A Guide to Utilization of the Microbiology Laboratory for Diagnosis of Infectious Diseases: 2018 Update by the Infectious Diseases Society of America and the American Society for Microbiology

The role of flexible bronchoscopy in children with Mycoplasma pneumoniae pneumonia

PURPOSE

To explore the effectiveness of flexible bronchoscopy in pediatric Mycoplasma pneumoniae pneumonia (MPP).

METHODS

This retrospective cohort study included children with MPP admitted between 2016 and 2019 in Shanghai. Tracheobronchial manifestations, etiologic findings, therapeutic effect, and health-economic indicators were assessed in bronchoscopy (plus bronchoalveolar lavage (BAL)) and non-bronchoscopy group. We used propensity-score matching and multivariable logistic regression to investigate the effect of bronchoscopy and BAL on disease recovery.

RESULTS

In 900 children with MPP, 24/278 (8.6%) of those who underwent bronchoscopy had sputum plugs. Coinfection rate was four-fold enhanced by BAL (19.6% vs. 4.5%, p < 0.01) in patients with severe MPP (SMPP) and nearly doubled (10.8% vs. 5.9%, p = 0.03) in those without SMPP, compared with no BAL. Total of 224 (24.9%) patients had multilobar consolidation; after BAL, a significantly shorter lesion-resolution duration was observed on imaging (OR: 0.2, 95% CI: 0.0-0.7). However, longer fever duration (OR: 2.8, 95% CI: 1.7-4.8), hospital stay (OR: 3.1, 95% CI: 1.9-5.1), and higher costs were found in the bronchoscopy group than in the non-bronchoscopy group.

CONCLUSIONS

Through BAL, coinfection may explain one-fifth of causes for SMPP. Bronchoscopy with BAL may increase the detection rate of pathogen and resolve pulmonary lesions in patients with multilobar consolidation.

IMPACT

Flexible bronchoscopy with bronchoalveolar lavage is of great assistance in the timely detection of coinfection, sputum plug and inflammatory polyps in children with Mycoplasma pneumoniae pneumonia (MPP), and improves the recovery of lung damage in MPP patients with multilobar consolidation. This study provides new insights into the indications of flexible bronchoscopy for the diagnosis and treatment of pediatric patients with MPP.

An initiative to improve effluent culture detection among pediatric patients undergoing peritoneal dialysis through process improvement

BACKGROUND

Peritonitis is a significant cause of morbidity and healthcare cost among pediatric patients undergoing peritoneal dialysis. Culture-negative peritonitis has been associated with an increased risk of technique failure. Known risk factors for culture-negative peritonitis are related to the process of collection and sample processing for culture, but additional studies are needed. A culture detection rate of 16.7% was identified among our patients undergoing peritoneal dialysis, which is below the national benchmark of ≥ 85%. Our primary objective of this quality improvement project was to improve culture detection rates.

METHODS

Interventions were developed aimed at standardizing the process of effluent collection and laboratory processing, timely collection and processing of samples, and addressing other modifying risk factors for lack of bacterial growth from culture. These interventions included direct inoculation of effluent into blood culture bottles at bedside and use of an automated blood culture system. Two Plan-Do-Study-Act cycles were completed prior to moving to the sustain phase.

RESULTS

The culture detection rate improved from 16.7% (pre-intervention) to 100% (post-intervention). A decrease in the median process time also occurred from 83 min (pre-intervention) to 53 min (post-intervention). An individual and moving range chart identified a decrease in both the centerline (mean) and upper control limit, indicating that the process became more reliable during the sustain phase.

CONCLUSIONS

An improvement in process time and culture positivity rate occurred following standardization of our PD fluid culture process. Future studies should be aimed at the impact of the components of collection and processing methods on the effluent culture yield. A higher resolution version of the Graphical abstract is available as Supplementary information.

Pharmacokinetic/Pharmacodynamic Analysis of Continuous-Infusion Fosfomycin in Combination with Extended-Infusion Cefiderocol or Continuous-Infusion Ceftazidime-Avibactam in a Case Series of Difficult-to-Treat Resistant Pseudomonas aeruginosa Bloodstream Infections and/or Hospital-Acquired Pneumonia

Objectives: To perform a pharmacokinetic/pharmacodynamic (PK/PD) analysis of continuous-infusion (CI) fosfomycin combined with extended-infusion (EI) cefiderocol or CI ceftazidime-avibactam in a case series of severe difficult-to-treat Pseudomonas aeruginosa (DTR-PA) infections. Methods: A single-center retrospective study of patients who were treated with CI fosfomycin plus EI cefiderocol or CI ceftazidime-avibactam for severe DTR-PA infections and who underwent therapeutic drug monitoring (TDM), from 1 September 2021 to 30 June 2022 was performed. Concentrations were measured at steady-state (Css) for CI fosfomycin and ceftazidime-avibactam and at trough (Cmin) for EI cefiderocol. Joint PK/PD targets of combination therapy were analyzed (thresholds: area-under-the curve to minimum inhibitory concentration (AUC/MIC) ratio > 40.8 for fosfomycin; ceftazidime Css/MIC ratio ≥ 4 coupled with avibactam Css > 4 mg/L for ceftazidime-avibactam; Cmin/MIC ratio ≥ 4 for cefiderocol). Joint PK/PD targets of the combination therapy were analyzed and defined as optimal when both were achieved, quasi-optimal if only one of the two was achieved, and suboptimal if none of the two was achieved). The relationship between joint PK/PD target attainment and microbiological response was assessed. Results: Six patients (three pneumonia, two BSI + pneumonia, and one BSI) were included. The joint PK/PD targets were optimal in four cases and quasi-optimal in the other two. Microbiological eradication (ME) occurred in 4/4 of patients with optimal joint PK/PD targets and in one of the two patients with quasi-optimal joint PK/PD targets. Conclusions: Attaining optimal joint PK/PD targets with a combo-therapy of CI fosfomycin plus EI cefiderocol or CI ceftazidime-avibactam could represent an effective strategy for granting favorable microbiological outcomes in patients with DTR-PA pneumonia and/or BSI.

Antibacterial action mechanisms and mode of trypsin inhibitors: a systematic review

This systematic review (SR) aimed to gather studies describing the antibacterial action mechanisms and mode of trypsin inhibitors. The review protocol was registered (PROSPERO: CRD42020189069). Original articles resulting from studies in animal models, in bacterial culture, and using cells that describe antibacterial action of trypsin inhibitor-type peptides or proteins were selected in PubMed, Science Direct, Scopus, Web of Science, BVS, and EMBASE. The methodological quality assessment was performed using the PRISMA and OHAT tool. 2382 articles were retrieved, 17 of which were eligible. Four studies demonstrated the action mechanism directly on the bacterial membrane, and the fifth study on endogenous proteases extracted from the bacteria themselves. The antibacterial action mode was presented in the other studies, which can generate bacteriostatic or bactericidal effects without describing the mechanisms. This study generated information to enable new preclinical or clinical studies with molecules contributing to public health.

The comparative accuracy of pooled vs. individual blood culture sampling methods for diagnosis of catheter-related bloodstream infection

Background

Catheter-related bloodstream infection (CRBSI) is associated with increased morbidity, mortality, and cost of treatment in critically ill patients. A differential time to positivity (DTP) of 120 min or more between blood cultures obtained through the catheter vs. peripheral vein is an indicator of CRBSI with high sensitivity and specificity. However, it is no clear whether pooled sampling would be as efficient as individual sampling in order to reduce costs, contamination, or anemia.

Methods

This was a prospective diagnostic study conducted at the medical ICU and semi-ICU of Khon Kaen University’s Srinagarind Hospital in Thailand from May 2020 to November 2021. Fifty patients with triple-lumen central venous catheters (CVCs) who were clinically suspected of CRBSI were enrolled. 15 mL of blood was drawn through each catheter lumen, 10 mL of which was inoculated into three blood culture bottles, and the remaining 5 mL was pooled into a single bottle. Sensitivity, specificity, accuracy, and time to positivity of the pooled blood cultures were calculated using individual blood cultures as a reference.

