Efficacy of targeted next generation sequencing for pathogen detection in lower respiratory tract infections.

OBJECTIVE: To investigate the diagnostic utility of targeted next-generation sequencing (tNGS) in the diagnosis of lower respiratory tract infections. METHODS: Patients with lower respiratory tract infection in East Area of Yantai Yantaishan Hospital from December 2021 to September 2023 were retrospectively analyzed. Sputum samples were tested using both tNGS technology and conventional microbiological examination. Data were collected on general clinical features and test outcomes. The study evaluated the efficacy of tNGS by comparing its positive detection rate against traditional methods and analyzing detection differences among patients with varying clinical characteristics. Receiver operating characteristic (ROC) analysis was used to determine the diagnostic accuracy of both testing methods. RESULTS: A total of 281 patients were included, with corresponding sputum specimens. The tNGS method showed a higher positivity rate of 90.0%, significantly outperforming the conventional method's rate of 70.82% (P<0.05). Among 199 patients with concordant positive results, 38.22% fully agreed, while 53.40% completely disagreed between the two methods. Mycobacterium tuberculosis, Candida albicans, and Pseudomonas aeruginosa were the most frequently detected pathogens, respectively. tNGS significantly reduced the time required for pathogen detection (P<0.001) and identified a higher rate of mixed infections compared to conventional methods (49.11% vs 2.85%, P<0.001). Positive tNGS detection rates significantly differed between patients with abnormal vs normal C-reactive protein or procalcitonin levels. The AUC for tNGS was 0.867, indicating superior diagnostic accuracy over the conventional method (P<0.05). CONCLUSIONS: tNGS technology demonstrates a high positivity rate and rapid pathogen detection in lower respiratory tract infections, with notable advantages in identifying mixed infections. This method shows potential for enhancing diagnostic accuracy and treatment decisions in clinical settings.

Evaluation of Oral Microflora-Related to Dental Caries and Salivary pH in type II Diabetic Patients.

Background: Diabetes mellitus is one of the chronic diseases and a group of metabolic disorders characterized by a high blood sugar level over a prolonged period. The present study aimed to evaluate and correlate HbA1c, salivary pH, and oral bacterial microflora (streptococcus and lactobacillus colony-forming unit (CFU)) related to dental caries in normal, controlled, and uncontrolled type II diabetic patients. Materials and Methods: A total of 90 samples were taken for this study. The HbA1c test was recorded and grouped into three (normal, prediabetic, and diabetic). CFUs (streptococcus and lactobacillus) were evaluated by the spit-and-swab method. Salivary pH was measured with a pH strip with color coding. By using the post hoc test, the P-value was significant. Results: The CFU of streptococcus and lactobacillus in the saliva spit and swab method is statistically significant for P <0.005 and P <0.01 among normal, prediabetic, and diabetic groups. In diabetic patients, there is a higher incidence of dental caries (s.d. 6.7), a higher CFU (s.d. 6194.5) in the bacterial microflora, and a lower salivary pH (s.d. 0.6) than in prediabetic and normal patients. Conclusion: From the present study, we conclude that there is a slight increase in the CFU of Streptococcus mutans in diabetic patients compared to non-diabetic patients. This CFU increase and decrease in salivary PH were strongly associated with increased dental caries in diabetic patients.

Clarifications on the Intended Use of USP <61> Microbiological Examination of Nonsterile Products: Microbial Enumeration Tests.

In the execution of its legislated responsibilities, the United States Food and Drug Administration commonly refers to standard test methods detailed in the United States Pharmacopeia (USP). Microbiological test methods (contained in general chapters) are listed in chapters <51> to <80> with details regarded as enforceable where referenced as a test method. USP <61> "Microbiological Examination of Nonsterile Products: Microbial Enumeration Tests" is a globally harmonized chapter that has been successfully employed for the enumeration of microorganisms recoverable from nonsterile finished drug products. The content of USP <61> is not always scientifically principled nor emphatically understood by all pharmaceutical microbiologists. Consequently, misunderstanding and misapplication of USP <61> may result in analyses and assessments of microbiological quality that are flawed or erroneous. In this article, clarification is provided to assist the pharmaceutical microbiologist in the appropriate and intended use of USP <61>, including provision of details not always commonly known or understood.

