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

From Prevention to Management: Understanding Postoperative Infections in Gynaecology

This narrative review examines the multifaceted realm of postoperative infections in gynaecology, addressing their significance, types, risk factors, prevention, management, and emerging trends. Postoperative infections, encompassing surgical site infections, urinary tract infections, and pelvic inflammatory disease, pose considerable challenges in patient care, warranting comprehensive exploration. Strategies for prevention include preoperative patient assessment, antimicrobial prophylaxis, and aseptic techniques. Intraoperative measures encompass infection control and instrument sterilization, while postoperative care involves wound management and early infection detection. Diagnostic tools, including blood tests, imaging, and microbiological cultures, aid in timely identification. Management strategies encompass antibiotic therapy, surgical interventions, supportive care, and addressing complications. The review underscores the necessity of personalized approaches, multidisciplinary collaboration, and innovative technologies in future infection management. It calls for ongoing research, heightened awareness, and meticulous care to minimize the impact of postoperative infections and optimize patient outcomes.

Appropriateness of antibiotic use for patients with asymptomatic bacteriuria or urinary tract infection with positive urine culture: a retrospective observational multi-centre study in Korea

BACKGROUND

Antibiotic resistance threatens public health worldwide, and inappropriate use of antibiotics is one of the main causes.

AIM

To evaluate qualitative use of antibiotics in asymptomatic bacteriuria (ABU) and urinary tract infection (UTI).

METHODS

Cases of positive urine culture (≥105 colony-forning units/mL) performed in inpatient, outpatient and emergency departments in April 2021 were screened in 26 hospitals in the Republic of Korea. The cases were classified as ABU, lower UTI and upper UTI. The appropriateness of antibiotic use was evaluated retrospectively by infectious disease specialists using quality indicators based on clinical guidelines for ABU and UTI.

RESULTS

This study included a total of 2697 patients with ABU or UTI. The appropriateness of antibiotic use was assessed in 1157 patients with ABU, and in 677 and 863 patients with lower and upper UTI, respectively. Among the 1157 patients with ABU, 251 (22%) were prescribed antibiotics without appropriate indications. In 66 patients with ABU in which antibiotics were prescribed with appropriate indications, the duration was adequate in only 23 (34.8%) patients. The appropriateness of empirical and definite antibiotics was noted in 527 (77.8%) and 353 (68.0%) patients with lower UTI, and 745 (86.3%) and 583 (78.2%) patients with upper UTI, respectively. The duration of antibiotics was adequate in 321 (61.8%) patients with lower UTI and 576 (78.7%) patients with upper UTI.

CONCLUSIONS

This nationwide qualitative assessment of antibiotic use in ABU and UTI revealed that antibiotics were often prescribed inappropriately, and the duration of antibiotics was unnecessarily prolonged.

Antibiotic management of urinary tract infections in the post-antibiotic era: a narrative review highlighting diagnostic and antimicrobial stewardship

BACKGROUND

As one of the most common indications for antimicrobial prescription in the community, the management of urinary tract infections (UTIs) is both complicated by, and a driver of, antimicrobial resistance.

OBJECTIVES

To highlight the key clinical decisions involved in the diagnosis and treatment of UTIs in adult women, focusing on clinical effectiveness and both diagnostic and antimicrobial stewardship as we approach the post-antimicrobial era.

SOURCES

Literature reviewed via directed PubMed searches and manual searching of the reference list for included studies to identify key references to respond to the objectives. A strict time limit was not applied. We prioritised recent publications, randomised trials, and systematic reviews (with or without meta-analyses) where available. Searches were limited to English language articles. A formal quality assessment was not performed; however, the strengths and limitations of each paper were reviewed by the authors throughout the preparation of this manuscript.

CONTENT

We discuss the management of UTIs in ambulatory adult women, with particular focus on uncomplicated infections. We address the diagnosis of UTIs, including the following: definition and categorisation; bedside assessments and point-of-care tests; and the indications for, and use of, laboratory tests. We then discuss the treatment of UTIs, including the following: indications for treatment, antimicrobial sparing approaches, key considerations when selecting a specific antimicrobial agent, specific treatment scenarios, and duration of treatment. We finally outline emerging areas of interest in this field.

IMPLICATIONS

The steady increase in antimicrobial resistance among common uropathogens has had a substantial affect on the management of UTIs. Regarding both diagnosis and treatment, the clinician must consider both the patient (clinical effectiveness and adverse effects, including collateral damage) and the community more broadly (population-level antimicrobial selection pressure).

Diagnostic and antibiotic stewardship lessons: an outpatient assessment of symptomatic reflex urinalysis ordering accuracy using an electronic best-practice alert

BACKGROUND

It is not well known how reliably clinicians order reflex urinalysis to microscopy and culture (rUA-cx) for outpatient urinary tract infection (UTI) workup. Antibiotic appropriateness cannot be fully appreciated until the prevalence of UTIs and asymptomatic bacteriuria (ASB) are realized.

OBJECTIVE

This quality improvement study has two major aims, first to determine UTI symptom accuracy for rUA-cx ordering and second, to confirm UTI and ASB cases by integrating rUA-cx and cascaded urinalysis results. Antibiotic utilization and diagnostic coding were secondarily linked to UTIs and ASB.

METHODS

An electronic best-practice alert informed the ordering of two rUA-cx options: symptomatic- rUA-cx specifically for dysuria, frequency, urgency, costovertebral pain, suprapubic pain or fever versus non-specific-rUA-cx for vague complaints. UTI symptoms were verified by chart review. Confirmed UTI was defined as a significant culture with UTI symptoms and ASB as a significant culture without UTI symptoms.

RESULTS

rUA-cx (2065) were prospectively collected over 6 months from female patients at risk for uncomplicated UTIs. Symptomatic-rUA-cx and non-specific-rUA-cx were associated with UTI symptoms for 53% (809/1527) and 20% (107/538), respectively. Overall, 44% (916/2065) of all rUA-cx had UTI symptoms. rUA-cx were overordered by a factor of 9 (2065/225) for every confirmed UTI. The UTI-to-ASB relative ratio was 2.6 (225/86). Regarding UTI-relevant antibiotics, 39% (214/553) were appropriately associated with UTI whereas only 22% (74/339) of inappropriate antibiotics were captured by the ASB definition, underestimating the problem 4-fold.

CONCLUSIONS

UTI and ASB remain challenging to categorize despite a meticulous method that applied acceptable criteria.

Diagnostic capacity for cutaneous fungal diseases in the African continent

BACKGROUND

Cutaneous fungal infections are very common, especially in poorer communities and with intercurrent HIV infection. Determining the fungal pathogen in skin-related fungal neglected tropical diseases (NTDs) determines optimal therapy. We undertook a country survey across many African countries to determine the diagnostic capacity for skin fungal diseases.

METHODS

A detailed questionnaire was delivered to country contacts to collect data on availability, frequency, and location of testing for key diagnostic procedures and followed up with 2 rounds of validation by video call and by confirmation of individual country data confirmation by email.

RESULTS

Of 47 countries with data, seven (15%) and 21 (45%) do not offer skin biopsy in the public or private sector, respectively, but 22 (46%) countries do it regularly, mostly in university hospitals. Direct microscopy is often performed in 20 of 48 (42%) countries in the public sector and not done in 10 (21%). Fungal cultures are often performed in 21 of 48 (44%) countries in the public sector but not done in nine (20%) or 21 (44%) in either public or private facilities. Histopathological examination of tissue is frequently used in 19 of 48 (40%) countries but not in nine (20%) countries in the public sector. The cost of diagnostics to patients was a major limiting factor in usage.

CONCLUSION

Major improvements in the availability and use of diagnostic tests for skin, hair, and nail fungal disease are urgently needed across Africa.

ESMO/ASCO Recommendations for a Global Curriculum in Medical Oncology Edition 2023

The European Society for Medical Oncology (ESMO) and ASCO are publishing a new edition of the ESMO/ASCO Global Curriculum (GC) with contributions from more than 150 authors. The purpose of the GC is to provide recommendations for the training of physicians in medical oncology and to establish a set of educational standards for trainees to qualify as medical oncologists. This edition builds on prior ones in 2004, 2010, and 2016 and incorporates scientific advances and input from an ESMO ASCO survey on GC adoption conducted in 2019, which revealed that GC has been adopted or adapted in as many as two thirds of the countries surveyed. To make GC even more useful and applicable, certain subchapters were rearranged into stand-alone chapters, that is, cancer epidemiology, diagnostics, and research. In line with recent progress in the field of multidisciplinary cancer care new (sub)chapters, such as image-guided therapy, cell-based therapy, and nutritional support, were added. Moreover, this edition includes an entirely new chapter dedicated to cancer control principles, aiming to ensure that medical oncologists are able to identify and implement sustainable and equitable cancer care, tailored to local needs and resources. Besides content renewal, modern didactic principles were introduced. GC content is presented using two chapter templates (cancer-specific and non-cancer-specific), with three didactic points (objectives, key concepts, and skills). The next step is promoting GC as a contemporary and comprehensive document applicable all over the world, particularly due to its capacity to harmonize education in medical oncology and, in so doing, help to reduce global disparities in cancer care.