Results

Of the 50 patients enrolled, 14 (28%) were diagnosed with CRBSI, 57.9% of whom were infected with gram-negative bacteria as the causative pathogen (57.9%). Extensively drug-resistant (XDR) Klebsiella pneumoniae was the most common organism. Sensitivity and specificity of the pooled blood sampling method were 69.23% (95% CI [0.44–0.94]) and 97.3% (95% CI [0.92–1.02]), respectively. The area under the ROC curve (AUC) was 0.83 (95% CI [0.68–0.99]). A paired T-Test to compare time to positivity of the pooled blood bottle and the first positive culture from the individual bottles indicated statistical significance (14.9 and 12.4 h, respectively). The mean difference was 2.5 [0.9–4.1] h, with a 95% CI and a p-value of 0.006.

Conclusion

Pooled blood sampling results in a lower sensitivity and longer time to positivity for CRBSI diagnosis in patients with triple-lumen CVCs than individual lumen sampling.

Trial registration Retrospectively registered at Thai Clinical Trials Registry. The study was reviewed and approved on 08/03/2022. TCTR identification number is TCTR20220308002

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07605-x.

Changes in Use of Blood Cultures in a COVID-19-Dedicated Tertiary Hospital

Blood cultures should be collected within an hour in the setting of sepsis/septic shock. The contamination rate should be below 3%. Worldwide reports have described an increase in blood contamination rates during the COVID-19 pandemic. We performed a retrospective analysis of the blood cultures collected during a 10-month period (March−December 2020) at NIID “Prof. Dr. Matei Balș”. The results were compared with data from the pre-pandemic period (March−December 2016) and with the existing data in the literature. During the pandemic, there was a significant decrease in the number of blood cultures collected (1274 blood cultures in 2020 vs. 5399 in 2016). The contamination rate was higher in 2020 (11.7%) compared to 2016 (8.2%), p < 0.001. The rate of infectious episodes in which the etiological agent was identified was constant: 11% in 2020 versus 11.9% in 2016, p = 0.479, but there were fewer invasive bacterial/fungal infections: 0.95/1000 patient days in 2020 vs. 2.39/1000 patient days in 2016, p < 0.001. We observed a change in the species distribution. The Gram-negative isolate’s proportion increased from 50.6% to 63.1% and the gram-positive isolate’s proportion decreased from 31.8% to 19%. Collection of a low number of blood cultures and a high contamination rate was identified in our clinic. In order to improve the usefulness of blood cultures as a diagnostic method, at least two sets should be collected in aseptic conditions.

Bacterial isolates, their antimicrobial susceptibility pattern, and associated factors of external ocular infections among patients attending eye clinic at Debre Markos Comprehensive Specialized Hospital, Northwest Ethiopia

Background

External eye infection caused by bacteria can lead to reduced vision and blindness. Therefore, pathogen isolation and antimicrobial susceptibility testing are vital for the prevention and control of ocular diseases.

Objective

The main aim of this study was to assess bacterial isolates, their antimicrobial susceptibility pattern, and associated factors of external ocular infection (EOI) among patients attended eye clinic at Debre Markos Comprehensive Specialized Hospital (DMCSH), Northwest Ethiopia.

Methods

We conducted a cross-sectional study in patients with external ocular infections from January 1, 2021, to June 30, 2021, at DMCSH. Socio-demographic and clinical data were collected using semi-structured questionnaires. Following standard protocols, external ocular swabs were collected and inoculated onto blood agar, chocolate agar, MacConkey agar and mannitol salt agar (MSA). Finally, bacterial isolates were identified by Gram stain, colony morphology, and biochemical tests. Antimicrobial susceptibility testing was done by using the modified Kirby-Bauer disk diffusion technique according to Clinical and Laboratory Standards Institute (CLSI) guideline. Cleaned and coded data were entered into EpiData version 4.2 software and exported to Statistical Packages for Social Sciences (SPSS) version 22 for analysis. Bivariate logistic regression was applied to investigate the association between predictors and outcome variables. P-values ≤ 0.05 with 95% confidence interval were considered statistically significant.

Results

Two hundred seven study participants were enrolled in this study. More than half of them (57.5%, 119/207) were males, and 37.7% (78/207) of them were ≥ 65 years old. A total of 130 (62.8%) bacterial isolates were identified, with Gram-positive bacteria accounting for 78.5% (102/130) of the isolates. Staphylococcus aureus was the most common isolate with a 46.2% (60/130) prevalence. Ciprofloxacin was comparatively effective against Gram-positive and Gram-negative bacteria. The prevalence of culture-confirmed bacteria was significantly associated with age groups 15–24 (AOR: 9.18, 95%CI: 1.01–82.80; P = 0.049) and 25–64 (AOR: 7.47, 95%CI: 1.06–52.31; P = 0.043). Being farmer (AOR: 5.33, 95% CI: 1.04–37.33; P = 0.045), previous history of eye surgery (AOR: 5.39, 95% CI: 1.66–17.48; P = 0.005), less frequency of face washing (AOR: 5.32, 95% CI: 1.31–7.23; P = 0.010) and face washing once a day (AOR: 3.07, 95% CI: 1.13–25.13; P = 0.035) were also significantly associated with the prevalence of culture-confirmed bacteria.

Conclusion

The prevalence of culture-confirmed bacteria among patients with EOI was high in the study area. A considerable proportion of bacterial isolates exhibited mono and/or multi-drug resistance. Age (15–64 years), being farmer, previous history of eye surgery and less frequency of face washing were significantly associated with the prevalence of culture-confirmed bacteria. Bacterial isolation and antibiotic susceptibility testing should be routinely performed in the study area to combat the emergence of antibiotic resistance.

Nasopharyngeal aspirates in children with severe community-acquired pneumonia collected within 3 days before bronchoscopy can partially reflect the pathogens in bronchoalveolar lavage fluids

BACKGROUND

There is little evidence about consistency between nasopharyngeal and pulmonary pathogens in children with severe pneumonia. This study aims to compare the difference of pathogens between nasopharyngeal aspirates (NPAs) collected before bronchoscopy and bronchoalveolar lavage fluids (BALFs) in children with severe community-acquired pneumonia (SCAP).

METHODS

NPAs and BALFs were collected form pediatric SCAP cases hospitalized from January 2018 to March 2019. NPAs were colleced within 3 days before bronchoscopy. Samples were detected by direct immunofluorescence assay (DFA) for seven respiratory viruses and by routine bacterial culture in the clinical microbiology laboratory. Respiratory syncytial virus (RSV), Adenovirus (ADV), Influenza virus types A, B (IV-A and IV-B), Parainfluenza virus 1-3 (PIV1-3) were detected with a commercial assay. The virological and bacteriological detention results of NPAs were compared with the results of BALFs.

RESULTS

In total 204 cases with mean age of 3.4 ± 2.8 years (IQR, 1 month-14 years) were included in the study. Both NPA and BALF were collected from those cases. The positive rates of pathogen in NPAs and BALFs were 25.0% (51/204) and 36.7% (75/204), respectively (x² = 6.614, P = 0.010). Respiratory viruses were found in 16.1% (33/204) from NPAs and 32.3% (66/204) from BALFs (x² = 14.524, P < 0.001). RSV and ADV were the two most frequent detected viruses in NPAs and BALFs. High consistentcy of pathogens between NPAs and BALFs was observed, and 96.9% (32/33) viruses detected in NPAs were also found in BALFs. While bacteria were isolated from 12.7% (26/204) and 10.7% (22/204) of the two kinds of samples, respectively (x² = 0.378, P = 0.539). In addition, Haemophilus influenzae (HI) was the dominant germ in both samples.

CONCLUSION

The DFA method used to detect seven respiratory viruses from NPAs collected within 3 days before bronchoscopy can partially reflect the pathogens in the lungs in children with SCAP.

Current methods for microbiological diagnosis of acute central nervous system infections

The incidence of infections affecting the central nervous system has increased in recent years, making neuroinfections a current global health problem. The central nervous system is quite well protected from the external and internal environments, although it is susceptible to infection by a wide variety of pathogens. The etiological diversity further complicates the management of such infections because it is important to identify correctly the specific cause in order to choose the most appropriate antimicrobial therapy. Diagnosis is made not only based on clinical and epidemiological data but also on the results of clinical laboratory and microbiological examination of cerebrospinal fluid. This article aims to review current microbiological methods in the diagnosis of acute central nervous system infections and help healthcare providers to recognize their advantages and limitations in order to manage their patients appropriately.

