Comparison of 16S Ribosomal RNA Targeted Sequencing and Culture for Bacterial Identification in Normally Sterile Body Fluid Samples: Report of a 10-Year Clinical Laboratory Review

Suture Contamination During Arthroscopic Rotator Cuff Repair Is Associated With Significantly Higher Retear Rates in Magnetic Resonance Imaging: A Matched-Pair Analysis

PURPOSE

To evaluate the correlation between suture contamination and rotator cuff tendon retear after arthroscopic rotator cuff repair.

METHODS

Patients undergoing primary arthroscopic rotator cuff repair from April 1, 2020, to September 30, 2022, were enrolled. Those younger than 18 years, with a history of shoulder surgeries or shoulder infection episodes, or who declined participation were excluded. A 5-cm section of the first-cut suture, originating from the anchor eyelet ends, in each rotator cuff repair surgery was subjected to bacteria culture and polymerase chain reaction analysis. Patients with positive culture findings were matched 1:1 to those with negative culture reports based on age, sex, tear size as well as involved tendons, preoperative fatty infiltration grade (Goutallier grade), and preoperative muscle atrophy grade (Warner score). Postoperative rotator cuff tendon retear assessments were conducted at the 6-month mark using the Sugaya classification via magnetic resonance imaging. The Wilcoxon signed-rank test was used for matched-pair comparisons between the groups.

RESULTS

A total of 141 patients (60 men and 81 women) with a mean age of 61.0 ± 8 years were finally enrolled. Twenty-six patients (18 men and 8 women) had a positive culture, while 115 patients (42 men and 73 women) had a negative culture. After the propensity score matching process, 24 culture-negative patients (16 men and 8 women) were selected as the culture-negative group. Age, fatty infiltration grade, and muscle atrophy grade were not significantly different between matched groups. The retear grade in the culture-positive group was significantly higher than that in the culture-negative group (P = .020) under the matched-pair comparison. Cutibacterium acnes was the most prevalent bacterial species responsible for suture contamination.

CONCLUSIONS

The matched-pair analysis revealed that the presence of bacterial contamination on sutures was associated with a higher risk of retear on magnetic resonance imaging following arthroscopic rotator cuff repair.

LEVEL OF EVIDENCE

Level III, retrospective cohort study.

Development of a scoring system to identify high-yield specimens for bacterial broad-range 16S rRNA gene PCR with sequencing at a tertiary care medical center

OBJECTIVES

Broad-range bacterial polymerase chain reaction with sequencing (BRBPS) provides valuable diagnostic data, especially in cases of culture-negative infections. However, as BRBPS testing demonstrates generally low positivity, cost per impactful result can be high and commonly involves longer turnaround times compared with other methods, targeting use of this assay to high-yield situations remains a challenging goal. Diagnostic stewardship can help alleviate these challenges and increase clinical utility, yet not all laboratories have a dedicated stewardship team, and little formal guidance exists on identifying high-yield samples outside of specific clinical syndromes. In this study, we performed a retrospective review of 86 BRBPS orders from a tertiary care medical center, with a focus on identifying high-yield cases using an infectious markers scoring system, visualized inflammation or organism (VIO) score, to predict return of actionable diagnostic data.

METHODS

Using chart review, we evaluated how results from high VIO score or low VIO score specimens contributed to clinical management.

RESULTS

Testing low VIO score samples identified an organism in only 10% of samples, and of these positive results, 33% were considered to represent contamination. Despite negative routine workup and no identified pathogen via BRBPS, broad antimicrobial treatment was continued in 85% of cases with a low VIO score. In contrast, specimens with high VIO scores were more predictably positive by BRBPS, identified organisms that were universally considered pathogens, and provided opportunities to target or de-escalate antimicrobial therapy.

CONCLUSIONS

This study describes the VIO scoring system to guide the identification of high-yield samples and steward the appropriate use of BRBPS testing.

Bloodstream infection, peritonitis, and pneumonia caused by Pasteurella multocida in a patient with liver cirrhosis despite no animal contact: case report and literature review

Pasteurella multocida is an opportunistic pathogen. Previously reported infections associated with P. multocida have often been linked to contact with cats, dogs, and other animals. Cases of systemic multiple-site infections following P. multocida infection are rare. This case study presents a 49-year-old middle-aged man with post-hepatitis B cirrhosis and no history of animal contact. The patient was admitted with symptoms of fever accompanied by diarrhea, abdominal distension, and cough. Blood tests showed elevated levels of CRP, PCT, and IL-6, and blood culture revealed the growth of P. multocida. CT scans revealed a large amount of abdominal effusion, a small amount of pleural effusion, and pulmonary infection foci. The patient's condition improved after successive administration of ceftriaxone and levofloxacin to fight the infection, and abdominal puncture and drainage. Multiple-site infections caused by P. multocida are rarely encountered in patients with liver cirrhosis but without animal contact, which could be regarded as serious conditions warranting careful attention in terms of clinical diagnosis and treatment.