Oral doxycycline to carbapenem-resistant Acinetobacter baumannii infection as a polymyxin-sparing strategy: results from a retrospective cohort

Acinetobacter baumannii infection presents a high mortality rate and few therapeutic options. This study aimed to evaluate clinical-microbiological characteristics and prognosis factors of patients diagnosed with A. baumanni. infections treated with oral doxycycline. A retrospective cohort of hospitalized patients with confirmed Acinetobacter spp. infection between 2018 and 2020 receives at least 3 days of oral doxycycline. Clinical and microbiological data were evaluated, including the outcome and molecular characterization of A. baumannii. Doxycycline minimal inhibitory concentrations were evaluated by the broth dilution method. One hundred patients were included with a median age of 51 years. The leading site of infection was pulmonary (n = 62), followed by the soft tissues and skin (n = 28). A. baumannii resistant to carbapenem was found on 94%. The gene blaOXA-23 and blaOXA-51 were amplified in all recovered isolates of A. baumannii (n = 44). Doxycycline MIC50 and MIC90 were 1 µg/mL and 2 µg/mL, respectively. Death rate at 14 days and 28 days of follow-up was 9% and 14%, respectively. The prognostic factors related to death at end of follow-up were age > 49 years [85.7% vs. 46%, CI 95% 6.9 (1.4-32.6), P = 0.015] and hemodialysis [28.6% vs. 7%, CI 95% 5.33 (1.2-22.1), P = 0.021]. Patients treated with doxycycline to A. baumannii presented a relatively low death rate, and risk factors related to death were age and hemodialysis. Further and larger studies should compare polymyxin to doxycycline to better understand the differences between these therapeutic options.

Use and Quality of Blood Cultures for the Diagnosis of Bloodstream Infections: A Cross-Sectional Study in the Ho Teaching Hospital, Ghana, 2019-2021

Blood Culture and Drug Susceptibility Testing (CDST) remains vital for the diagnosis and management of bloodstream infections (BSIs). While the Ghana National Standard Treatment Guidelines require CDST to be performed in each case of suspected or clinically diagnosed BSI, these are poorly adhered to in the Ho Teaching Hospital (HTH). This study used secondary medical and laboratory records to describe blood CDST requests by clinicians and the quality of CDST processes for the diagnosis of BSI among patients admitted to HTH from 2019 to 2021. Of 4278 patients, 33% were infants. Pneumonia and neonatal sepsis cases were 40% and 22%, respectively. Only 8% (351/4278) had blood CDST requested. Of 94% (329/351) blood CDST processed and reported, only 7% (22/329) were culture-positive, with likely contaminants being recovered from 16% (52/329) of the specimens. The duration from admission to request was 2 days (IQR: 0-5), and Further qualitative studies must be conducted to understand the reasons for low blood CDST utilisation among clinicians and the patient outcomes. Targeted interventions are required to enhance the utilisation of blood CDST by clinicians and the quality of laboratory processes.

Laboratory Surveillance, Quality Management, and Its Role in Addressing Antimicrobial Resistance in Africa: A Narrative Review

AMR is a major public health concern that calls for extensive work and a multidisciplinary team approach. The high prevalence of infectious diseases in African nations leads to widespread antibiotic usage and eventual antimicrobial resistance, which has significant negative effects on people's health, the economy, and society. Additionally, inadequate or nonexistent antimicrobial drug regulations, inappropriate prescription practices, and restrictions on public health prevention initiatives such as immunization, water and sanitation, and sexual health may all contribute to the emergence of AMR. Despite the need for laboratory quality assurance, many African laboratories confront substantial difficulties in implementing efficient quality assurance programs. AMR surveillance in Africa is hampered by a lack of laboratory capacity, insufficient data collection and analysis, and poor stakeholder collaboration. Several initiatives and programs, including the World Health Organization's Global Antimicrobial Resistance and Use Surveillance System (GLASS), the Africa Centres for Disease Control and Prevention (Africa CDC) Antimicrobial Resistance Surveillance Network (AMRSNET), and the Fleming Fund, a UK government initiative aimed at tackling AMR in low- and middle-income countries, have been established to strengthen AMR surveillance in Africa and globally.

Candida Biofilm Eye Infection: Main Aspects and Advance in Novel Agents as Potential Source of Treatment

Fungi represent a very important cause of microbial eye infections, especially in tropical and developing countries, as they could cause sight-threating disease, such as keratitis and ocular candidiasis, resulting in irreversible vision loss. Candida species are among the most frequent microorganisms associated with fungal infection. Although Candida albicans is still the most frequently detected organism among Candida subspecies, an important increase in non-albicans species has been reported. Mycotic infections often represent an important diagnostic-clinical problem due to the difficulties in performing the diagnosis and a therapeutic problem due to the limited availability of commercial drugs and the difficult penetration of antifungals into ocular tissues. The ability to form biofilms is another feature that makes Candida a dangerous pathogen. In this review, a summary of the state-of-the-art panorama about candida ocular pathology, diagnosis, and treatment has been conducted. Moreover, we also focused on new prospective natural compounds, including nanoparticles, micelles, and nanocarriers, as promising drug delivery systems to better cure ocular fungal and biofilm-related infections. The effect of the drug combination has also been examined from the perspective of increasing efficacy and improving the course of infections caused by Candida which are difficult to fight.

SEPSIS UNIT IN THE EMERGENCY DEPARTMENT: IMPACT ON MANAGEMENT AND OUTCOME OF SEPTIC PATIENTS

ABSTRACT

Study hypothesis : Implementation of a new pathway dedicated to septic patients within the emergency department (ED) would improve early management, organ dysfunction, and outcome. Methods: During phase 1, all consecutive adult patients with infection and qualifying quick Sequential Organ Failure Assessment (qSOFA) score upon ED admission were managed according to standards of care. A multifaceted intervention was then performed (implementation phase): educational program, creation of a sepsis alert upon ED admission incorporated in the professional software, together with severity scores and Surviving Sepsis Campaign (SSC) bundle reminders, and dedication of two rooms to the management of septic patients (sepsis unit). During phase 2, patients were managed according to this new organization. Results: Of the 89,040 patients admitted to the ED over the two phases, 2,643 patients (3.2%) had sepsis including 277 with a qualifying qSOFA score on admission (phase 1, 141 patients; phase 2, 136 patients). Recommendations of SSC 3-h bundle significantly improved between the two periods regarding lactate measurement (87% vs. 96%, P = 0.006), initiation of fluid resuscitation (36% vs. 65%, P < 0.001), blood cultures sampling (83% vs. 93%, P = 0.014), and administration of antibiotics (18% vs. 46%, P < 0.001). The Sequential Organ Failure Assessment score between H0 and H12 varied significantly more during phase 2 (1.9 ± 1.9 vs. 0.8 ± 2.6, P < 0.001). Mortality significantly decreased during the second phase, on day 3 (28% vs. 15%, P = 0.008) and on day 28 (40% vs. 28%, P = 0.013). Conclusion: Systematic detection, education, and per protocol organization with a sepsis unit dedicated to the early management of septic patients appear to improve compliance with SSC bundles, organ dysfunction, and short-term mortality. These results warrant to be confirmed by prospective studies.

Metagenomic Next-Generation Sequencing for Pathogens in Bronchoalveolar Lavage Fluid Improves the Survival of Patients with Pulmonary Complications After Allogeneic Hematopoietic Stem Cell Transplantation

INTRODUCTION

Unbiased metagenomic next-generation sequencing (mNGS) has been used for infection diagnosis. In this study, we explored the clinical diagnosis value of mNGS for pulmonary complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS

From August 2019 to June 2021, a prospective study was performed to comparatively analyze the pathogenic results of mNGS and conventional tests for bronchoalveolar lavage fluid (BALF) from 134 cases involving 101 patients with pulmonary complications after allo-HSCT.

RESULTS

More pathogens were identified by mNGS than with conventional tests (226 vs 120). For bacteria, the diagnostic sensitivity (P = 0.144) and specificity (P = 0.687) were similar between the two methods. For fungus except Pneumocystis jirovecii (PJ), conventional tests had a significantly higher sensitivity (P = 0.013) with a similarly high specificity (P = 0.109). The sensitivities for bacteria and fungi could be increased with the combination of the two methods. As for PJ, both the sensitivity (100%) and specificity (99.12%) of mNGS were very high. For viruses, the sensitivity of mNGS was significantly higher (P = 0.021) and the negative predictive value (NPV) was 95.74% (84.27-99.26%). Pulmonary infection complications accounted for 90.30% and bacterium was the most common pathogen whether in single infection (63.43%) or mixed infection (81.08%). The 6-month overall survival (OS) of 88.89% in the early group (mNGS ≤ 7 days) was significantly higher than that of 65.52% (HR 0.287, 95% CI 0.101-0.819, P = 0.006) in the late group (mNGS > 7 days).

CONCLUSIONS

mNGS for BALF could facilitate accurate and fast diagnosis for pulmonary complications. Early mNGS could improve the prognosis of patients with pulmonary complications after allo-HSCT.

TRIAL REGISTRATION

ClinicalTrials.gov identifier, NCT04051372.

Shortening identification times: comparative observational study of three early blood culture testing protocols

Background

While early appropriate antibiotic therapy is a proven means of limiting the progression of infections, especially bacteremia, empirical antibiotic therapy in sepsis is ineffective up to 30%. The aim of this study was to compare early blood culture testing protocols in terms of their ability to shorten the delay between blood sampling and appropriate antibiotic therapy.

Methods

In this french observational study, we compared three blood culture testing protocols. Positive blood cultures were tested using either GenMark ePlex panels (multiplex PCR period), a combination of MRSA/SA PCR, β-Lacta and oxidase tests (multitest period), or conventional identification and susceptibility tests only (reference period). Conventional identification and susceptibility tests were performed in parallel for all samples, as the gold standard.

