Results: Due to the CP-induced variations in spatial structure, the early establishment of microecology in CP children was different from that in healthy children. Nasal bacterial composition showed greater changes than in the saliva. Moreover, such discrepancy also appeared in CP and postoperative adolescents who had even undergone surgery > 10 years previously. Interestingly, we found by Lefse analysis that part of bacterial biomarkers in the nasal cavity of CP subjects was common oral flora, suggesting bacterial translocation between the oral and nasal niches. Therefore, we defined the oral−nasal translocation bacteria as O-N bac. By comparing multiple groups, we took the intersection sets of O-N bacs selected from CP children, CP adolescents, and postoperative adolescents as TS O-N bacs with time−character, including Streptococcus, Gemella, Alloprevotella, Neisseria, Rothia, Actinomyces, and Veillonella. These bacteria were at the core of the nasal bacterial network in CP subjects, and some were related to infectious diseases. Conclusions: CP would lead to significant and long-term differences in oral and nasal flora. TS O-N bacs migrating from the oral to the nasal might be the key stone causing nasal flora dysbiosis in the CP patients.

Prevalence of Staphylococcus aureus nasal carriage and surgical site infection rate among patients undergoing elective cardiac surgery

BACKGROUND

Nasal carriers of Staphylococcus aureus are at increased risk of postoperative surgical site infection. Nasal decolonization with mupirocin is recommended in patients undergoing cardiac surgery to reduce surgical site infection. These data are still lacking in Thailand. Therefore, the aim of this study was to determine the prevalence of S. aureus nasal carriage in Thai patients undergoing elective cardiac surgery. The association of surgical site infection and S. aureus nasal carriage was also examined.

METHODS

This was a prospective cohort study of 352 patients who planned to undergo elective cardiac surgery. Nasal swab culture was performed in all patients preoperatively.

RESULTS

Of 352 patients, 46 (13.1%) had a positive nasal swab culture for methicillin-sensitive S. aureus (MSSA) and one patient (0.3%) harbored a methicillin-resistant S. aureus (MRSA) strain. The incidence of superficial and deep surgical site infection was 1.3% and 0.3%, respectively. After multivariate analysis, S. aureus nasal carriage was independently associated with superficial surgical site infection (odds ratio 13.04, 95% confidence interval 1.28-133.27; P=0.03).

CONCLUSIONS

The prevalence of MSSA and MRSA nasal carriage in Thai patients undergoing elective cardiac surgery was low. The incidence of surgical site infection was also very low in the population studied. Nevertheless, it was found that S. aureus nasal carriage increased the risk of superficial surgical site infection.