Effects of Sjogren's syndrome and high sugar diet on oral microbiome in patients with rampant caries: a clinical study.

OBJECTIVE: The purpose of this study was to assess the composition of the oral microbial flora of adults with rampant caries in China to provide guidance for treatment. PATIENTS AND METHODS: Sixty human salivary and supragingival plaque samples were collected. They were characterized into four groups: patients with rampant caries with Sjogren's syndrome (RC-SS) or high-sugar diet (RC-HD), common dental caries (DC), and healthy individuals (HP). The 16S rRNA V3-V4 region of the bacterial DNA was detected by Illumina sequencing. PCoA based on OTU with Bray-Curtis algorithm, the abundance of each level, LEfSe analysis, network analysis, and PICRUSt analysis were carried out between the four groups and two sample types. Clinical and demographic data were compared using analysis of variance (ANOVA) or the nonparametric Kruskal-Wallis rank-sum test, depending on the normality of the data, using GraphPad Prism 8 (P < 0.05). RESULTS: OTU principal component analysis revealed a significant difference between healthy individuals and those with RC-SS. In the saliva of patients with rampant caries, the relative abundance of Firmicutes increased significantly at the phylum level. Further, Streptocpccus, Veillonella, Prevotella, and Dialister increased, while Neisseria and Haemophilus decreased at the genus level. Veillonella increased in the plaque samples of patients with rampant caries. CONCLUSION: Both salivary and dental plaque composition were significantly different between healthy individuals and patients with rampant caries. This study provides a microbiological basis for exploring the etiology of rampant caries. CLINICAL RELEVANCE: This study provides basic information on the flora of the oral cavity in adults with rampant caries in China. These findings could serve as a reference for the treatment of this disease.

Exploring multidrug-resistant Klebsiella pneumoniae antimicrobial resistance mechanisms through whole genome sequencing analysis.

BACKGROUND: Antibiotic-resistant Klebsiella pneumoniae has emerged as a critical public health threat worldwide. Understanding the antimicrobial resistance mechanisms of multidrug-resistant K. pneumoniae (MDR-Kp) and its prevalence in time and space would provide clinical significance for managing pathogen infection. METHODS: Eighteen clinical MDR-Kp strains were analyzed by whole genome sequencing (WGS), and the antimicrobial resistance genes and associated resistance mechanisms were compared with results obtained from the conventional microbiological test (CMT). The sequence homology across strains in our study and those previously collected over time from a wide geographical region was assessed by phylogenetic analysis. RESULTS: MDR-Kp strains were collected from eighteen patients who had received empirical treatment before strain collection, with sputum (83.3%, 15/18) being the primary source of clinical samples. The commonly received treatments include ß-lactamase inhibitors (55.6%, 10/18) and carbapenems (50%, 9/18). Using CMT, we found that all 18 strains were resistant to aztreonam and ciprofloxacin, while 14 (77.8%) showed resistance to carbapenem. Polymyxin B and tigecycline were the only antibiotics to which MDR-Kp strains were sensitive. A total of 42 antimicrobial resistance mechanisms were identified by WGS, surpassing the 40 detected by the conventional method, with 25 mechanisms shared between the two techniques. Despite a 100% accuracy rate of WGS in detecting penicillin-resistant strains, the accuracy in detecting cephalosporin-resistant strains was only at 60%. Among all resistance genes identified by WGS, Klebsiella pneumoniae carbapenemase-2 (KPC-2) was present in all 14 carbapenem-resistant strains. Phenotypic analysis indicated that sequence type (ST) 11 isolates were the primary cause of these MDR-Kp infections. Additionally, phylogenic clustering analysis, encompassing both the clinical and MDR-Kp strains previously reported in China, revealed four distinct subgroups. No significant difference was observed in the sequence homology between K. pneumoniae strains in our study and those previously collected in East China over time. CONCLUSION: The application of WGS in identifying potential antimicrobial-resistant genes of MDR-Kp has demonstrated promising clinical significance. Comprehensive genomic information revealed by WGS holds the promise of guiding treatment decisions, enabling surveillance, and serving as a crucial asset in understanding antibiotic resistance.