Results

Among the 270 patients with positive blood cultures included, early and conventional results were in good agreement, especially for the multitest period. The delay between a blood culture positivity and initial results was 3.8 (2.9-6.9) h in the multiplex PCR period, 2.6 (1.3-4.5) h in the multitest period and 3.7 (1.8-8.2) h in the reference period (p<0.01). Antibiotic therapy was initiated or adjusted in 68 patients based on early analysis results. The proportion of patients receiving appropriate antibiotic therapy within 48 h of blood sampling was higher in the multiplex PCR and multitest periods, (respectively 90% and 88%) than in the reference period (71%).

Conclusion

These results suggest rapid bacterial identification and antibiotic resistance tests are feasible, efficient and can expedite appropriate antibiotic therapy.

A retrospective evaluation of the Euroarray STI-11 multiplex system for the detection of eight STI causing agents

With an incidence of more than > 1,000,000/day, sexually transmitted diseases remain a major challenge for health care systems worldwide. To reduce disease burden, complications, and spread, rapid diagnosis permitting early therapy is pivotal. The range of pathogens is wide and co-infections are common. This complicates pre-analytics, which are based on different laboratory techniques with potentially long turnaround times, e.g., cultivation and multistep serologies. Multiplex PCR provides the opportunity to overcome these limitations. In this study, we evaluated a novel assay, the Euroarray STI-11 microarray (EA; Euroimmun Medizinische Labordiagnostika), for the detection of eight obligate or facultative pathogens. Three-hundred-thirteen clinical specimens, which had been tested and pre-characterized for STI causing agents as part of routine diagnostics, were used as cases and controls in this retrospective study. The EA detected 34/44 Chlamydia trachomatis, 48/50 HSV-1, 50/50 HSV-2, 48/48 Mycoplasma hominis, 45/47 Neisseria gonorrhoeae, 9/11 Treponema pallidum, 46/46 Ureaplasma parvum, and 49/49 Ureaplasma urealyticum infections, respectively. 293 samples were EA positive, with polymicrobial infections (positive for two to six microbial or viral agents) detected in 130/293 cases. Specificities were 100% in the respective control groups (n = 18-48 depending on targeted pathogen) except for N. gonorrhoeae (25/26) and U. urealyticum (44/45). The broad spectrum of obligate and facultative pathogens targeted by the EA makes it a valuable tool in the setting of STI diagnostics and surveillance. The test has the potential to diagnose diseases neglected or overlooked in routine clinical practice. Besides a low sensitivity for C. trachomatis, the EA demonstrated high performance for all analyzed parameters. Further studies are warranted in order to capture a larger variety of the tested pathogens.

Contamination of Blood Cultures From Arterial Catheters and Peripheral Venipuncture in Critically Ill Patients: A Prospective Multicenter Diagnostic Study

BACKGROUND

Collecting blood cultures from indwelling arterial catheters is an attractive option in critically ill adult patients when peripheral venipuncture is difficult. However, whether the contamination proportion of blood cultures from arterial catheters is acceptable compared with that from venipuncture is inconclusive.

RESEARCH QUESTION

Is contamination of blood cultures from arterial catheters noninferior to that from venipuncture in critically ill adult patients with suspected bloodstream infection?

STUDY DESIGN AND METHODS

In this multicenter prospective diagnostic study conducted at five hospitals, we enrolled episodes of paired blood culture collection, each set consisting of blood drawn from an arterial catheter and another by venipuncture, were obtained from critically ill adult patients with cilinical indication. The primary measure was the proportion of contamination, defined as the number of false-positive results relative to the total number of procedures done. The reference standard for true bloodstream infection was blinded assessment by infectious disease specialists. We examined the noninferiority hypothesis that the contamination proportion of blood cultures from arterial catheters did not exceed that from venipuncture by 2.0%.

RESULTS

Of 1,655 episodes of blood culture from December 2018 to July 2021, 590 paired blood culture episodes were enrolled, and 41 of the 590 episodes (6.9%) produced a true bloodstream infection. In blood cultures from arterial catheters, 33 of 590 (6.0%) were positive, and two of 590 (0.3%) were contaminated; in venipuncture, 36 of 590 (6.1%) were positive, and four of 590 (0.7%) were contaminated. The estimated difference in contamination proportion (arterial catheter - venipuncture) was -0.3% (upper limit of one-sided 95% CI, +0.3%). The upper limit of the 95% CI did not exceed the predefined margin of +2.0%, establishing noninferiority (P for noninferiority < .001).

INTERPRETATION

Obtaining blood cultures from arterial catheters is an acceptable alternative to venipuncture in critically ill patients.

CLINICAL TRIAL REGISTRATION

University Hospital Medical Information Network Center (UMIN-CTR); No.: UMIN000035392; URL: https://center6.umin.ac.jp/.

Respiratory Syncytial Virus Infections in Neonates: A Persisting Problem

Respiratory syncytial virus (RSV) is the most common cause of lower respiratory tract infections in young infants. It is an enveloped, single-stranded, nonsegmented, negative-strand RNA virus, a member of the family Pneumoviridae. Globally, RSV is responsible for 2.3% of deaths among neonates 0-27 days of age. Respiratory syncytial virus infection is most common in children aged below 24 months. Neonates present with cough and fever. Respiratory syncytial virus-associated wheezing is seen in 20% infants during the first year of life of which 2-3% require hospitalization. Reverse transcriptase polymerase chain reaction (RT-PCR) gives fast results and has higher sensitivity compared with culture and rapid antigen tests and are not affected by passively administered antibody to RSV. Therapy for RSV infection of the LRT is mainly supportive, and preventive measures like good hygiene and isolation are the mainstay of management. Standard precautions, hand hygiene, breastfeeding and contact isolation should be followed for RSV-infected newborns. Recent AAP guidelines do not recommend pavilizumab prophylaxis for preterm infants born at 29-35 weeks without chronic lung disease, hemodynamically significant congenital heart disease and coexisting conditions. RSV can lead to long-term sequelae such as wheezing and asthma, associated with increased healthcare costs and reduced quality of life.

Evaluation of the Performance of the Novodiag® Stool Parasites Assay for the Detection of Intestinal Protozoa and Microsporidia

OBJECTIVES

We aimed to assess the performance of the Novodiag^® Stool Parasites (NSP) assay in the diagnosis of the most common intestinal protozoan and microsporidia infections.

METHODS

A panel of 167 selected stool samples was retrospectively analysed with the NSP assay and compared to routine microscopy and qPCR methods for the detection of pathogenic protozoa and microsporidia.

RESULTS

Whereas specificity was high for all protozoa and microsporidia, NSP sensitivity was strongly dependent on the comparative method used as reference. When compared to microscopic methods, NSP sensitivity was high (96.7 to 100%) for Blastocystis hominis, Entamoeba histolytica and Cyclospora cayetanensis but was lower for Giardia intestinalis (85.2%) and ≤50% for Cystoisospora belli and Dientamoeba fragilis. In comparison to conventional qPCR, the NSP assay demonstrated lower sensitivity characteristics dependent on parasite loads, reaching 60 to 70% for G. intestinalis, D. fragilis, Cryptosporidium spp. and E. histolytica. Sensitivity was 100% for Enterocytozoon bieneusi, but none of the five samples containing Encephalitozoon spp. were detected.

CONCLUSIONS

The overall performance of the NSP assay in the diagnosis of gastrointestinal protozoa and microsporidia seems to be better than or equivalent to that observed with microscopic methods but inferior to that obtainable with classical targeted qPCR.

Unexplained hypothermia is associated with bacterial infection in the Emergency Department

BACKGROUND

Early recognition and antibiotic therapy improve the prognosis of bacterial infections. Triage temperature in the Emergency department (ED) constitutes a diagnostic and prognostic marker of infection. The objective of this study was to assess the prevalence of community-acquired bacterial infections and the diagnostic ability of conventional biological markers in patients presenting to the ED with hypothermia.

METHODS

We conducted a retrospective single-center study over a 1-year period before the COVID-19 pandemic. Consecutive adult patients admitted to the ED with hypothermia (body temperature < 36.0 °C) were eligible. Patients with evident cause of hypothermia and patients with viral infections were excluded. Diagnosis of infection was based on the presence of at least two among the three following pre-defined criteria: (i) the presence of a potential source of infection, (ii) microbiology data, and (iii) patient outcome under antibiotic therapy. The association between traditional biomarkers (white blood cells, lymphocytes, C-reactive protein [CRP], Neutrophil to Lymphocyte Count Ratio [NLCR]) and underlying bacterial infections was evaluated using a univariate and a multivariate (logistic regression) analysis. Receiver operating characteristic curves were built to determine threshold values yielding the best sensitivity and specificity for each biomarker.