Disease- and Medication-Specific Differences of the Microbial Spectrum in Perianal Fistulizing Crohn's Disease-Relevant Aspects for Antibiotic Therapy

Perianal fistulizing Crohn's Disease (CD) with abscess formation represents an aggressive phenotype in Inflammatory Bowel Disease (IBD) with increased morbidity. Treatment is multidisciplinary and includes antibiotics, but knowledge about the microbial spectrum is rare often resulting in inadequate antimicrobial therapy. In this single center retrospective study, all patients who were operated due to perianal abscess formation were retrospectively analyzed and the microbial spectrum evaluated. Patients were divided into a CD and non-CD group with further subgroup analysis. 138 patients were finally included in the analysis with 62 patients suffering from CD. Relevant differences were detected for the microbial spectrum with anaerobic bacteria being significantly more often isolated from non-CD patients. In a subgroup-analysis of CD patients only, medical therapy had a relevant effect on the microbial spectrum since Streptococcus groups and Enterobacterales were significantly more often isolated in patients treated with steroids compared to those being treated by antibodies. In conclusion, the microbial spectrum of patients suffering from CD varies significantly from non-CD patients and immunosuppressive medication has a relevant effect on isolated pathogens. Based on that, adaption of antibiotic treatment might be discussed in the future.

Expiratory Technique versus Tracheal Suction to Obtain Good-Quality Sputum from Patients with Suspected Lower Respiratory Tract Infection: A Randomized Controlled Trial

Microbiological diagnostics of good-quality sputum samples are fundamental for infection control and targeted treatment of lower respiratory tract infections (LRTI). This study aims to compare the expiratory technique and tracheal suction on the quality of sputa from adults acutely hospitalized with suspected LRTI. We performed an open-label, randomized controlled trial. Patients were randomized to sputum sampling by tracheal suction (standard care) or the expiratory technique. The primary outcome was quality of sputum evaluated by microscopy and was analysed in the intention-to-treat population. The secondary outcomes were adverse events and patients experience. In total, 280 patients were assigned to tracheal suction (n = 141, 50.4%) or the expiratory technique (n = 139, 49.6%). Sputum samples were collected from 122 (86.5%) patients with tracheal suction and 67 (48.2%) patients with expiratory technique. Good-quality sputa were obtained more often with tracheal suction than with expiratory technique (odds ratio 1.83 [95% CI 1.05 to 3.19]; p = 0.035). There was no statistical difference in adverse events (IRR 1.21 [95% CI, 0.94 to 1.66]; p = 0.136), but patient experience was better in the expiratory technique group (p < 0.0001). In conclusion, tracheal suction should be considered a routine procedure in emergency departments for patients with suspected LRTI.

Analysis of Blood Culture Collection and Laboratory Processing Practices in Israel

IMPORTANCE

Blood culturing is a critical diagnostic procedure affecting patient outcomes and antibiotic stewardship. Although there are standards for blood culturing, the process is not often measured.

OBJECTIVES

To evaluate processes related to the diagnosis of bloodstream infection and compare them with best practices.

DESIGN, SETTING, AND PARTICIPANTS

A quality improvement study using laboratory data from January 1 to June 30, 2019, was conducted in 28 (96.6%) Israeli acute care hospitals. All blood cultures (BCs) performed on samples from adults and children in a period of 147 hospital-months were analyzed. Data analysis was performed from April 12, 2021, to September 9, 2022.

MAIN OUTCOMES AND MEASURES

True pathogen detection rate, contamination rate, proportion of adults with blood cultures performed, proportion of adult culturing episodes with only 1 set or bottle used, and median time of steps from sample collection to pathogen identification.

RESULTS

The data set consisted of 348 987 BC bottles. Bloodstream infection was detected in a median of 6.7% (IQR, 5.8%-8.2%) of adult culturing episodes and 1.1% (IQR, 0.7%-1.9%) of pediatric episodes. Eleven of 27 hospitals (40.7%) with adult patients met the standard of a contamination rate of less than 3% and only 2 hospitals (7.4%) met the more stringent standard of less than or equal to 1% contamination rate. The percentage of adults with blood cultures ranged from 2.7% to 29.0% (mean [SD], 15.7% [6.0%]). There was an association between sampling rate and pathogen detection until BCs were performed in 17% of adult admissions. The percentage of solitary BCs ranged from 47.8% to 94.4%. An estimated 1745 of 7436 (23.5%) adult bloodstream infections went undetected because solitary BCs were performed, anaerobic bottles were not used, or BCs were not performed. Median processing time was 51.2 (IQR, 33.9-78.0) hours, 3 times the optimal time: 4.4 (IQR, 1.7-12.5) hours for the preanalytical stage, 15.9 (IQR, 10.2-23.6) hours from incubation to growth detection, 4.5 (IQR, 1.5-10.7) hours from detection to Gram stain, and 30.9 (IQR, 22.0-41.9) hours from detection to isolate identification. An 8.6-hour delay was related to off-hours operating of laboratories.

CONCLUSIONS AND RELEVANCE

The findings of this study suggest that the multistep process of blood culturing is not managed comprehensively in Israel, leading to poor clinical practices and delayed results.

[Impact of Staphylococcus aureus bacteremia in COVID-19 patients]

OBJECTIVE

The disease caused by SARS-CoV-2 (COVID-19) has been a challenge for healthcare professionals since its appearance. Staphylococcus aureus has been described as one of the main pathogens causing bacterial infections in viral pandemics. However, co- infection with S. aureus causing bacteremia in patients with COVID-19 has yet to be well studied.

METHODS

We performed a e study of S. aureus bacteremia (SAB) at Hospital Miguel Servet (Zaragoza) from March 2020 to February 2021. The clinical characteristics, mortality and risk factors of adults hospitalized patients with BSA associated COVID-19 compared to patients without COVID-19.

RESULTS

A total of 95 patients with SAB were identified. 27.3% were positive for SARS-CoV-2. SAB represented 9.9% of bacteremia, being the second agent in frequency after E. coli. Nosocomial bacteremia was more frequent in the group of COVID-19 patients. The most frequent source of BSA in these patients was the respiratory source (26.9% vs 0%; P<0.001) followed by the skin (15.5% vs 15.9%; P=1). The development of sepsis was more frequent in COVID-19 patients (61,5% vs 7,8%; P=0,336) and among them, who received dexamethasone at doses > 6 mg/day (62.5% vs. 37.5%, P<0.05).

CONCLUSIONS

Our data suggest that BSA has a negative impact on the evolution of patients with COVID-19. However, further and preferably prospective studies are required to obtain solid data on the impact of BSA on coronavirus patients.

Routine Use of Anaerobic Blood Culture Bottles for Specimens Collected from Adults and Children Enhances Microorganism Recovery and Improves Time to Positivity

The utility of anaerobic blood culture bottles remains controversial, especially for specimens from children. Data are limited on the inclusion of an anaerobic bottle as part of a blood culture "set" when using contemporary blood culture instruments and media. Here, we evaluated the clinical utility of anaerobic blood culture bottles (FN Plus) and aerobic bottles (FA Plus) for the BacT/Alert Virtuo blood culture system (bioMérieux). A total of 158,710 bottles collected between November 2018 and October 2019 were evaluated. There were 6,652 positive anaerobic bottles, of which 384 (5.8%) contained 403 obligate anaerobes. In patients <19 years old, there were 389 positive anaerobic bottles, with 15 (1.8%) containing 16 obligate anaerobes. If not for anaerobic bottles, all but 8 obligate anaerobes would have gone undetected. Furthermore, anaerobic bottles were advantageous for some facultative anaerobes. Staphylococcus aureus from anaerobic bottles demonstrated statistically significant increased recovery (1,992 anaerobic versus 1,901 aerobic bottles, P = 0.009) and faster mean time to positivity (1,138 versus 1,174 min, P = 0.027). Only 25 microorganisms had statistically significant improved recovery and/or faster time to positivity from aerobic versus anaerobic bottles, suggesting anaerobic bottles offer comparable growth for most species. Finally, if only an aerobic bottle had been collected, 2,027 fewer positive cultures would have been detected and 7,452 fewer isolates would have been reported, including cultures with S. aureus (413 isolates, 10.6% less), Pseudomonas aeruginosa (9 isolates, 3.1% less) and Escherichia coli (193 isolates, 14.0% less). Taken together, these findings support the practice of routinely including an anaerobic bottle for blood culture collection.