The number of erupted teeth as a risk factor for dental caries in eighteen-month-old children: a cross­sectional study.

BACKGROUND: Dental caries is one of the most common chronic diseases worldwide, affecting lifelong as well as children. Therefore, it is important to clarify factors related to early childhood caries (ECC) in a younger population in terms of caries prevention. However, the prevalence of ECC is low in developed countries in the twenty-first century and a large-scale survey is needed to clarify the risk factors. Furthermore, earlier tooth eruption is not taken into consideration in most studies of ECC, even though it may be a factor of ECC. The present study investigated the prevalence and risk factors of dental caries in children aged 18 months in a core city of Japan. METHODS: Findings from a total of 7351 children aged 18 months were analyzed. Anthropometric measurements of height and weight, as well as an oral examination and a microbiological caries-risk test, were performed. Additionally, a structured interview sheet was provided to the parents or guardians. Findings of dental caries at 18 months of age were evaluated using a logistic regression model. RESULTS: Of the enrolled children, 1.2% had experienced dental caries. Multivariable logistic regression analysis results indicated a significant association with dental caries at 18 months of age for the following factors: second child (OR = 1.78; 95% CI:1.08-2.93, P < 0.05), third and later child (OR = 2.08; 95% CI:1.12-3.89, P < 0.05), 12 or fewer erupted teeth (OR = 0.47; 95% CI:0.24-0.96, P < 0.05), 17 or more erupted teeth (OR = 4.37; 95% CI:1.63-11.7, P < 0.01), Cariostat score (+ + +) (OR = 3.99; 95% CI:1.29-12.31, P < 0.05), daily eating before bed (OR = 2.62; 95% CI: 1.55-4.45, P < 0.001), three or more snacks per day (OR = 2.03; 95% CI:1.15-3.58, P < 0.05), and breastfeeding (OR = 3.30; 95% CI:2.00-5.44, P < 0.001). CONCLUSIONS: These results suggest that the number of erupted teeth, as well as birth order, eating habits, and breastfeeding, are significant factors in dental caries occurrence at 18 months of age.

Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status.

Purpose: Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions. Patients and Methods: A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status. Results: In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, P=9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was Acinetobacter baumannii (42/180, 23.3%) in bacterum level, Candida albicans in fungus level (44/180, 24.4%), and Human herpesvirus 1 (39/180, 27.5%) in virus level. However, for mNGS results, Candida albicans in 34.9% of positive patients, and Human herpesvirus 1 in 7.7% of positive cases were confirmed as pathogens causing pneumonia. Acinetobacter baumannii detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. Pneumocystis jirovecii was more likely to infect immunocompromised patients (P=0.002). Pseudomonas aeruginosa (14.8% vs 0.0%, P=0.008) and Human herpesvirus 1 (26.1% vs 5.3%, P=0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including Streptococcus pneumoniae, Enterococcus faecium, Pneumocystis jirovecii, and majority of viruses. Conclusion: mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.

Corrigendum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.

[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].

Erratum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.

[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].

Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.

Background: Community-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging. Methods: A total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection. Results: The positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only. Conclusion: mNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.

Improved accuracy of etiological diagnosis of spinal infection by metagenomic next-generation sequencing.

Currently, the use of metagenomic next-generation sequencing (mNGS), a new approach to identify organisms in infectious diseases, is rarely reported in the diagnosis of spinal infection. This study aimed to evaluate the potential value of mNGS in etiological diagnosis of spinal infection. In this retrospective study, the clinical data of patients with suspected spinal infection were collected by electronic medical records. Specimens obtained from each patient were tested via mNGS assay and other conventional microbiological tests (CMTs). The sensitivity and specificity of mNGS and CMTs were calculated using the final clinical diagnosis as the golden standard. In total, 108 patients were eligible for the study, with the mean length of stay of 42.8 days. Regarding the overall identification of pathogens, mNGS exhibited a better performance than CMTs, and several nontuberculous mycobacteria, fungi, and bacteria were newly discovered. In the diagnosis of spinal infection, the sensitivity, specificity, and area under the curve of mNGS were 90.72%, 81.82%, and 0.89, respectively, which were all higher than 52.17%, 56.25%, and 0.72 of the CMTs. At hospital discharge, the C-reactive protein, erythrocyte sedimentation rate, and white blood cell count of patients significantly decreased compared with hospitalization (all p < 0.05), and 88.89% showed good outcomes. These findings may suggest that mNGS has a better diagnostic accuracy in pathogenic identification of patients with suspected spinal infection, and patients treated with NGS-guided antimicrobial therapy mostly seem to have good outcomes.