RESULTS

Of 490 patients admitted to the ED with hypothermia during the study period, 281 were excluded for circumstantial or viral origin, and 209 were finally studied (108 men; mean age: 73 ± 17 years). A bacterial infection was diagnosed in 59 patients (28%) and was mostly related to Gram-negative microorganisms (68%). The area under the curve (AUC) for the CRP level was 0.82 with a confidence interval (CI) ranging from 0.75 to 0.89. The AUC for the leukocyte, neutrophil and lymphocyte counts were 0.54 (CI: 0.45-0.64), 0.58 (CI: 0.48-0.68) and 0.74 (CI: 0.66-0.82), respectively. The AUC of NLCR and quick Sequential Organ Failure Assessment (qSOFA) reached 0.70 (CI: 0.61-0.79) and 0.61 (CI: 0.52-0.70), respectively. In the multivariate analysis, CRP ≥ 50 mg/L (OR: 9.39; 95% CI: 3.91-24.14; p < 0.01) and a NLCR ≥10 (OR: 2.73; 95% CI: 1.20-6.12; p = 0.02) were identified as independent variables associated with the diagnosis of underlying bacterial infection.

CONCLUSION

Community-acquired bacterial infections represent one third of diagnoses in an unselected population presenting to the ED with unexplained hypothermia. CRP level and NLCR appear useful for the diagnosis of causative bacterial infection.

Etiology and Multi-Drug Resistant Profile of Bacterial Infections in Severe Burn Patients, Romania 2018-2022

Infections in severe burns and their etiology are and will remain a big concern for the medical field. The multi-drug resistant strains of bacteria are a challenge of today's medicine. The aim of our study was to identify the etiological spectrum of bacterial infections in severe burn patients in Romania and their multi-drug resistant patterns. We performed a prospective study that included 202 adult patients admitted to the intensive care unit (ICU) of the Clinical Emergency Hospital of Plastic, Reconstructive Surgery and Burns, Bucharest, Romania (CEHPRSB), from 1 October 2018 to 1 April 2022, a period which includes the first 2 years of the outbreak of COVID-19. From each patient, wound swabs, endotracheal aspirates, blood for blood culture, and urine were collected. The most frequently isolated bacterium was Pseudomonas aeruginosa (39%), followed by Staphylococcus aureus (12%), Klebsiella spp. (11%), and Acinetobacter baumannii (9%). More than 90% of Pseudomonas aeruginosa and Acinetobacter baumannii were MDR, regardless of the clinical specimen from which they were isolated.

Improving Blood Culture Quality with a Medical Staff Educational Program: A Prospective Cohort Study

Purpose

Blood cultures (BCs) are essential laboratory tests for diagnosing blood stream infections. BC diagnostic improvement depends on several factors during the preanalytical phase outside of innovative technologies. In order to evaluate the impact of an educational program on BC quality improvement, a total of 11 hospitals across China were included from June 1st 2020 to January 31st 2021.

Methods

Each hospital recruited 3 to 4 wards to participate. The project was divided into three different periods, pre-implementation (baseline), implementation (educational activities administered to the medical staff) and post-implementation (experimental group). The educational program was led by hospital microbiologists and included professional presentations, morning meetings, academic salons, seminars, posters and procedural feedback.

Results

The total number of valid BC case report forms was 6299, including 2739 sets during the pre-implementation period and 3560 sets during the post-implementation period. Compared with the pre-implementation period, some indicators, such as the proportion of patients who had 2 sets or more, volume of blood cultured, and BC sets per 1000 patient days, were improved in the post-implementation period (61.2% vs 49.8%, 18.56 vs 16.09 sets, and 8.0 vs 9.0mL). While BC positivity and contamination rates did not change following the educational intervention (10.44% vs 11.97%, 1.86% vs 1.94%, respectively), the proportion of coagulase negative staphylococci-positive samples decreased in BSI patients (6.87% vs 4.28%).

Conclusion

Therefore, medical staff education can improve BC quality, especially increasing volume of blood cultured as the most important variable to determine BC positivity, which may lead to improved BSI diagnosis.

Acute Bacterial Meningitis in Healthy Adult Patients: A Prospective Cohort Study

Spontaneous bacterial meningitis (BM) is more common among patients with underlying conditions, but its characteristics in previously healthy patients are not well described. We analyzed the time trends of BM in terms of characteristics, and outcomes in patients without comorbidities.

PATIENTS AND METHODS

Single-center, prospective observational cohort study of 328 adults with BM hospitalized in a tertiary university hospital in Barcelona (Spain). We compared the features of infections diagnosed in 1982-2000 and 2001-2019. The main outcome measure was in-hospital mortality.

RESULTS

The median age of the patients increased from 37 to 45 years. Meningococcal meningitis significantly diminished (56% versus 31%, p < 0.000) whereas listerial meningitis increased (1.2% versus 8%, p = 0.004). Systemic complications were more common in the second period, although mortality did not vary significantly between periods (10.4% versus 9.2%). However, after adjusting for relevant variables, infection in the second period was associated with lower risk death.

CONCLUSIONS

Adult patients without underlying comorbidities that developed BM in recent years were older and more likely to have pneumococcal or listerial infections and systemic complications. In-hospital death was less likely in the second period, after adjusting for risk factors of mortality.

Necrotising pneumonia caused by Curvularia hawaiiensis (syn. Bipolaris hawaiiensis) and Mycobacterium tuberculosis coinfection in a patient with ascariasis: a case report and review

INTRODUCTION

Curvularia hawaiiensis (formerly Bipolaris hawaiiensis) is a plant pathogen often isolated from soil and vegetative material. However, only a few cases of opportunistic invasive infections in humans have been described.

CASE

A 16-year-old female patient without comorbidities was admitted to the emergency department because of fever and chest pain. We described the first coinfection of Curvularia hawaiiensis and Mycobacterium tuberculosis necrotising pneumonia.

DISCUSSION

Multiple infections can alter immune responses. However, immunosuppression is the most critical risk factor for infection with species of the genus Curvularia. Therefore, it is crucial to carefully examine patients with tuberculosis, as they may rarely be coinfected with unusual fungi.

Adenovirus-Associated Acute Interstitial Nephritis With Graft Survival and Novel Follow-Up Biopsy Findings Including Karyomegaly: A Case Series

Adenoviral infections in post-transplant patients have been described in multiple organ systems, most classically the lung, liver, and alimentary tract. In the genitourinary tract, hemorrhagic cystitis is most frequently observed. Clinically apparent renal involvement with adenovirus is rare, and adenovirus-associated interstitial nephritis (AAIN) is an uncommon cause of renal allograft failure. Here, we present three cases of AAIN in patients who, after prompt diagnosis and treatment adjustment, experienced a return of allograft function. All patients were on standard triple therapy with tacrolimus levels within the target range at the time of biopsy. None of the patients had respiratory symptoms, and despite diarrhea, colon biopsies were negative. Only case one had positive adenovirus serology (IgG only) and case three had positive urine; two patients had leukopenia without neutropenia. Renal biopsies showed a characteristic granulomatous tubulocentric mixed lymphocytic and neutrophilic infiltrate. Adenovirus immunohistochemistry (IHC) showed strong staining in the tubular epithelium (nuclear and cytoplasmic) while staining for polyomavirus was negative. A follow-up biopsy two months after the diagnosis of AAIN in one patient revealed persistent cytopathic effects with negative adenoviral IHC staining while a biopsy at one year in another patient showed glomerular and tubulointerstitial scarring. AAIN is an uncommon but important etiology to consider in cases of acute renal allograft dysfunction. Although the presenting symptoms for AAIN are nonspecific, hematuria is frequently noted. Adenovirus IHC should be considered in cases with granulomatous inflammation associated with necrosis and mixed inflammatory infiltrate. As demonstrated in this single-institution case series, prompt diagnosis can result in the preservation of the renal allograft. Lasting cytopathic effects after adenoviral infection should also be considered in patients with a history, or potential history, of AAIN.

Management of Lumbar Pyogenic Spondylodiscitis in Germany: A Cross-Sectional Analysis of Spine Specialists

OBJECTIVE

The incidence of pyogenic spondylodiscitis is increasing, and the disease is associated with considerable morbidity, mortality, long-term healthcare utilization and societal costs. Disease-specific treatment guidelines are lacking and there is little consensus regarding optimal conservative and surgical management. This cross-sectional survey of German specialist spinal surgeons sought to determine practice patterns and degree of consensus regarding the management of lumbar pyogenic spondylodiscitis (LPS).

METHODS

An electronic survey covering provider information, diagnostic approaches, treatment algorithms, and follow-up care of patients with LPS was distributed to members of the German Spine Society.

RESULTS

Seventy-nine survey responses were included in the analysis. Magnetic resonance imaging is the diagnostic imaging modality of choice for 87% of respondents; 100% routinely measure C-reactive protein in suspected LPS and 70% routinely take blood cultures before therapy initiation; 41% believe that surgical biopsy to obtain microbiological diagnosis should be carried out in all cases of suspected LPS, whereas 23% believe that surgical biopsy should only be carried out when empirical antibiotic therapy proves ineffective; 38% believe an intraspinal empyema should always be surgically evacuated, regardless of spinal cord compression. The median intravenous antibiotic duration is 2 weeks. The median total duration of the antibiotic therapy (intravenous and oral) is 8 weeks. Magnetic resonance imaging is the preferred imaging modality for follow-up of both conservatively and operatively treated LPS.

CONCLUSIONS

There exists considerable variation of care in the diagnosis, management, and follow-up of LPS among German spine specialists with little agreement on key aspects of care. Further research is required to understand this variation in clinical practice and to enhance the evidence base in LPS.

A descriptive pharmacokinetic/pharmacodynamic analysis of continuous infusion ceftazidime-avibactam for treating DTR gram-negative infections in a case series of critically ill patients undergoing continuous veno-venous haemodiafiltration (CVVHDF)

PURPOSE

To explore pharmacokinetic/pharmacodynamic (PK/PD) profile of continuous infusion (CI) ceftazidime-avibactam for treating difficult-to-treat resistant Gram-negative (DTR-GN) infections in critical patients undergoing continuous venovenous haemodiafiltration (CVVHDF).