Metagenomic next-generation sequencing may assist diagnosis of cat-scratch disease

Bartonella henselae, the pathogen that causes cat-scratch disease (CSD), is relatively rare in the clinic. CSD usually causes mild clinical manifestations, which self-heal in a matter of weeks. However, in immunocompromised patients, CSD may cause systemic disorders that can lead to critical illness. Due to the diversity of symptom signs and the lack of a golden standard for diagnosis, identifying atypical CSD in a timely manner presents a challenge. Metagenomic next-generation sequencing (mNGS), is a promising technology that has been widely used in the detection of pathogens in clinical infectious diseases in recent years. mNGS can detect multiple pathogens quickly and accurately from any given source. Here, we present a case of atypical CSD, which was diagnosed using mNGS. The patient manifested a fever of unknown infectious origin, and routine antibiotic treatment was ineffective. mNGS was employed to test the patient’s peripheral blood, which led to the detection of B. henselae. This was rarely seen in previous CSD reports. We surmised that the patient presented with atypical CSD and thus a targeted therapy was recommended. Crucially, the patient recovered rapidly. Based on this case study findings, we recommend that CSD should be included in the differential diagnosis for fever of unknown origin and that mNGS may be helpful in the diagnosis of CSD.

Chi-square automatic interaction detector decision tree analysis model: Predicting cefmetazole response in intra-abdominal infection

BACKGROUND

Cefmetazole is used as the first-line treatment for intra-abdominal infections. However, only a few studies have investigated the risk factors for cefmetazole treatment failure.

AIMS

This study aimed to develop a decision tree-based predictive model to assess the effectiveness of cefmetazole in initial intra-abdominal infection treatment to improve the clinical treatment strategies.

METHODS

This retrospective cohort study included adult patients who were unexpectedly hospitalized due to intra-abdominal infections between 2003 and 2020 and initially treated with cefmetazole. The primary outcome was clinical intra-abdominal infection improvement. The chi-square automatic interaction detector decision tree analysis was used to create a predictive model for clinical improvement after cefmetazole treatment.

RESULTS

Among 2,194 patients, 1,807 (82.4%) showed clinical improvement post-treatment; their mean age was 48.7 (standard deviation: 18.8) years, and 1,213 (55.3%) patients were men. The intra-abdomせinal infections were appendicitis (n = 1,186, 54.1%), diverticulitis (n = 334, 15.2%), and pancreatitis (n = 285, 13.0%). The chi-square automatic interaction detector decision tree analysis identified the intra-abdominal infection type, C-reactive protein level, heart rate, and body temperature as predictive factors by categorizing patients into seven groups. The area under the receiver operating characteristic curve was 0.71 (95% confidence interval: 0.68-0.73).

CONCLUSION

This predictive model is easily understandable visually and may be applied in clinical practice.

Lower airway microbiota and decreasing lung function in young Brazilian cystic fibrosis patients with pulmonary Staphylococcus and Pseudomonas infection

Cystic fibrosis (CF) is a genetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator gene that leads to respiratory complications and mortality. Studies have shown shifts in the respiratory microbiota during disease progression in individuals with CF. In addition, CF patients experience short cycles of acute intermittent aggravations of symptoms called pulmonary exacerbations, which may be characterized by a decrease in lung function and weight loss. The resident microbiota become imbalanced, promoting biofilm formation, and reducing the effectiveness of therapy. The aim of this study was to monitor patients aged 8–23 years with CF to evaluate their lower respiratory microbiota using 16S rRNA sequencing. The most predominant pathogens observed in microbiota, Staphylococcus (Staph) and Pseudomonas (Pseud) were correlated with clinical variables, and the in vitro capacity of biofilm formation for these pathogens was tested. A group of 34 patients was followed up for 84 days, and 306 sputum samples were collected and sequenced. Clustering of microbiota by predominant pathogen showed that children with more Staph had reduced forced expiratory volume in one second (FEV₁) and forced vital capacity (FVC) compared to children with Pseud. Furthermore, the patients’ clinical condition was consistent with the results of pulmonary function. More patients with pulmonary exacerbation were observed in the Staph group than in the Pseud group, as confirmed by lower body mass index and pulmonary function. Additionally, prediction of bacterial functional profiles identified genes encoding key enzymes involved in virulence pathways in the Pseud group. Importantly, this study is the first Brazilian study to assess the lower respiratory microbiota in a significant group of young CF patients. In this sense, the data collected for this study on the microbiota of children in Brazil with CF provide a valuable contribution to the knowledge in the field.

Diagnosis of bacteriospermia and its impact on spermogram parameters in adolescents with varicocele

Infectious etiology is the cause of about 15% of cases of male infertility. And if sexually transmitted infections are easily diagnosed, the role of asymptomatic bacteriospermia in the formation of infertility in men, and especially in adolescents against the background of the existing pathology of the reproductive sphere (varicocele), remains insufficiently studied. A microbiological study in the ejaculate of adolescents revealed the following types of bacteria: Escherichia coli, Enterococcus faecalis, Corynebacterium glucuronolyticum, Corynebacterium minitissimum, Streptococcus anginosus, Staphylococcus epidermidis, Staphylococcus haemolyticus. Bacteria in the ejaculate were also detected during semen analysis and electron microscopic examination of spermatozoa. With abundant growth of microorganisms in a monoculture or an association of two microorganisms present in a moderate amount, in all cases, violations of sperm motility, an increase in the viscosity of the ejaculate, the presence of leukocytes in the seminal fluid were detected, and damage to the chromatin, acrosome and mitochondria was recorded at the ultrastructural level, which may indicate active infection. When bacterial flora was detected in a small and moderate amount (<10 CFU/ml), no pathological changes in the ejaculate were observed. The microflora of the ejaculate of the examined adolescents is represented by gram-positive microflora. Simultaneous study of the ejaculate sample by bacteriological seeding, the performance of spermogram and EMIS allowed to increase the detection of bacteriospermia. Opportunistic pathogens with abundant growth or their various combinations can serve as a factor in the development of pathospermia. It is possible to distinguish an active infection from commensal microflora or sample contamination not only by the presence of bacteria in the ejaculate and their quantitative accounting, but also by the degree of damage to the function of spermatozoa and pathological changes in the parameters of the ejaculate, by combining diagnostic methods. Most often, in the presence of bacteria in the ejaculate, asthenozoospermia is diagnosed.

Clinical Value of Metagenomic Next-Generation Sequencing in Immunocompromised Patients with Sepsis

BACKGROUND Sepsis is a serious threat to human life, particularly in immunocompromised patients; hence, early diagnosis and targeted treatment are important. Metagenomic next-generation sequencing (NGS) has significant advantages over traditional diagnostic methods. This study investigated the clinical value of NGS for pathogen identification in immunocompromised patients with sepsis. MATERIAL AND METHODS From July 2020 to September 2021, 90 consecutive patients with sepsis were enrolled in this prospective study. The patients were divided into 2 groups: an immunocompromised group (n=30) and an immunocompetent group (n=60). The pathogens causing sepsis were concurrently identified using NGS and traditional diagnostic methods. The pathogen detection rates and the spectrum of pathogens identified were compared according to the method of detection and between the immunocompromised and immunocompetent groups. RESULTS Of the 90 patients, 77 (86%) were positive for 1 or more pathogens using NGS, and 50 (56%) were positive using traditional detection methods. The positivity rate of sputum and bronchoalveolar lavage fluid was higher than that of blood samples. Pneumocystis jirovecii and cytomegalovirus infections were more common in the immunocompromised group than in the immunocompetent group. CONCLUSIONS The performance of NGS in identifying pathogens for patients with sepsis is better than that of traditional detection methods, especially in immunocompromised patients. Pneumocystis jirovecii and cytomegalovirus infections are more common in immunocompromised patients.

Revisiting factors associated with blood culture positivity: Critical factors after the introduction of automated continuous monitoring blood culture systems

Blood culture is the main tool used to identify causative pathogens. Adequate volume and number of culture sets are considered key to blood culture positivity rate. It is not known whether these factors remain critical to the positivity rate after the introduction of automated continuous blood culture system monitoring. We measured blood volume per bottle and described the distribution of blood volume and number of culture sets. Multivariate logistic regression was performed to determine the independent association of blood volume, number of culture sets, diagnosis of sepsis in a patient, and other covariates with blood culture results. Only 6.9% of the blood culture bottle volumes complied with the guidance (8-10 mL), with the highest culture positivity rate (18%). Of the culture events, only one set of blood was cultured in 60.9% of events. In the multivariate analysis, blood culture volume per event (odds ratio [OR], 1.09 [95% confidence interval [CI], 1.06-1.11]), patients with a diagnosis of sepsis (OR, 2.86 [95% CI, 2.06-3.98]), and samples from the emergency department (OR, 2.29 [95% CI, 1.72-3.04]), but not the number of culture sets (OR, 0.74 [95% CI, 0.50-1.12]), were observed to be statistically significant with respect to blood culture positivity rate. Our results revealed that the total blood culture volume and the diagnosis of sepsis were critical factors affecting blood culture positivity rate. However, the proportion of blood culture bottles with the optimal blood volume was very low, and optimizing blood volume would be key to increasing blood culture positivity rate.