Microbiological Testing for Coronavirus Disease 2019.

Microbiological diagnosis of coronavirus disease 2019 (COVID-19) is mainly performed through nucleic acid amplification test (NAAT) and antigen test. Although NAAT is the standard diagnostic test, its use is limited by insufficient laboratory resources and long turnaround time. Point-of-care NAAT tests have been introduced to address these shortcomings, but their varied sensitivity and resource constraints remain a concern. Antigen tests require fewer resources but have low sensitivity. Nevertheless, low-sensitivity tests may be useful depending on the situation. In contrast, in some clinical phases of COVID-19, high-sensitivity tests may provide false-negative results. Therefore, the right testing strategy is needed for an accurate diagnosis. In this review, the characteristics and clinical applications of microbiological tests available in Japan (NAAT, antigen test, and antibody test) are discussed. The clinical diagnosis of COVID-19 is slightly complicated, and cases in which the infection spreads from asymptomatic infected individuals are many; hence, laboratory diagnosis is essential to prevent further transmission.

Electronic reporting of diagnostic laboratory test results from all healthcare sectors is a cornerstone of national preparedness and control of COVID-19 in Denmark.

The COVID-19 pandemic has led to an unprecedented demand for real-time surveillance data in order to inform critical decision makers regarding the management of the pandemic. The aim of this review was to describe how the Danish national microbiology database, MiBa, served as a cornerstone for providing data to the real-time surveillance system by linkage to other nationwide health registries. The surveillance system was established on an existing IT health infrastructure and a close network between clinical microbiologists, information technology experts, and public health officials. In 2020, testing capacity for SARS-CoV-2 was ramped up from none to over 10,000 weekly PCR tests per 100,000 population. The crude incidence data mirrored this increase in testing. Real-time access to denominator data and patient registries enabled adjustments for fluctuations testing activity, providing robust data on crude SARS-CoV-2 incidence during the changing diagnostic and management strategies. The use of the same data for different purposes, for example, final laboratory reports, information to the public, contact tracing, public health, and science, has been a critical asset for the pandemic response. It has also raised issues concerning data protection and critical capacity of the underlying technical systems and key resources. However, even with these limitations, the setup has enabled decision makers to adopt timely interventions. The experiences from COVID-19 may motivate a transformation from traditional indicator-based public health surveillance to an all-encompassing information system based on access to a comprehensive set of data sources, including diagnostic and reference microbiology.

A questionnaire-based crossover study on the association of microbiological testing with prescription of systemic antibiotics following initial periodontal therapy.

AIM: (1) To assess prescription of systemic antibiotics following initial periodontal therapy with and without the availability of microbiological information; (2) To identify factors associated with prescription of systemic antibiotics following initial periodontal therapy. MATERIALS AND METHODS: Twenty-four clinicians were invited to complete a questionnaire on 20 patient records with respect to periodontal treatment planning, once with microbiological information available and once without. Randomization determined when the microbiological information was provided, and a 3-month washout period was respected between scoring sessions. Regression analysis was performed to identify factors associated with prescription of systemic antibiotics. RESULTS: Twenty-one clinicians completed both scoring sessions. Clinicians prescribed systemic antibiotics in on average 56% (95% Confidence Interval (CI) [0.51; 0.61]) of the cases having microbiological information, and in 52% (95% CI [0.47; 0.57]) of the same cases not having that information (p = 0.094). The odds for prescribing systemic antibiotics were 3.34 (95% CI [2.06; 5.42]) times higher when the clinician had at least 3 years of experience, 2.55 (95% CI [1.40; 4.66]) times higher for patients diagnosed with periodontitis stage IV when compared to stage III, 1.08 (95% CI [1.04; 1.11]) times higher for younger patients, 2.78 times (95% CI [1.37; 5.56]) times higher for non-smokers and 2.22 (95% CI [1.27; 3.85]) times higher when less than three teeth would require extraction. No significant associations with the prescription of systemic antibiotics were found for detection of A.actinomycetemcomitans (p = 0.287), grade of periodontitis (p = 0.499) and gender of the patient (p = 0.067). CONCLUSIONS: Based on a limited number of cases and clinicians, several patient and clinician related factors were associated with prescription of systemic antibiotics following initial periodontal therapy. However, microbiological testing was not.