MATERIALS AND METHODS

Patients treated with CI ceftazidime-avibactam for DTR-GN infections during CVVHDF were retrospectively assessed. Ceftazidime and avibactam concentrations were measured at steady-state and the free fraction (fC_ss) was calculated. Total clearance (CL_tot) of both agents were calculated and the impact of CVVHDF intensity was assessed by linear regression. The joint PK/PD target of ceftazidime-avibactam was defined as optimal when both fC_ss/MIC≥4 for ceftazidime and fC_ss/C_T > 1 for avibactam were achieved. Relationship between ceftazidime-avibactam PK/PD targets and microbiological outcome was assessed.

RESULTS

Eight patients with DTR-GN infections were retrieved. Median fC_ss were 84.5 (73.7-87.7 mg/L) for ceftazidime and 24.8 mg/L (20.7-25.8 mg/L) for avibactam. Median CL_tot was 2.39 L/h (2.05-2.96 L/h) for ceftazidime and 2.56 L/h (2.12-2.98 L/h) for avibactam. Median CVVHDF dose was 38.6 mL/h/kg (35.9-40.0 mL/kg/h). CL_tot were linearly correlated with CVVHDF dose (r = 0.53;p = 0.03, and r = 0.64;p = 0.006, respectively). The joint PK/PD targets were optimal granting microbiological eradication in all the assessable cases.

CONCLUSION

CI administration of 1.25-2.5 g q8h ceftazidime-avibactam may allow prompt attainment and maintenance of optimal joint PK/PD targets during high-intensity CVVHDF.

A Dedicated Mycosis Flask Increases the Likelihood of Identifying Candidemia Sepsis

Introduction: Candidemia is a severe condition associated with high mortality, and fungi are often not covered by empiric antimicrobial regimes for sepsis. Therefore, the shortest possible time to detection of yeast in the blood is of the essence. Materials and methods: We performed a cohort study of blood culture flasks drawn from patients aged 18 or older in the capital region of Denmark. In 2018 a blood cultures set consisted of two aerobic and two anaerobic flasks. This was changed in 2020 to two aerobic, one anaerobic, and one mycosis flask. We used time-to-event statistics to model time to positivity and compared 2018 with 2020; further, we stratified analyses on the blood culture system used (BacTAlert™ vs. BACTEC™) and high-risk vs. low-risk departments. Results: We included 175,416 blood culture sets and 107,077 unique patients. We found an absolute difference in the likelihood of identifying fungi in a blood culture set of 1.2 (95% CI: 0.72; 1.6) pr. 1.000 blood culture sets corresponding to the number needed to treat 853 (617; 1382). In high-risk departments, the absolute difference was profound, whereas it was negligible and statistically non-significant in low-risk departments 5.2 (95% CI: 3.4; 7.1) vs. 0.16 (−0.17; 0.48) pr. 1.000 blood culture sets. Conclusions: We found that including a mycosis flask in a blood culture set increases the likelihood of identifying candidemia. The effect was mainly seen in high-risk departments.

How to manage skin and soft-tissue infections in the emergency department

PURPOSE OF REVIEW

Our purpose is to review the state-of-the-art on the management of skin and soft tissue infections (SSTI) in emergency departments (ED).Although the information is scarce, SSTI may account for 3-30% of all cases presenting to an ED, of which 25-40% require hospital admission.SSTI include very different entities in aetiology, location, pathogenesis, extension, and severity. Therefore, no single management can be applied to them all. A simple approach is to classify them as non-purulent, purulent, and necrotising, to which a severity scale based on their systemic repercussions (mild, moderate, and severe) must be added.The initial approach to many SSTIs often requires no other means than anamnesis and physical examination, but imaging tests are an indispensable complement in many other circumstances (ultrasound, computerized tomography, magnetic resonance imaging…). In our opinion, an attempt at etiological filiation should be made in severe cases or where there is suspicion of a causality other than the usual one, with tests based not only on cultures of the local lesion but also molecular tests and blood cultures.

RECENT FINDINGS

Recent contributions of interest include the value of bedside ultrasound and the potential usefulness of biomarkers such as thrombomodulin to differentiate in early stages the presence of necrotising lesions not yet explicit.New antimicrobials will allow the treatment of many of these infections, including severe ones, with oral drugs with good bioavailability and for shorter periods.

SUMMARY

The ED has an essential role in managing SSTIs, in their classification, in decisions on when and where to administer antimicrobial treatment, and in the rapid convening of multidisciplinary teams that can deal with the most complex situations.

Polysegmental and multilevel lesions in hematogenous vertebral osteomyelitis: assessment of immediate and long-term results

Objective. To analyze the results of treatment of disseminated (polysegmental and multilevel) forms of hematogenous vertebral osteomyelitis (HVO) as compared with those of monosegmental and monovertebral lesions.

Material and Methods. A retrospective analysis of a monocenter cohort of 266 patients with hematogenous osteomyelitis of the spine for 2006 to 2019 was carried out. Patients were divided into two groups: Group A (polysegmental and multilevel lesions) included 33 (12.4 %) patients and Group B (monosegmental and monovertebral lesions) – 233 (87.6 %) patients. The main examination methods were: clinical, radiological (standardized roentgenography, CT), MRI, microbiological, histological and statistical ones.

Results. Comparison revealed that involvement of the cervical (p < 0.001) and thoracic (p = 0.014) spine was more typical for polysegmental and multilevel lesions. There was a tendency to the predominance of type A lesions according to the Pola classification in patients with local forms (p = 0.078) and to the increase in type C lesions in polysegmental and multilevel processes (p = 0.035). The number of neurological complications was higher in polysegmental and multilevel lesions (p = 0.003). There were no significant differences in the treatment results, the number of relapses and mortality rate between the compared groups.

Conclusion. Lesions of the cervical and thoracic spine and the presence of a neurological deterioration are typical for multilevel and polysegmental HVO. The formation of a multilevel lesion in different regions of the spine with a gap of 2–4 weeks or more requires a separate implementation of the diagnostic algorithm, defining of classification criteria and differentiated treatment tactics for each focus.

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.

Urinalysis exhibits excellent predictive capacity for the absence of urinary tract infection

OBJECTIVES

To assess predictive value of urinalysis for negative urine culture and absence of urinary tract infection, re-evaluate the microbial growth threshold for positive urine culture result, and describe antimicrobial resistance features. Urine culture is associated with 27% of U.S. hospitalizations, and unnecessary antibiotic prescription is a main antibiotic resistance contributor.

SUBJECTS AND METHODS

Urinalyses with urine culture from women ages 18-49 from 2013 to 2020 were studied. Clinically-diagnosed urinary tract infection (CUTI) was defined as 1) uropathogen growth, 2) documented diagnosis of urinary tract infection, and 3) antibiotic prescription. Sensitivity, specificity, and diagnostic predictive values were used to assess urinalysis performance in predicting isolation of a uropathogen by culture and in detection of CUTI.

RESULTS

12,252 urinalyses were included. 41% of urinalyses were associated with positive urine culture and 1287 (10.5%) with CUTI. Negative urinalysis exhibited high predictive accuracy for negative urine culture (specificity 90.3%, PPV 87.3%) and absence of CUTI (specificity 92.2%, PPV 97.4%). 24% of patients not meeting the CUTI definition were still prescribed antibiotics. 22% of cultures associated with CUTI exhibited growth less than 100,000 CFU/ml. Escherichia coli was implemented as causing 70% of CUTIs, and 4.2% of these produced an extended spectrum beta-lactamase.

CONCLUSIONS

Negative urinalysis exhibits high predictive accuracy for absence of CUTI. A reporting threshold of 10,000 CFU/ml is more clinically appropriate than a 100,000 CFU/ml cutpoint. Reflex culture based on urinalysis results could complement clinical judgement and improve laboratory and antibiotic stewardship in pre-menopausal women.

Impact of a strategy based on unique blood culture sampling on contamination rate and detection of bloodstream infections in critically ill patients

BACKGROUND

Unique blood culture (UBC) has been proposed to limit the number of venipuncture and to decrease the risk of BC contaminations (BCC) without affecting their yield. We hypothesized that a multi-faceted program based on UBC in the ICU may reduce the rate of contaminants with a similar performance for bloodstream infections (BSI) identification.

METHODS

In a before and after design, we compared the proportion of BSI and BCC. A first 3-year period with multi-sampling (MS) strategy followed by a 4-month washout period, where staff received education and training for using UBC, and a 32-month period, where UBC was routinely used, while education and feedback were maintained. During the UBC period, a large volume of blood (40 mL) was sampled through a unique venipuncture with additional BC collections discouraged for 48 h.

RESULTS

Of the 4,491 patients included (35% female patients, mean age 62 years) 17,466 BC were collected. The mean volume of blood per bottle collected increased from 2.8 ± 1.8 mL to 8.2 ± 3.9 mL between the MS and UBC periods, P < 0.01. A 59.6% reduction (95% CI 56.7-62.3; P < 0.001) of BC bottles collected per week was observed between the MS and UBC periods. The rate of BCC per patient decreased between the two periods from 11.2% to 3.8% (73.4% reduction; P < 0.001) for the MS and UBC periods, P < 0.001. Meanwhile, the rate of BSI per patient remained stable at 13.2% and 13.2% for the MS and UBC periods, P = 0.98.