Relationship between Pharmacokinetic/Pharmacodynamic Target Attainment and Microbiological Outcome in Critically Ill COVID-19 Patients with Documented Gram-Negative Superinfections Treated with TDM-Guided Continuous-Infusion Meropenem

Objectives: The objective of this study was to explore the relationship between pharmacokinetic/pharmacodynamic (PK/PD) target attainment of continuous-infusion (CI) meropenem and microbiological outcome in critical COVID-19 patients with documented Gram-negative superinfections. Methods: Patients receiving CI meropenem for documented Gram-negative infections at the COVID ICU of the IRCCS Azienda Ospedaliero-Universitaria di Bologna and undergoing therapeutic drug monitoring from January 2021 to February 2022 were retrospectively assessed. Average steady-state meropenem concentrations (Css) were calculated and the Css/MIC ratio was selected as a pharmacodynamic parameter of meropenem efficacy. The Css/MIC ratio was defined as optimal if ≥4, quasi-optimal if between 1 and 4, and suboptimal if <1. The relationship between Css/MIC and microbiological outcome was assessed. Results: Overall, 43 critical COVID-19 patients with documented Gram-negative infections were retrieved. Combination therapy was implemented in 26 cases. Css/MIC ratios were optimal in 27 (62.8%), quasi-optimal in 7 (16.3%), and suboptimal in 9 cases (20.9%). Microbiological failure occurred in 21 patients (48.8%), with no difference between monotherapy and combination therapy (43.8% vs. 53.8%; p = 0.53). The microbiological failure rate was significantly lower in patients with an optimal Css/MIC ratio compared to those with a quasi-optimal or suboptimal Css/MIC ratio (33.3% vs. 75.0%; p = 0.01). Conclusion: Suboptimal attainment of meropenem PK/PD targets may be a major determinant impacting on microbiological failure in critical COVID-19 patients with Gram-negative superinfections.

Microbial Spectrum and Antibiotic Resistance in Patients Suffering from Penetrating Crohn's Disease

Intraabdominal abscess formation occurs in up to 30% of patients suffering from Crohn´s disease (CD). While international guidelines recommend a step-up approach with a combination of empiric antibiotic therapy and percutaneous drainage to delay or even avoid surgery, evidence about microbial spectrum in penetrating ileitis is sparse. We retrospectively assessed outcomes of 46 patients with terminal penetrating Ileitis where microbial diagnostics have been performed and compared microbial spectrum and antibiotic resistance profile of CD patients with patients suffering from diverticulitis with intraabdominal abscess formation. In both groups, the most frequently isolated pathogen was the gram-negative bacterium E.coli belonging to the family of Enterobacterales. However, overall Enterobacterales were significantly more often verifiable in the control group than in CD patients. Furthermore, microbial analysis showed significant differences regarding isolation of anaerobic pathogens with decreased frequency in patients with CD. Subgroup analysis of CD patients to evaluate a potential influence of immunosuppressive therapy on microbial spectrum only revealed that Enterobacterales was less frequently detected in patients treated with steroids. Immunosuppressive therapy did not show any impact on all other groups of pathogens and did not change antibiotic resistance profile of CD patients. In conclusion, we were able to demonstrate that the microbial spectrum of CD patients does differ only for some pathogen species without increased rate of antibiotic resistance. However, the empiric antibiotic therapy for CD-associated intra-abdominal abscess remains challenging since different points such as local epidemiological and microbiological data, individual patient risk factors, severity of infection, and therapy algorithm including non-surgical and surgical therapy options should be considered before therapeutical decisions are made.

The absolute number of leukocytes per vial as a major cause of early false positive blood cultures: proof-of-concept and application

Blood cultures detected as positive by the automated system but negative by microscopy and subculture are considered as "false-positives." Several causes have been identified, including hyperleukocytosis or the presence of fastidious bacteria, but as many cases remain unexplained we aimed to investigate the false positives occurring in our laboratory. We retrospectively collected data on blood cultures received over a period of 12 months to determine factors associated with the false-positive vials. We then prospectively validated our findings on the false-positive results occurring over a 3.5-month period. We finally applied scanning electron microscopy (SEM) on 63 false positives and molecular approaches on a subset of them. In the retrospective study, 154 (85%) of the 181 false-positive identified were positive following less than 4 h of incubation and were considered as "early false-positives." By performing ROC curves on these early false positives, we demonstrate that the absolute number of leukocytes is in fact the most discriminating factor of early false positivity (p < 0.001). This phenomenon can be the consequence of either a high blood culture volume (p < 0.001) or hyperleukocytosis (p < 0.001). In the prospective study, the use of a threshold of 219 million of leukocytes per vial enabled the identification of 97% of the early false positives. Finally, SEM and specific qPCR enabled three additional identifications while 16S rRNA/nanopore sequencing enabled the detection of Helicobacter cinaedi bacteremia and a polymicrobial infection. A high absolute number of leukocytes in blood cultures explains most false positives, thereby making it possible to target additional microbiological investigations.

The Novodiag® Stool parasites assay, an innovative high-plex technique for fast detection of protozoa, helminths and microsporidia in stool samples: a retrospective and prospective study

OBJECTIVES

We provide the first evaluation of the CE-IVD marked Novodiag® stool parasites assay (NVD), allowing rapid and high-plex detection of 26 distinct targets, encompassing protozoans, helminths and microsporidia in stool samples.

METHODS

A total of 254 samples (n = 205 patients) were prospectively processed by the NVD and our routine procedure (RP). Performances of the NVD were compared with RP. Samples only positive by the NVD assay were investigated by external PCR assays. Sensitivity and specificity (Se/Sp) and time from sample receipt to results were determined for each method. The NVD was also evaluated against 77 additional samples positive for a wide range of parasites.

RESULTS

Overall positivity rate was 16.9% for RP compared with 34% using the NVD assay, and 164 samples (66%) were negative by both methods. Only 30 positive samples (12%) showed full concordance between RP and NVD. Fifty-three discordant samples were sent for external investigations. Except for Giardia intestinalis and Trichuris spp., higher Se was observed for the NVD assay for Blastocystis spp. (100% vs. 63%), Dientamoeba fragilis (100% vs. 0%), Schistosoma spp. (100% vs. 17%), and Enterobius vermicularis (100% vs. 67%) but roughly similar to RP for the remaining parasites tested. False-positive results were identified for Blastocystis spp., G. intestinalis, and Trichuris spp. using the NVD assay. The NVD mostly provides a diagnosis on the day of sample receipt compared with a mean of three days with RP.

CONCLUSIONS

Besides some limitations, the NVD is a new diagnostic strategy allowing rapid and high-plex detection of gastrointestinal parasites from unpreserved stools.

Development and validation of MicrobEx: an open-source package for microbiology culture concept extraction

Objective

Microbiology culture reports contain critical information for important clinical and public health applications. However, microbiology reports often have complex, semistructured, free-text data that present a barrier for secondary use. Here we present the development and validation of an open-source package designed to ingest free-text microbiology reports, determine whether the culture is positive, and return a list of Systemized Nomenclature of Medicine (SNOMED)-CT mapped bacteria.

Materials and Methods

Our concept extraction Python package, MicrobEx, is built upon a rule-based natural language processing algorithm and was developed using microbiology reports from 2 different electronic health record systems in a large healthcare organization, and then externally validated on the reports of 2 other institutions with manually reviewed results as a benchmark.

Results

MicrobEx achieved F1 scores &gt;0.95 on all classification tasks across 2 independent validation sets with minimal customization. Additionally, MicrobEx matched or surpassed our MetaMap-based benchmark algorithm performance across positive culture classification and species capture classification tasks.

Discussion

Our results suggest that MicrobEx can be used to reliably estimate binary bacterial culture status, extract bacterial species, and map these to SNOMED organism observations when applied to semistructured, free-text microbiology reports from different institutions with relatively low customization.