Microbiological Response to Periodontal Therapy: A Retrospective Study.

BACKGROUND: Periodontitis is a multifactorial infection caused by a complex of pathogenic bacterial species that induce the destruction of periodontal structures. OBJECTIVE: The aim of this study is to evaluate the presence and bacterial load of six periodontal pathogens bacteria, measured at initial visit and after osseous surgery in patients affected by chronic periodontitis and treated between 2005 and 2007. METHODS: This cohort study was carried out on a sample of 38 consecutive patients affected by severe chronic periodontitis, diagnosed at baseline on the basis of probing depths equal to 6.68 ± 1.47 mm. On each subject, a microbiological test was performed before periodontal initial therapy and after osseous surgery (one year later). Five compromised teeth were chosen for each patient (the same teeth, before and after surgery), for a total of 190 teeth. Real-time PCR based analysis computed total bacterial load of the samples and quantified six periodontal pathogens: Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Treponema denticola, Fusobacterium nucleatum and Prevotella intermedia. Data collection was made consulting medical charts. RESULTS: Pocket probing depth reduction after surgery was 4.50 ± 1.54 mm (p=0.0001). The mean number of sites with bleeding at baseline was 2.08 ± 1.17 and 0.58 ± 1.00 after surgery (p=0.001). The mean number of sites with suppuration at baseline was 0.26 ± 0.86 and 0 after surgery (p=0.02). Cell count of each pathogen and total cell count were significantly higher at baseline than after surgery. Almost all bacteria presented a mean percentage reduction equal to that of the total count, except for Aa and Pi, which seemed to show a greater resistance. The difference of bacterial load, both before and after surgery, between smokers and non-smokers was not statistically significant (p<0.05). A statistically significant correlation was detected between pocket probing depth variation and bleeding on probing variation before and after the surgery, controlling for age (r=0.6, p=0.001). No significant correlations were observed between pocket probing depth and bacterial loads, except for Pg (r=0.5, p=0.001), Tf (r=0.6, p=0.001) and Td (r=0.4, p=0.02). CONCLUSIONS: Reduction of presence and bacterial load of the examined periodontal pathogens bacteria after osseous surgery, along with periodontal pocket reduction, appeared to be essential to achieve and maintain periodontal stability over years.

The application value of DNA hybridization probe test in the diagnosis of bacterial vaginosis and vulvovagi-nal candidiasis / 实用医学杂志

Objective To investigate the sensitivity and specificity of DNA hybridization probe test(Af-firm VPIII) in the identification related microorganisms of bacterial vaginosis(BV),vulvovaginal candidiasis (VVC). Methods Vaginal secretion were detected in 103 patients with symptom and sign of vaginitis in the out patient department. According to Nungent score,the fungal culture as the gold standard. BV blue reagent assay and wet mount microscopy as a common detection method,evaluated the sensitivity and specificity of Affirm VPIII. Results Compared with the Nungent score,the sensitivity and specificity of Affirm VPIII were 98% and 96.2%. Compared with the fungi culture,the sensitivity and specificity of Affirm VPIII were 89.4% and 98.3%. Conclusion Affirm VPIII has high sensitivity and specificity which can identify pathogenic microorganisms of BV,VVC,especially in BV diagnosis.