CONCLUSIONS

In ICU patients, a strategy based on UBC reduces the contamination rate of cultures without affecting their yield.

Multidimensional analysis using low-dose computed tomography to evaluate the severity of Mycoplasma pneumoniae pneumonia in children

Background

It is unclear whether local pathological pulmonary changes truly reflect the severity of childhood Mycoplasma pneumoniae infection, which is characterized by rapid progress and potential mortality. This study multi-dimensionally analyzed low-dose computed tomography findings to assess the severity of Mycoplasma pneumoniae infection and predict its progress in such patients.

Methods

In all, 752 children with Mycoplasma pneumoniae pneumonia (MPP) who underwent low-dose computed tomography examinations from February 2016 to July 2020 were retrospectively enrolled to conduct a cohort study. Clinical and radiological variables were analyzed using univariate analysis, and radiological variables were further analyzed using multivariable logistic regression in severe cases. Then, the correlation between the key computed tomography features and clinical symptoms, laboratory indicators, and medical costs were assessed using the chi-squared and Kruskal-Wallis H tests. Kaplan-Meier curves and Cox regression models were created to evaluate the correlations between the key computed tomography features, fever duration, and the length of hospital stay.

Results

Of the 752 included patients, 16.2% (122/752) developed severe MPP. Atelectasis, pleural effusion, and lung consolidation occurred in 9.7% (73/752), 15.8% (119/752), and 90.3% (679/752) of patients, respectively. In addition to pleural effusion, the number of lobes of lung consolidation was the highest risk feature of severe MPP. Patients with consolidation in 2, 3, and 4 lobes had a 1.0-, 3.1-, and 7.5-fold increased risk of severe MPP, compared with patients with consolidation in fewer than 1 lobe. The duration of fever prior to admission had no effect on the proportions of the lobar consolidation (P=0.14) but did have significant effect on the incidence of pleural effusion (P=0.004). Levels of inflammatory markers and medical costs rose consistently with the increase in the number of lobar consolidations (P<0.001). After adjustments for pleural effusion, 1, 2, 3, and 4 lobes of consolidation remained positively associated with fever duration [1 lobe: hazard ratio (HR) =1.55, 95% CI: 1.10-2.18; 2 lobes: HR =1.65, 95% CI: 1.13-2.42l; 3 lobes: HR =1.82, 95% CI: 1.11-2.98; 4 lobes: HR =2.87, 95% CI: 1.25-6.61] compared to 0 lobes of consolidation. Compared to 0 lobes of consolidation, 1, 2, 3, and 4 lobes of consolidation were also positively correlated with the length of hospital stay (1 lobe: HR =2.24, 95% CI: 1.73-2.89; 2 lobes: HR =2.56, 95% CI: 1.91-3.43; 3 lobes: HR =2.87, 95% CI: 1.90-4.32; 4 lobes: HR =4.12, 95% CI: 2.01-8.46).

Conclusions

Lobar consolidation is a stable and reliable computed tomography feature that can be used to assess the severity of MPP in children. Quantitative analysis of lobar consolidation can comprehensively and accurately predict the progression of Mycoplasma pneumoniae. Low-dose computed tomography is recommended for children with severe MPP with complicated courses.

Empiric versus culture-based antibiotic therapy for UTIs in menopausal women

PURPOSE

To assess the benefits and risks associated with empiric prescription of antibiotic therapy for treatment of a urinary tract infection (UTI).

METHODS

Following IRB approval menopausal women presenting with a symptomatic UTI to a single urology clinic were prospectively assigned to one of the two treatment groups based on day of presentation: culture-based treatment (CB) (Monday, Tuesday, Wednesday) or empiric treatment (ET) (Thursday, Friday) and started on nitrofurantoin (NF) pending culture results. Both groups were contacted at 7 and 14 days following treatment. Side effects and answers to a standardized questionnaire (UTISA) were recorded. Success was defined as a total UTISA score < 3. Any NF retreatment, use of another antibiotic therapy, or extension of the original antibiotic course was considered treatment failures.

RESULTS

From July 2020 to March 2022, 65 women with 80 UTI events were included in the study, with CB treatment used for 60 UTIs and ET used for 23 UTIs. At 7 days after start of treatment, questionnaire failure rate was 44% (20/45) for the CB group and 16% (3/19) for the ET group (P = 0.076). At 14 days following start of treatment, questionnaire failure rate was 31% (13/42) for the CB group and 17% (3/18) for the ET group (P = 0.3). In the ET group, 11% of cultures were found to be resistant to NF.

CONCLUSION

Outcomes for the empiric treatment of uncomplicated UTI with NF at both 7 and 14 days are not significantly different than outcomes with culture-based treatment.

Use of Severe Acute Respiratory Syndrome Coronavirus 2 Antibody Tests by US Infectious Disease Physicians: Results of an Emerging Infections Network Survey, March 2022

Background

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibody tests have had limited recommended clinical application during the coronavirus disease 2019 (COVID-19) pandemic. To inform clinical practice, an understanding is needed of current perspectives of United States-based infectious disease (ID) physicians on the use, interpretation, and need for SARS-CoV-2 antibody tests.

Methods

In March 2022, members of the Emerging Infections Network (EIN), a national network of practicing ID physicians, were surveyed on types of SARS-CoV-2 antibody assays ordered, interpretation of test results, and clinical scenarios for which antibody tests were considered.

Results

Of 1867 active EIN members, 747 (40%) responded. Among the 583 who managed or consulted on COVID-19 patients, a majority (434/583 [75%]) had ordered SARS-CoV-2 antibody tests and were comfortable interpreting positive (452/578 [78%]) and negative (405/562 [72%]) results. Antibody tests were used for diagnosing post-COVID-19 conditions (61%), identifying prior SARS-CoV-2 infection (60%), and differentiating prior infection and response to COVID-19 vaccination (37%). Less than a third of respondents had used antibody tests to assess need for additional vaccines or risk stratification. Lack of sufficient evidence for use and nonstandardized assays were among the most common barriers for ordering tests. Respondents indicated that statements from professional societies and government agencies would influence their decision to order SARS-CoV-2 antibody tests for clinical decision making.

Conclusions

Practicing ID physicians are using SARS-CoV-2 antibody tests, and there is an unmet need for clarifying the appropriate use of these tests in clinical practice. Professional societies and US government agencies can support clinicians in the community through the creation of appropriate guidance.

Use and Cost Analysis of Comprehensive Respiratory Panel Testing in a Pediatric Emergency Department

OBJECTIVES

Fever and respiratory infections are among the leading causes of pediatric emergency department visits and hospitalizations. Although typically self-resolving, clinicians may perform diagnostic tests to determine microbial etiologies of these illnesses. Although comprehensive respiratory viral panels can quickly identify causative organisms, cost to the hospital and patient may be significant. The objective of this study was to analyze the financial impact of comprehensive respiratory viral panel use in relation to associated clinical outcomes.

METHODS

This study was a single-center, retrospective chart review of pediatric emergency department patients who were evaluated between October 1, 2016, and April 30, 2018, with International Classification of Diseases, Tenth Revision (ICD-10) code diagnoses of acute upper respiratory infection, fever unspecified, and/or bronchiolitis. Our primary outcome was the effect of comprehensive respiratory viral panel testing and results on the total health care charge to patients. Secondary outcomes were the effect of comprehensive respiratory viral panel testing and results on emergency department length of stay and antimicrobial use.

RESULTS

A total of 5766 visits were included for primary analysis, with 229 (4%) undergoing comprehensive respiratory viral panel testing. Of these, 163 had a positive result (71%) for at least 1 organism. The total cost was significantly higher in the group that underwent comprehensive respiratory viral panel testing ($643.39 [$534.18-$741.15] vs $295.15 [$249.72-$353.92]; P < 0.001). There was no decrease in emergency department length of stay or significant change in antimicrobial use associated with comprehensive respiratory viral panel use.

CONCLUSIONS

This study demonstrates that the utilization of comprehensive respiratory viral panels in pediatric emergency department patients with bronchiolitis, unspecified fever, and/or acute upper respiratory infection adds significant cost to patient care without a decrease in their length of stay or antimicrobial use. Further studies are needed to determine the appropriate targeted use of comprehensive respiratory viral panels.

Droplet Encoding-Pairing Enabled Multiplexed Digital Loop-Mediated Isothermal Amplification for Simultaneous Quantitative Detection of Multiple Pathogens

Despite the advantages of digital nucleic acid analysis (DNAA) in terms of sensitivity, precision, and resolution, current DNAA methods commonly suffer a limitation in multiplexing capacity. To address this issue, a droplet encoding-pairing enabled DNAA multiplexing strategy is developed, wherein unique tricolor combinations are deployed to index individual primer droplets. The template droplets and primer droplets are sequentially introduced into a microfluidic chip with a calabash-shaped microwell array and are pairwise trapped and merged in the microwells. Pre-merging and post-amplification image analysis with a machine learning algorithm is used to identify, enumerate, and address the droplets. By incorporating the amplification signals with droplet encoding information, simultaneous quantitative detection of multiple targets is achieved. This strategy allows for the establishment of flexible multiplexed DNAA by simply adjusting the primer droplet library. Its flexibility is demonstrated by establishing two multiplexed (8-plex) droplet digital loop-mediated isothermal amplification (mddLAMP) assays for individually detecting lower respiratory tract infection and urinary tract infection causative pathogens. Clinical sample analysis shows that the microbial detection outcomes of the mddLAMP assays are consistent with those of the conventional assay. This DNAA multiplexing strategy can achieve flexible high-order multiplexing on demand, making it a desirable tool for high-content pathogen detection.