Conclusion

MicrobEx offers an open-source software solution (available on both GitHub and PyPI) for bacterial culture status estimation and bacterial species extraction from free-text microbiology reports. The package was designed to be reused and adapted to individual institutions as an upstream process for other clinical applications such as: machine learning, clinical decision support, and disease surveillance systems.

Diagnosis of Bloodstream Infections: An Evolution of Technologies towards Accurate and Rapid Identification and Antibiotic Susceptibility Testing

Bloodstream infections (BSI) are a leading cause of death worldwide. The lack of timely and reliable diagnostic practices is an ongoing issue for managing BSI. The current gold standard blood culture practice for pathogen identification and antibiotic susceptibility testing is time-consuming. Delayed diagnosis warrants the use of empirical antibiotics, which could lead to poor patient outcomes, and risks the development of antibiotic resistance. Hence, novel techniques that could offer accurate and timely diagnosis and susceptibility testing are urgently needed. This review focuses on BSI and highlights both the progress and shortcomings of its current diagnosis. We surveyed clinical workflows that employ recently approved technologies and showed that, while offering improved sensitivity and selectivity, these techniques are still unable to deliver a timely result. We then discuss a number of emerging technologies that have the potential to shorten the overall turnaround time of BSI diagnosis through direct testing from whole blood-while maintaining, if not improving-the current assay's sensitivity and pathogen coverage. We concluded by providing our assessment of potential future directions for accelerating BSI pathogen identification and the antibiotic susceptibility test. While engineering solutions have enabled faster assay turnaround, further progress is still needed to supplant blood culture practice and guide appropriate antibiotic administration for BSI patients.

Value of syndromic panels in the management of severe community-acquired pneumonia

Community-acquired pneumonia requiring hospital admission is a prevalent and potentially serious infection, especially in high-risk patients (e.g., those requiring ICU admission or immunocompromised). International guidelines recommend early aetiological diagnosis to improve prognosis and reduce mortality. Syndromic panels that detect causative pathogens by molecular methods are here to stay. They are highly sensitive and specific for detecting the targets included in the test. A growing number of studies measuring their clinical impact have observed increased treatment appropriateness and decreased turnaround time to aetiological diagnosis, need for admission, length of hospital stay, days of isolation, adverse effects of medication and hospital costs. Its use is recommended a) per a pre-established protocol on making the diagnosis and managing the patient, b) together with an antimicrobial stewardship programme involving both the Microbiology Service and the clinicians responsible for the patient, and c) the final evaluation of the whole process. However, we recall that microbiological diagnosis with traditional methods remains mandatory due to the possibility that the aetiological agent is not included among the molecular targets and to determine the antimicrobial susceptibility of the pathogens detected.

Current international and national guidelines for managing skin and soft tissue infections

PURPOSE OF REVIEW

Skin and soft tissue infections account for a significant percentage of both community and nosocomial infections. Several nosological entities are included in this concept. However, there is a very scarce body of doctrine for their treatment based on randomised trials. Therefore, we considered it necessary to review current treatment guidelines to bring new recommendations and improvements to our colleagues. In this review of recent literature, we identified updated guidelines in this area by searching the databases PubMed, evidence-based medicine online, York University reviewers group, Cochrane, MBE-Trip and Sumsearch using the terms: soft tissue infection, therapy, guideline.

RECENT FINDINGS

Developments focus on using new antimicrobials and on the prescription of shorter antibiotic treatment courses.

SUMMARY

With the development of new drugs and the current evidence of their use, there is a need to refine the appropriate drug's decision-making. Drugs with a long half-life, which allows weekly administration, can reduce hospital admission and length of stay with fewer healthcare resources. Shorter courses of antibiotics are recommended. The role of stewardship programmes will continue to expand. The surgical indication and its value are evident in many patients. Therefore, management should rely on a collaborative group with experience in this disease.

Comparison of a Point-of-Care FilmArray Test to Standard-of-Care Microbiology Test in Diagnosis of Healthcare Associated Infections in a Tertiary Care Pediatric Intensive Care Unit

Background: Rapid and accurate identification of healthcare associated pathogens is crucial for early diagnosis and treatment of infections. This study aimed to assess the performance of a point-of-care multiplex polymerase chain reaction (PCR) in diagnosis of pathogens and their antibiotic resistance genes in bloodstream infections, pneumonia and meningitis/encephalitis in a pediatric intensive care unit (PICU). Methods: A retrospective cross-sectional study was conducted on pediatric patients diagnosed with healthcare associated infections at Alexandria University PICU, Egypt. A total of 111 samples from 98 patients were subjected simultaneously to standard-of-care microbiology testing (SOCMT) and molecular testing by BioFire multiplex PCR. Results: In comparison to SOCMT, the BioFire FilmArray^® had a better diagnostic yield with broncho-alveolar lavage (BAL) (45 vs. 21) and cerebrospinal fluid (CSF) samples (five vs. none) (p ≤ 0.0001). Klebsiella pneumoniae was the most common pathogen in BAL (n = 19 by BioFire, n = 9 by SOCMT) and blood (n = 7, by SOCMT and BioFire) samples, while Streptococcus pneumoniae was the most common in CSF samples. BioFire showed 95.8% overall percent agreement, 100% positive percent agreement and 95.6% negative percent agreement with SOCMT. All phenotypically confirmed resistant isolates had resistance genes by the BioFire FilmArray^® (100%). The turnaround time (TAT) of positive results by the FilmArray panels was 1–1.5 h in comparison to 48–72 h by SOCMT (p ≤ 0.001). Conclusions: The results of the current study confirm the utility of the BioFire FilmArray^® in making early decisions regarding patients’ diagnosis and management of infection in the PICU, in terms of rapid TAT and appropriate antimicrobial use.

High prevalence of infections in non-COVID-19 patients admitted to the Emergency Department with severe lymphopenia

Background

In the Emergency Department (ED), early and accurate recognition of infection is crucial to prompt antibiotic therapy but the initial presentation of patients is variable and poorly characterized. Lymphopenia is commonly associated with bacteraemia and poor outcome in intensive care unit patients. The objective of this retrospective study was to assess the prevalence of community-acquired infection in a cohort of unselected patients admitted to the ED with undifferentiated symptoms and severe lymphopenia.

Methods

This is a retrospective single-center study conducted over a 1 year-period before the COVID-19 pandemic. Consecutive adult patients admitted to the ED with severe lymphopenia (lymphocyte count < 0.5 G/L) were studied. Patients with hematological or oncological diseases, HIV infection, hepato-cellular deficiency, immunosuppression, or patients over 85 years old were excluded. Diagnoses of infection were validated by an independent adjudication committee. The association between various parameters and infection was assessed using a multivariate logistic regression analysis.

Results

Of 953 patients admitted to the ED with severe lymphopenia, 245 were studied (148 men; mean age: 63 ± 19 years). Infection was confirmed in 159 patients (65%) (bacterial: 60%, viral: 30%, other: 10%). Only 61 patients (25%) were referred to the ED for a suspected infection. In the univariate analysis, SIRS criteria (OR: 5.39; 95%CI: 3.04–9.70; p < 0.001) and temperature ≥ 38.3 °C (OR: 10.95; 95%CI: 5.39–22.26; p < 0.001) were strongly associate with infection. In the multivariate analysis, only SIRS criteria (OR: 2.4; 95%CI: 1.48–3.9; p < 0.01) and fever (OR: 3.35; 95%CI: 1.26–8.93; p = 0.016) were independently associated with infection.

Conclusions

The prevalence of underlying infection is high in patients admitted to the ED with lymphopenia, irrespective of the reason for admission. Whether lymphopenia could constitute a valuable marker of underlying infection in this clinical setting remains to be confirmed prospectively in larger cohorts.

Trial registration: No registration required as this is a retrospective study.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-022-07295-5.

To wait or not to wait: Optimal time interval between the first and second blood-culture sets to maximize blood-culture yield

The optimal timing of blood culture (BCx) sets collection has not been evaluated with continuous BCx detection systems. The yield of BCx was similar between short intervals (median, 3 minutes) and longer intervals (median, 16 or 43 minutes) among 5,856 BCx, except for improved polymicrobial bacteremia detection with long-interval BCx.