Preliminary study on WPBL teaching method in microbiological test teaching / 中华医学教育探索杂志

Objective To explore the effect of WPBL teaching method in microbiologicla test teach-ing. Method A total of 120 students majoring in clinical laboratory medicine were divided into the experi-mental group (WPBL teaching) and the control group (the traditional teaching) with 60 in each group in 2015. Results Questionnaire survey showed that in the experimental group, 92.6％of the students believe that WPBL teaching method can stimulate learning interest and promote student self-directed learning, 97.3％ believe that WPBL teaching method can improve the ability to analyze and solve problems, 94.7％believe that WPBL teaching method can strengthen teamwork and promote learning exchanges, and 99.6％hold that WPBL teaching method can help them recognize the importance of microbiological tests in the di-agnosis of clinical infectious diseases. The final scores and the usual performance of the experimental group were (75.23 ±11.21) and (24.15 ±1.71), respectively, while those of the control group were (63.42 ±8.21) and (20.26±1.48), respectively. The differences were statistically significant (P<0.005). Conclusions PBL teaching method can fully integrate teaching resources, stimulate students' enthusiasm and initiative, improve students' comprehensive qualities, including the ability to analyze and solve problems, teamwork ability and critical thinking ability, and improve the quality and effect of microbiological test teaching.

Knowledge, attitude and practice of Gambian health practitioners towards antibiotic prescribing and microbiological testing: a cross-sectional survey.

Background: Inappropriate antibiotic use is the leading cause of antibiotic resistance worldwide. At the same time, the practice of antibiotic prescribing in Africa is less well documented when compared to developed countries. The objective of the study was to assess the knowledge, attitude, and practice (KAP) of health practitioners towards antibiotic prescribing and microbiological testing in The Gambia. Methods: A KAP survey was conducted in The Gambia from March to May 2016. Self-administered paper-based questionnaires were distributed to health practitioners working in 12 health facilities. Results: Out of 241 questionnaires distributed, 216 (89.6%) were returned. One third of respondents reported making a request for microbiological tests or using results as a guide in less than 25% of patients with possible infectious disease. Thirty-two percent of the participants reported that '25-50%' of antibiotic prescriptions in their departments were inappropriate. Only 16.1% of the participants had some training on antibiotic prescribing in the last 12 months. Respondents agreed with the options 'inadequate supervision' (82.6%) and 'insufficient laboratory support' (82.5%) as the main causes of inappropriate antibiotic use in their settings. Conclusions: There are deficits related to antibiotic prescriptions in The Gambia. Availability and use of microbiological services and training should be emphasized.

The Application of Noninvasive Headspace Analysis to Media Fill Inspection.

The results of a proof-of-principle study demonstrating a new analytical technique for detecting microbial growth directly in pharmaceutical containers are described. This analytical technique, laser-based headspace analysis, uses tunable diode laser absorption spectroscopy to nondestructively determine gas concentrations in the headspace of a media-filled pharmaceutical container. For detecting microbial growth, the levels of headspace oxygen and carbon dioxide are measured. Once aerobic microorganisms begin to divide after the lag phase and enter the exponential growth phase, there will be significant consumption of oxygen and concomitant production of carbon dioxide in the sealed container. Laser-based headspace analysis can accurately measure these changes in the headspace gas composition. The carbon dioxide and oxygen measurement data for the representative microorganisms Staphylococcus aureus, Bacillus subtilis, Candida albicans, and Aspergillus brasiliensis were modeled using the Baranyi-Roberts equation. The mathematical modeling allowed quantitative comparisons to be made between the data from the different microorganisms as well as to the known growth curves based on microbial count. Because laser-based headspace analysis is noninvasive and can be automated to analyze the headspace of pharmaceutical containers at inspection speeds of several hundred containers per minute on-line, some potential new applications are enabled. These include replacing the current manual human visual inspection with an automated analytical inspection machine to determine microbial contamination of media fill and pharmaceutical drug product vials. LAY ABSTRACT: A novel analytical technique has been demonstrated for detecting microbial growth in media-filled pharmaceutical containers. This analytical technique, laser-based headspace analysis, uses tunable diode laser absorption spectroscopy to determine gas concentrations in the headspace of a pharmaceutical container. For detecting microbial growth, the levels of headspace oxygen and carbon dioxide are measured. The study shows that once aerobic microorganisms begin to grow after the lag phase and enter the exponential growth phase there will be a significant consumption of oxygen in the sealed container as well as a corresponding production of carbon dioxide. Headspace analysis can accurately measure and monitor these changes in the headspace gas composition and could therefore be used to detect contaminated pharmaceutical containers. Because the technique can be automated to analyze hundreds of containers a minute on-line, there are opportunities for implementing a headspace inspection machine to perform automated inspection of media fills used to validate aseptic filling operations.