Bacterial Co-Infections and Antimicrobial Resistance in Patients Hospitalized with Suspected or Confirmed COVID-19 Pneumonia in Kazakhstan

Our study was carried out to characterize respiratory tract microbiota in patients with “COVID-like pneumonia” in Kazakhstan and analyze differences between COVID-19 positive and negative groups. Sputum samples were collected from hospitalized patients, ≥18 years old, in the three cities in Kazakhstan with the highest COVID-19 burden in July 2020. Isolates were identified by MALDI-TOF MS. Susceptibility testing was performed by disk diffusion. We used SPSS 26 and MedCalc 19 for statistical analysis. Among 209 patients with pneumonia, the median age was 62 years and 55% were male. RT-PCR-confirmed SARS-CoV-2 cases were found in 40% of patients, and 46% had a bacterial co-infection. Co-infection was not associated with SARS-CoV-2 RT-PCR test results, but antibiotic use was. The most frequent bacteria were Klebsiella pneumoniae (23%), Escherichia coli (12%), and Acinetobacter baumannii (11%). Notably, 68% of Klebsiella pneumoniae had phenotypic evidence of extended-spectrum beta-lactamases in disk diffusion assays, 87% of Acinetobacter baumannii exhibited resistance to beta-lactams, and >50% of E. coli strains had evidence of ESBL production and 64% were resistant to fluoroquinolones. Patients with a bacterial co-infection had a higher proportion of severe disease than those without a co-infection. The results reinforce the importance of using appropriate targeted antibiotics and effective infection control practices to prevent the spread of resistant nosocomial infections.

Empirical treatment and mortality in bacteremia due to extended spectrum β-lactamase producing Enterobacterales (ESβL-E), a retrospective cross-sectional study in a tertiary referral hospital from Colombia

BACKGROUND

Infections caused by extended spectrum β-lactamase (ESβL) producing bacteria are common and problematic. When they cause bloodstream infections, they are associated with significant morbidity and mortality.

METHODS

A retrospective cross-sectional observational study was conducted in a single center in Pereira, Colombia. It included people hospitalized with bacteremia due to gram-negative bacilli with the extended-spectrum β-lactamase producing phenotype. A logistic regression analysis was constructed. Clinical characteristics and risk factors for death from sepsis were established.

RESULTS

The prevalence of bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype was 17%. 110 patients were analyzed. Most patients were men (62%) with a median age of 58 years, hospital mortality was 38%. Admission to intensive care was 45%. The following risk factors for mortality were established: shock requiring vasoactive support, Pitt score > 3 points, and not having an infectious disease consultation (IDC).

CONCLUSIONS

bacteremia due to Enterobacterales with extended-spectrum β-lactamase producing phenotype have a high mortality. Early recognition of sepsis, identification of risk factors for antimicrobial resistance, and prompt initiation of appropriate empiric antibiotic treatment are important. An infectious disease consultation may help improve outcomes.

Best methods for urine sample collection for diagnostic accuracy in women with urinary tract infection symptoms: a systematic review

BACKGROUND

Most guidelines recommend a midstream urine (MSU) or a midstream clean-catch (MSCC) sample for urinalysis. However, whether this sample is better than others is still controversial.

OBJECTIVES

To assess the most adequate non-invasive method to collect a urine specimen for diagnosing urinary tract infections (UTI) in symptomatic non-pregnant women.

METHODS

This review was conducted according to the Systematic Reviews of Diagnostic Test Accuracy guidelines (PROSPERO CRD42021241758). PubMed was searched paired sample studies and controlled trials. Studies comparing MSCC, MSU without cleaning, first-void urine, and random voiding samples were considered. Studies evaluating invasive methods were excluded. The main outcome was diagnostic accuracy of urine cultures. Contamination rates were evaluated. The risk of bias tool for systematic reviews on diagnostic accuracy (QUADAS-2) was assessed.

RESULTS

Six studies including 1,010 patients were evaluated. Only two studies used paired samples. No study was considered as having low risk of bias. There was no difference in contamination for MSU specimens collected with or without cleansing and between random void urine collection and MSCC. In one study comparing first-void urine with MSU samples, the contamination rate was lower in the latter, but the gold standard of urine culture was only used for one sampling collection.

CONCLUSIONS

To the best of our knowledge, this systematic review is the first to assess the evidence available from different exclusively non-invasive urine sampling. Despite being widely recommended, our review did not find consistent evidence that asking women to provide midstream samples with or without cleansing is better.

Gram Stain and Culture of Sputum Samples Detect Only Few Pathogens in Community-Acquired Lower Respiratory Tract Infections: Secondary Analysis of a Randomized Controlled Trial

Identification of the bacterial etiology of lower respiratory tract infections (LRTI) is crucial to ensure a narrow-spectrum, targeted antibiotic treatment. However, Gram stain and culture results are often difficult to interpret as they depend strongly on sputum sample quality. We aimed to investigate the diagnostic yield of Gram stain and culture from respiratory samples collected by tracheal suction and expiratory technique from adults admitted with suspected community-acquired LRTI (CA-LRTI). In this secondary analysis of a randomized controlled trial, 177 (62%) samples were collected by tracheal suction, and 108 (38%) by expiratory technique. We detected few pathogenic microorganisms, and regardless of sputum quality, there were no significant differences between the sample types. Common pathogens of CA-LRTI were identified by culture in 19 (7%) samples, with a significant difference between patients with or without prior antibiotic treatment (p = 0.007). The clinical value of sputum Gram stain and culture in CA-LRTI is therefore questionable, especially in patients treated with antibiotics.

Regulatory Approach to Point-of-Care/At-Home Testing in the United States

The Clinical Laboratory Improvement Amendments (CLIA) classifications were activated in the 1990s in partnership with the Centers for Medicare and Medicaid Services and Food and Drug Administration and included waived, moderate, and high complexity testing. The waived section of CLIA certificates allows laboratories to perform testing of analytes and methods of samples by the Food and Drug Administration. During the COVID-19 pandemic, many molecular or antigen laboratory testing methods for COVID-19 virus were quickly approved by emergency use authorization. Waived testing is now done in highly complex, moderately complex, and waived testing laboratories, and some at-home testing.

IPVS policy statement on HPV nucleic acid testing guidance for those utilising/considering HPV as primary precancer screening: Quality assurance and quality control issues

We advise that only clinically validated HPV assays which have fulfilled internationally accepted performance criteria be used for primary cervical screening. Further, assays should be demonstrated to be fit for purpose in the laboratory in which they will ultimately be performed, and quality materials manuals and frameworks will be helpful in this endeavor. Importantly, there is a fundamental shortage of well validated, low-cost, low complexity HPV tests that have demonstrated utility in a near-patient setting; representing a significant challenge and focus for future development in order to reach the WHO's goal of eliminating cervical cancer.

Evaluation of hospital blood culture utilization rates to identify opportunities for diagnostic stewardship

OBJECTIVES

To evaluate the pattern of blood-culture utilization among a cohort of 6 hospitals to identify potential opportunities for diagnostic stewardship.

METHODS

We completed a retrospective analysis of blood-culture utilization during adult inpatient or emergency department (ED) encounters in 6 hospitals from May 2019 to April 2020. We investigated 2 measures of blood-culture utilization rates (BCURs): the total number of blood cultures, defined as a unique accession number per 1,000 patient days (BCX) and a new metric of blood-culture events per 1,000 patient days to account for paired culture practices. We defined a blood-culture event as an initial blood culture and all subsequent samples for culture drawn within 12 hours for patients with an inpatient or ED encounter. Cultures were evaluated by unit type, positivity and contamination rates, and other markers evaluating the quality of blood-culture collection.

RESULTS

In total, 111,520 blood cultures, 52,550 blood culture events, 165,456 inpatient admissions, and 568,928 patient days were analyzed. Overall, the mean BCUR was 196 blood cultures per 1,000 patient days, with 92 blood culture events per 1,000 patient days (range, 64-155 among hospitals). Furthermore, 7% of blood-culture events were single culture events, 55% began in the ED, and 77% occurred in the first 3 hospital days. Among all blood cultures, 7.7% grew a likely pathogen, 2.1% were contaminated, and 5.9% of first blood cultures were collected after the initiation of antibiotics.

CONCLUSIONS

Blood-culture utilization varied by hospital and was heavily influenced by ED culture volumes. Hospital comparisons of blood-culture metrics can assist in identifying opportunities to optimize blood-culture collection practices.

The clinical implications of bacterial pathogenesis and mucosal immunity in chronic urinary tract infection

Urinary tract infections (UTIs) exert a significant health and economic cost globally. Approximately one in four people with a previous history of UTI continue to develop recurrent or chronic infections. Research on UTI has primarily concentrated on pathogen behavior, with the focus gradually shifting to encompass the host immune response. However, these are centered on mouse models of Escherichia coli infection, which may not fully recapitulate the infective etiology and immune responses seen in humans. The emerging field of the urobiome also inadvertently confounds the discrimination of true UTI-causing pathogens from commensals. This review aims to present a novel perspective on chronic UTI by linking microbiology with immunology, which is commonly divergent in this field of research. It also describes the challenges in understanding chronic UTI pathogenesis and the human bladder immune response, largely conjectured from murine studies. Lastly, it outlines the shortcomings of current diagnostic methods in identifying individuals with chronic UTI and consequently treating them, potentially aggravating their disease due to mismanagement of prior episodes. This discourse highlights the need to consider these knowledge gaps and encourages more relevant studies of UTIs in humans.