Blood Culture Utilization in the Hospital Setting: a Call for Diagnostic Stewardship

There has been significant progress in detection of bloodstream pathogens in recent decades with the development of more sensitive automated blood culture detection systems and the availability of rapid molecular tests for faster organism identification and detection of resistance genes. However, most blood cultures in clinical practice do not grow organisms, suggesting that suboptimal blood culture collection practices (e.g., suboptimal blood volume) or suboptimal selection of patients to culture (i.e., blood cultures ordered for patients with low likelihood of bacteremia) may be occurring. A national blood culture utilization benchmark does not exist, nor do specific guidelines on when blood cultures are appropriate or when blood cultures are of low value and waste resources. Studies evaluating the potential harm associated with excessive blood cultures have focused on blood culture contamination, which has been associated with significant increases in health care costs and negative consequences for patients related to exposure to unnecessary antibiotics and additional testing. Optimizing blood culture performance is important to ensure bloodstream infections (BSIs) are diagnosed while minimizing adverse events from overuse. In this review, we discuss key factors that influence blood culture performance, with a focus on the preanalytical phase, including technical aspects of the blood culture collection process and blood culture indications. We highlight areas for improvement and make recommendations to improve current blood culture practices among hospitalized patients.

Derivation and Validation of a Predictive Scoring Model of Infections Due to Acinetobacter baumannii in Patients with Hospital Acquired Pneumonia by Gram-Negative Bacilli

Background

The prognosis of ABA-HAP patients is very poor. This study aimed to develop a scoring model to predict ABA-HAP in patients with GNB-HAP.

Methods

A single center retrospective cohort study was performed among patients with HAP caused by GNB in our hospital during January 2019 to June 2019 (the derivation cohort, DC). The variables were assessed on the day when qualified respiratory specimens were obtained. A prediction score was formulated by using independent risk factors obtained from logistic regression analysis. It was prospectively validated with a subsequent cohort of GNB-HAP patients admitted to our hospital during July 2019 to Dec 2019 (the validation cohort, VC).

Results

The final logistic regression model of DC included the following variables: transferred from other hospitals (3 points); blood purification (3 points); risk for aspiration (4 points); immunocompromised (3 points); pulmonary interstitial fibrosis (3 points); pleural effusion (1 points); heart failure (3 points); encephalitis (5 points); increased monocyte count (2 points); and increased neutrophils count (2 points). The AUROC of the scoring model was 0.845 (95% CI, 0.796 ~ 0.895) in DC and 0.807 (95% CI, 0.759 ~ 0.856) in VC. The scoring model clearly differentiated the low-risk patients (the score < 8 points), moderate-risk patients (8 ≤ the score < 12 points) and high-risk patients (the score ≥ 12 points), both in DC (P < 0.001) and in VC (P < 0.001).

Conclusion

This simple scoring model could predict ABA-HAP with high predictive value and help clinicians to choose appropriate empirical antibiotic therapy.

Endophthalmitis After Intravitreal Anti-Vascular Endothelial Factor Injections: Outcomes of Eyes Managed Without Microbiologic Cultures

PURPOSE

To evaluate outcomes of eyes that developed endophthalmitis after intravitreal anti-vascular endothelial growth factor injections that were managed without microbiologic cultures.

DESIGN

Retrospective, single-center, comparative cohort study.

METHODS

We included all eyes with postinjection endophthalmitis from July 1, 2013, to September 1, 2019. Endophthalmitis cases were divided into the culture group if treated with intravitreal antibiotics and a vitreous or aqueous tap sent for microbiologic sampling or into the no culture group if treated with immediate injection of intravitreal antibiotics with an anterior chamber paracentesis that was not sent for microbiologic sampling. The main outcome measures were visual acuity, the incidence of retinal detachment, and the need for additional procedures.

RESULTS

Of 165 endophthalmitis cases identified, 119 (72%) were in the culture group and 46 (28%) were in the no culture group. At endophthalmitis presentation, eyes in the culture group had a mean logMAR VA of 1.98 (∼20/1900) compared with 1.90 (∼20/1600) for eyes in the no culture group (P = .589). At the 6-month follow-up, the mean vision loss was 5.5 lines lost from baseline for the culture group compared with 2.5 lines lost for the no culture group (P = .017). Eyes in the culture group required a subsequent pars plana vitrectomy in 29 of 119 cases (24%) compared with 7 of 46 cases (15%) in the no culture group (P = .29). Six of 119 eyes (5%) in the culture group developed secondary retinal detachments compared with none in the no culture group (P = .143).

CONCLUSIONS

When access to microbiologic facility is not available, the management of postinjection endophthalmitis using intravitreal antibiotics without microbiologic cultures may be an acceptable treatment strategy.

Faster infection diagnostics for intensive care unit (ICU) patients

INTRODUCTION

: The patient admitted to intensive care units (ICU) is critically ill, to some extent immunosuppressed, with a high risk of infection, sometimes by multidrug-resistant microorganisms. In this context, the intensivist expects from the microbiology service quick and understandable information so that appropriate antimicrobial treatment for that particular patient and infection can be initiated.

AREAS COVERED

: In this review of recent literature (2015-2021), we identified diagnostic methods for the most prevalent infections in these patients through a search of the databases Pubmed, evidence-based medicine online, York University reviewers group, Cochrane, MBE-Trip, and Sumsearch using the terms: adult, clinical laboratory techniques, critical care, early diagnosis, microbiology, molecular diagnostic techniques, spectrometry and metagenomics.

EXPERT OPINION

: There has been an exponential surge in diagnostic systems used directly on blood and other samples to expedite microbial identification and antimicrobial susceptibility testing of pathogens. Few studies have thus far assessed their clinical impact; final outcomes will also depend on preanalytical and post-analytical factors. Besides, many of the resistance mechanisms cannot yet be detected with molecular techniques, which impairs the prediction of the actual resistance phenotype.

Nonetheless, this is an exciting field with much yet to explore.

Role of the T2Dx magnetic resonance assay in patients with suspected bloodstream infection: a single-centre real-world experience

BACKGROUND

T2Dx was approved by the US Food and Drug Administration for the rapid detection of a modified panel of ESKAPE bacterial species or Candida spp. causing bloodstream infection (BSI).

PATIENTS AND METHODS

We performed a retrospective, observational study from January 1, 2018 to December 31, 2019 of all hospitalised patients with suspected BSI who underwent assessment using T2Dx in addition to standard blood culture (BC). T2-positive patients (cases) were compared to a matched group of patients with BSI documented only by BC (1:2 ratio) to investigate the possible impact of T2Dx on the appropriateness of empirical antimicrobial therapy and 21-day mortality.

RESULTS

In total, 78 T2Dx-analysed samples (49 patients) were analysed. The T2Dx assay result was positive for18 patients and negative for 31 patients. The concordance rates of the T2Bacteria Panel and T2Candida Panel results with those of standard BC were 74.4% and 91.4%, respectively. In the matched analysis, inappropriate empiric antimicrobial therapy administration was significantly less frequent in cases than in comparators (5.5% vs. 38.8%). The 21-day mortality rate was twofold lower in cases than in comparators (22.2% vs. 44.4%), although the difference was not significant. No other analysed variables were significantly different between the two groups.

CONCLUSIONS

This study illustrated that T2Dx might be associated with an increase in the appropriateness of empiric antimicrobial therapy in patients with BSI. Further studies are needed to evaluate whether the T2Dx assay can improve patient outcomes.

Ceftazidime/Avibactam versus Polymyxin B in the Challenge of Carbapenem-Resistant Pseudomonas aeruginosa Infection

Purpose

Ceftazidime/avibactam (CAZ/AVI) monotherapy and polymyxin B-based combination therapy are currently two treatment options for patients with carbapenem-resistant Pseudomonas aeruginosa (CRPA) infection; however, few studies have contrasted the relative efficacy of the two antibiotic regimens. The purpose of this study was to compare the effectiveness of CAZ/AVI and polymyxin B against CRPA infection and analyze the independent predictors of 30-day mortality or survival.

Patients and Methods

This single-center retrospective observational study included patients with CRPA infection treated with CAZ/AVI or polymyxin B between January 2018 and December 2020. The primary outcomes were the 14-day and 30-day mortality. The secondary outcomes were in-hospital mortality and bacterial clearance. Baseline characteristics and outcomes were compared between the two groups, and COX regression analysis was used to identify predictors of 30-day mortality.

Results

A total of 136 patients with CRPA infection were enrolled, including 51 patients in the CAZ/AVI group and 85 patients in the polymyxin B group. The 14-day mortality (5.9% vs 27.1%, p=0.002), 30-day mortality (13.7% vs 47.1%, p<0.001) and in-hospital mortality (29.4% vs 60.0%, p=0.001) in the CAZ/AVI group were significantly lower than the polymyxin B group. The bacterial clearance rate (45.1% vs 12.9%, p<0.001) in the CAZ/AVI group were higher than in the polymyxin B group. After adjustment by propensity score matching, the CAV/AVI group still had lower 30-day mortality (14.3% vs 42.9%, p=0.018) and higher bacterial clearance rate (42.9% vs 14.3%, p=0.018) than the polymyxin B group. The multivariate COX analysis showed that the age was identified as independent predictor of 30-day mortality while CAZ/AVI therapy and central venous catheterization emerged as independent predictors of 30-day survival.

Conclusion

CAZ/AVI therapy was superior to polymyxin B therapy for patients with CRPA infection, and provided significant survival benefits, but further larger studies were needed to substantiate our findings.

Isolation of Elizabethkingia anophelis From COVID-19 Swab Kits

Purpose: To investigate and characterize the putative Elizabethkingia anophelis contaminant isolated from throat and anal swab samples of patients from three fever epidemic clusters, which were not COVID-19 related, in Shenzhen, China, during COVID-19 pandemic. Methods: Bacteria were cultured from throat (n = 28) and anal (n = 3) swab samples from 28 fever adolescent patients. The isolated bacterial strains were identified using matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and the VITEK2 automated identification system. Nucleic acids were extracted from the patient samples (n = 31), unopened virus collection kits from the same manufacturer as the patient samples (n = 35, blank samples) and from unopened throat swab collection kits of two other manufacturers (n = 22, control samples). Metagenomic sequencing and quantitative real-time PCR (qPCR) detection were performed. Blood serum collected from patients (n = 13) was assessed for the presence of antibodies to E. anophelis. The genomic characteristics, antibiotic susceptibility, and heat resistance of E. anophelis isolates (n = 31) were analyzed. Results: The isolates were identified by MALDI-TOF/MS and VITEK2 as Elizabethkingia meningoseptica. DNA sequence analysis confirmed isolates to be E. anophelis. The patients' samples and blank samples were positive for E. anophelis. Control samples were negative for E. anophelis. The sera from a sub-sample of 13 patients were antibody-negative for isolated E. anophelis. Most of the isolates were highly homologous and carried multiple β-lactamase genes (bla _B, bla _GOB, and bla _CME). The isolates displayed resistance to nitrofurans, penicillins, and most β-lactam drugs. The bacteria survived heating at 56°C for 30 min. Conclusion: The unopened commercial virus collection kits from the same manufacturer as those used to swab patients were contaminated with E. anophelis. Patients were not infected with E. anophelis and the causative agent for the fevers remains unidentified. The relevant authorities were swiftly notified of this discovery and subsequent collection kits were not contaminated. DNA sequence-based techniques are the definitive method for Elizabethkingia species identification. The E. anophelis isolates were multidrug-resistant, with partial heat resistance, making them difficult to eradicate from contaminated surfaces. Such resistance indicates that more attention should be paid to disinfection protocols, especially in hospitals, to avoid outbreaks of E. anophelis infection.

Quality Management to Improve CSF Gram Stain Turnaround Time

BACKGROUND

With appropriate turnaround time (TAT), cerebrospinal fluid (CSF) Gram stains can provide rapid, clinically actionable information in patients with meningitis. Monitoring CSF Gram stain TAT at our institution revealed workflow gaps that were causing result reporting delays. We then implemented a new quality management program to improve TAT.

METHODS

We reviewed the TAT of all CSF specimens submitted for bacterial culture received between August 1, 2016, and July 31, 2020, and began prospectively monitoring CSF Gram stain TAT in January 2019. We then implemented the following changes in April 2019: (i) monthly reviews of TAT with staff, (ii) hand-off sheets for shift transitions, and (iii) pre- and post-shift walk throughs including centrifuge checks.

RESULTS

A total of 6913 samples were included in the analysis. CSF samples with TAT > 60 min decreased from 27.3% to 9.89% (P < 0.0001), and median TAT decreased by 9 min (P < 0.0001) with significantly reduced variability. These changes were sustained throughout the follow-up period across all shifts and shift transitions.

CONCLUSIONS

A new monthly quality metric allowed us to track CSF Gram stain TAT, identify barriers to TAT goals, and implement workflow changes that significantly improved TAT without the need for costly interventions.

Time to positivity of Corynebacterium in blood culture: Characteristics and diagnostic performance

The presence of Corynebacterium in blood samples can indicate true bacteremia or contamination, thus complicating the diagnosis of true bacteremia. We aimed to evaluate the usefulness of time to positivity (TTP) in diagnosing true bacteremia and contamination in cases where Corynebacterium was isolated from blood samples. We compared the TTP of the true-bacteremia group (n = 77) with that of the contamination group (n = 88). For the true-bacteremia cases that had only one set of positive blood cultures (n = 14), considering clinical and bacteriological data, additional cultures were performed on blood or other specimens. The same Corynebacterium spp. as in blood were isolated from these specimens. Receiver operating characteristic curves were generated, and the sensitivity and specificity of TTP were calculated for diagnosing true bacteremia. The median TTP of the true-bacteremia group (26.8 h) was shorter than that of the contamination group (43.3 h) (P < 0.0001). When considering TTP ≤ 25.0 h as true bacteremia, the sensitivity and specificity were 44.2% and 95.5%, respectively. Moreover, when considering TTP ≤ 69.4 h as true bacteremia, the sensitivity and specificity were 96.1% and 20.5%, respectively. Among the true-bacteremia groups with one set of positive blood cultures (n = 14), no case exhibited a TTP > 69.4 h. Only three cases showed TTP ≤ 25.0 h in the true-bacteremia group with one set of positive blood cultures. TTP > 69.4 h is likely to indicate contamination and may be useful to exclude true bacteremia in cases with one set of positive blood cultures. Meanwhile, diagnosing true bacteremia using the threshold of TTP 25.0 h would be difficult. Therefore, the clinical and bacteriological data are important for diagnosing bacteremia, especially in cases with TTP ≤ 69.4 h.

The Vaginal Microbiome: III. The Vaginal Microbiome in Various Urogenital Disorders

OBJECTIVE

This series of articles, titled The Vaginal Microbiome (VMB), written on behalf of the International Society for the Study of Vulvovaginal Disease, aims to summarize the recent findings and understanding of the vaginal bacterial microbiota, mainly regarding areas relevant to clinicians specializing in vulvovaginal disorders.

MATERIALS AND METHODS

A search of PubMed database was performed, using the search terms "vaginal microbiome" with "Candida," "vaginitis," "urinary microbiome," "recurrent urinary tract infections," "sexually transmitted infections," "human immunodeficiency virus," "human papillomavirus," "nonspecific vaginitis," "vulvodynia," and "vulvovaginal symptoms." Full article texts were reviewed. Reference lists were screened for additional articles. The third article in this series describes VMB in various urogenital disorders.

RESULTS

Variable patterns of the VMB are found in patients with vulvovaginal candidiasis, challenging the idea of a protective role of lactobacilli. Highly similar strains of health-associated commensal bacteria are shared in both the bladder and vagina of the same individual and may provide protection against urinary tract infections. Dysbiotic VMB increases the risk of urinary tract infection. Loss of vaginal lactic acid-producing bacteria combined with elevated pH, increase the risk for sexually transmitted infections, although the exact protective mechanisms of the VMB against sexually transmitted infections are still unknown.

CONCLUSIONS

The VMB may constitute a biological barrier to pathogenic microorganisms. When the predominance of lactobacilli community is disrupted, there is an increased risk for the acquisition of various vaginal pathogents. Longitudinal studies are needed to describe the association between the host, bacterial, and fungal components of the VMB.

Machine learning early prediction of respiratory syncytial virus in pediatric hospitalized patients

Respiratory syncytial virus (RSV) causes millions of infections among children in the US each year and can cause severe disease or death. Infections that are not promptly detected can cause outbreaks that put other hospitalized patients at risk. No tools besides diagnostic testing are available to rapidly and reliably predict RSV infections among hospitalized patients. We conducted a retrospective study from pediatric electronic health record (EHR) data and built a machine learning model to predict whether a patient will test positive to RSV by nucleic acid amplification test during their stay. Our model demonstrated excellent discrimination with an area under the receiver-operating curve of 0.919, a sensitivity of 0.802, and specificity of 0.876. Our model can help clinicians identify patients who may have RSV infections rapidly and cost-effectively. Successfully integrating this model into routine pediatric inpatient care may assist efforts in patient care and infection control.