Epidemiology of bacteremia in a pediatric population - A 10-year study

INTRODUCTION

With the widespread introduction of conjugate meningococcal and pneumococcal vaccines, the prevalence and etiology of invasive bacterial infections have changed. We aimed to review all cases of bacteremia in a level II pediatric department over a ten-year period in the post-pneumococcal conjugate vaccine era.

METHODS

We reviewed all positive blood cultures (BC) obtained in our department between 2007 and 2016. Results were classified as contaminants, potential pathogens or confirmed pathogens, based on species, number of positive BC in the episode and the patients' medical history. Demographic and clinical data were collected for patients with identified pathogens.

RESULTS

A total of 638 positive BC were identified (6.6% of total BC); 120 (1.2%) were considered to represent true bacteremia. The most frequently identified microorganism was Streptococcus pneumoniae (29.2%), with a decrease in the number of cases between 2008 and 2015. Staphylococcus aureus was the second most common organism (19.2%) being 21.7% of these methicillin-resistant. Escherichia coli was the most common isolate in children aged less than three months.

CONCLUSION

We found a rate of true bacteremia in children similar to recent studies. Although Streptococcus pneumoniae remains the most common microorganism, its prevalence may be declining. Monitoring microbiological data in children has implications in practice, particularly in local antibiotic prescription.

Mucormycosis threats: A systemic review

During the catastrophic wave of Coronavirus disease 2019, health agencies started to report an infrequent but lethal mucormycosis or black fungal infection. Primarily, it causes sinusitis by affecting nasal, oral, lung, brain, ocular, and other body tissues. It becomes more fatal, especially in diabetic, cancer, and immune-compromised patients. Before 2020, the prevalence of mucormycosis was very rare but it has rapidly emerged globally from late 2020 to mid-2021. Recently, the mucormycosis got worse and epidemic with more than 30,000 cases reported across India. The etiology of infection can be diagnosed by molecular, serological, microscopic, and clinical methods. However, early diagnosis of this ailment is still a challenging task due to no standalone diagnostic tool available along with clinical manifestations of the ailment resembling other fungal diseases. The treatment of mucormycosis is also challenging and frequently requires long-term treatment. Amphotericin B was found to be an effective antifungal for preventing mucormycosis but it failed if infection disseminated to necrotizing tissues or adjacent organs. Removal of infected tissue/organ by surgery is an alternative treatment to control mucormycosis. In addition, reversal of underlying predisposing conditions based on therapy is also in practice for its prevention. This review highlights different aspects of mucormycosis such as pathogenesis, diagnosis, treatment, and their challenges and so on. We also emphasized the epidemiological shift during the recent outbreak and its influence on the different regions of India.

The Impact of the COVID-19 Pandemic on Respiratory Syncytial Virus Infection: A Narrative Review

Respiratory syncytial virus (RSV) is one of the most common respiratory viruses. It not only affects young children but also the elderly and immunocompromised patients. After the emergence of SARS-CoV-2 and the corona virus disease 2019 (COVID-19) era, a dramatic reduction in RSV activity was found, which coincided with the implementation of public health and social measures (PHSMs). However, the correlation is more complicated than we initially thought. After PHSMs were gradually lifted, a seasonality shift and a delayed RSV outbreak with greater number of infected patients were found in numerous countries, such as Israel, Australia, South Africa, New Zealand, France, United States, and Japan. Several hypotheses and possible reasons explaining the interaction between SARS-CoV-2 and RSV were mentioned. Since RSV vaccinations are still under investigation, administration of palivizumab should be considered in high-risk patients. In the post-COVID-19 era, greater attention should be paid to a further resurgence of RSV. In this narrative review, we conducted a thorough review of the current knowledge on the epidemiology of RSV during the COVID-19 era, the out-of-season outbreak of RSV, and the data on co-infection with RSV and SARS-CoV-2.

Pulmonary hypertension at admission predicts ICU mortality in elderly critically ill with severe COVID-19 pneumonia: retrospective cohort study

BACKGROUND

Point-of-care ultrasound (POCUS) is a useful diagnostic tool for non-invasive assessment of critically ill patients. Mortality of elderly patients with COVID-19 pneumonia is high and there is still scarcity of definitive predictors. Aim of our study was to assess the prediction value of combined lung and heart POCUS data on mortality of elderly critically ill patients with severe COVID-19 pneumonia.

METHODS

This was a retrospective observational study. Data of patients older than 70 years, with severe COVID-19 pneumonia admitted to mixed 25-bed, level 3, intensive care unit (ICU) was analyzed retrospectively. POCUS was performed at admission; our parameters of interest were pulmonary artery systolic pressure (PASP) and presence of diffuse B-line pattern (B-pattern) on lung ultrasound.

RESULTS

Between October 2020 and March 2021, 117 patients aged 70 years or more (average age 77 ± 5 years) were included. Average length of ICU stay was 10.7 ± 8.9 days. High-flow oxygenation, non-invasive ventilation and invasive mechanical ventilation were at some point used to support 36/117 (31%), 39/117 (33%) and 75/117 (64%) patients respectively. ICU mortality was 50.9%. ICU stay was shorter in survivors (8.8 ± 8.3 vs 12.6 ± 9.3 days, p = 0.02). PASP was lower in ICU survivors (32.5 ± 9.8 vs. 40.4 ± 14.3 mmHg, p = 0.024). B-pattern was more often detected in non-survivors (35/59 (59%) vs. 19/58 (33%), p = 0.005). PASP and B-pattern at admission, and also mechanical ventilation and development of VAP, were univariate predictors of mortality. PASP at admission was an independent predictor of ICU (OR 1.061, 95%CI 1.003-1.124, p = 0.039) and hospital (OR 1.073, 95%CI 1.003-1.146, p = 0.039) mortality.

CONCLUSIONS

Pulmonary artery systolic pressure at admission is an independent predictor of ICU and hospital mortality of elderly patients with severe COVID-19 pneumonia.

Development of Quality Indicators to Evaluate the Appropriateness of Empiric Antimicrobial Use in Pediatric Patients

Background

Use of quality indicators is one strategy recommended to assess antimicrobial prescribing for pediatric inpatients.

Objective

To achieve consensus from infectious diseases clinicians on quality indicators that characterize appropriate empiric antimicrobial use for the management of infectious syndromes in pediatric inpatients.

Methods

This study was completed using the Delphi technique. The research team developed an initial list of quality indicators, informed by a literature search. A multidisciplinary group of health care providers with expertise in infectious diseases was invited to participate. The list was disseminated to this panel of experts using Opinio survey software. The experts were asked to rate the indicators on a 9-point Likert scale in relation to the following criterion: "The importance of each item in determining appropriateness considering benefit or harm at the individual or population level". Consensus was defined as at least 75% agreement and a median score of 7 or higher.

Results

Twelve of 31 invited experts completed at least 1 round of the survey, and 10 completed all rounds. Consensus was achieved on 28 of 31 proposed indicators after 3 rounds. Indicators with consensus were categorized under "empiric choice" (n = 12 indicators), "dose" (n = 5), "duration" (n = 2), "administration" (n = 4), "diagnosis" (n = 2), and "documentation" (n = 3). Six of the indicators for which consensus was achieved were rephrased by the experts.

Conclusions

Consensus was achieved on quality indicators to assess the appropriateness of empiric antimicrobial use in pediatric patients. Clinicians and researchers can use these consensus-based indicators to assess adherence to best practice.

Evaluation of the Diagnostic Performance of mNGS in Detecting Intra-Abdominal Infections of the Emergency Department Patients

Purpose

Intra-abdominal infections (IAI) are gradually becoming common in the emergency department, though the incidence is low and the prognosis is fair, as the symptoms are similar to other intra-abdominal diseases, rapid and accurate diagnosis of the causative agents is essential for clinical management. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in detecting IAI in the emergency department.

Patients and Methods

This was a retrospective, single-centered study including patients admitted to the emergency department from January 1st, 2021 to August 31st, 2022 with diagnosis of IAI. The comparison between mNGS and microbial culture using paracentesis fluid samples was performed to evaluate the diagnostic performance of mNGS for IAI. Meanwhile, paracentesis fluid and peripheral blood mNGS were compared to explore the sample specificity. Further, the microbial community structure of the patients with pyogenic liver abscesses (PLA) was analyzed.

Results

Thirty-four IAI patients including 23 with pyogenic liver abscesses (PLA), 3 with parapancreatic abscesses, and 8 with other IAI were included in this study. Compared with the conventional microbial culture of paracentesis fluid, mNGS using paracentesis fluid detected more positive cases of IAI (93.75% vs 81.25%), and identified more species of pathogens, especially in obligate anaerobes and viral pathogens. Peripheral blood mNGS presented a relatively high consistency with the paracentesis fluid mNGS (91% mutual positive). The microbial community structure of PLA patients with diabetes is less diverse than that of those without diabetes. Patients with diabetes are at high risk of PLA caused by Klebsiella pneumonia.

Conclusion

mNGS has advantages in detecting IAI in the emergency department, and peripheral blood mNGS can be a non-invasive choice for early diagnosis.