Clinical Evaluation of Metagenomic Next-Generation Sequencing Method for the Diagnosis of Suspected Ascitic Infection in Patients with Liver Cirrhosis in a Clinical Laboratory

Metagenomic next-generation sequencing (mNGS), mostly carried out in independent clinical laboratories, has been increasingly applied in clinical pathogen diagnosis. We aimed to explore the feasibility of mNGS in clinical laboratories and analyze its potential in the diagnosis of infectious ascites. Two reference panels composed of 12 strains commonly appearing in peritonitis were constructed to evaluate the performance metrics based on in-house mNGS protocols. The mNGS clinical detection value was analyzed in 211 ascitic samples and compared with culture and composite standards. Finally, eight patients with cirrhosis were prospectively enrolled to verify the clinical value of mNGS in peritoneal infection diagnosis. The mNGS analytical performance showed that the assay had great linearity, specificity, stability, interference, and limits of detection of 33 to 828 CFU/mL. The sensitivity and specificity of mNGS for bacterial or fungal detection using culture standards were 84.2% and 82.0%, respectively. After adjustment using digital PCR and clinical judgment, the sensitivity and specificity increased to 87.2% and 90.1%, respectively. Compared with culture, mNGS detected a broad range of pathogens and more polymicrobial infections (49% versus 9%, P < 0.05). The pathogen results were obtained within 24 h using mNGS in eight prospective cases, which effectively guided antibiotics therapy. mNGS testing in clinical laboratories affiliated with a hospital has certain advantages. It has unique superiority in pathogens detection, particularly in patients with polymicrobial infections. However, considering spectrum characteristics and test cost, pertinent pathogen panels should be developed in clinical practice. IMPORTANCE This study established and evaluated a complete metagenomics next-generation sequencing assay to improve the diagnosis of suspected ascitic infection in a clinical laboratory affiliated with a hospital. The assay is superior to traditional culture testing and will aid in the early and accurate identification of pathogens, particularly in patients with polymicrobial infections. This assay is also essential for precision therapy and can reduce the incidence of drug resistance stemming from irrational use of antibiotics.

Diagnostic Yield and Impact on Antimicrobial Management of 16S rRNA Testing of Clinical Specimens

16S rRNA gene sequencing is increasingly used in clinical practice for bacterial identification of clinical specimens. However, studies on its applicability to direct clinical specimens are limited. Here, we studied the diagnostic yield and impact of 16S rRNA gene sequencing from direct clinical specimens on antimicrobial management. Adult inpatients whose attending physician requested 16S rRNA gene sequencing and corresponding bacterial culture from a direct clinical specimen between January and December 2021 in a university hospital were prospectively included in this study. A total of 434 specimens from 374 patients were requested. Of these, 253 (58.3%) specimens were collected from patients whose final diagnosis indicated a bacterial infection, whereas 181 (41.7%) specimens were from nonbacterial infections. Using the final diagnosis as a "gold standard," the sensitivity and specificity of 16S rRNA gene sequencing were 38.3% and 93.9%, respectively. Among the bacterial infection cases, the proportion of 16S rRNA gene sequencing-positive and culture-positive cases was 32.4%, and the proportion of sequencing-positive and culture-negative cases was 5.9%. The impact on antimicrobial management was evident in 10 (2.3%) specimens, which all resulted in the continuation of antibiotics. The impact on antimicrobial management was highest in skin and soft tissue infections, followed by bone and joint infections. In this study, the long turnaround time of 16S rRNA gene sequencing of clinical specimens was a limiting factor. In conclusion, the overall diagnostic yield of 16S rRNA gene sequencing in bacterial infection cases was fair, being useful in selected cases. Restrictions on test requests may improve test utilization in this setting. IMPORTANCE 16S rRNA gene sequencing has been increasingly used in clinical practice. Using the final diagnosis as a gold standard, the sensitivity of 16S rRNA gene sequencing was fair. In the setting with no 16S rRNA gene sequencing test ordering restrictions, only small percentages of the test results had an impact on antimicrobial management. Restrictions on test requests should be developed to maximize the benefit of the test.

Nanopore Electrochemistry for Pathogen Detection

Pathogen infections have seriously threatened human health, and there is an urgent demand for rapid and efficient pathogen identification to provide instructions in clinical diagnosis and therapeutic intervention. Recently, nanopore technology, a rapidly maturing technology which delivers ultrasensitive sensing and high throughput in real-time and at low cost, has achieved success in pathogen detection. Furthermore, the remarkable development of nanopore sequencing, for example, the MinION sequencer from Oxford Nanopore Technologies (ONT) as a competitive sequencing technology, has facilitated the rapid analysis of disease-related microbiomes at the whole-genome level and on a large scale. Here, we highlighted recent advances in nanopore approaches for pathogen detection at the single-molecule level. We also overviewed the applications of nanopore sequencing in pathogenic bacteria identification and diagnosis. In the end, we discussed the challenges and future developments of nanopore technology as promising tools for the management of infections, which may be helpful to aid understanding as well as decision-making.

Targeted Metagenomic Sequencing-Based Approach Applied to 2,146 Tissue and Body Fluid Samples in Routine Clinical Practice

BACKGROUND

The yield of next generation sequencing (NGS) added to a Sanger sequencing-based 16S ribosomal RNA (rRNA) gene PCR assay was evaluated in clinical practice for diagnosis of bacterial infection.

METHODS

PCR targeting the V1 to V3 regions of the 16S rRNA gene was performed, with amplified DNA submitted to Sanger sequencing and/or NGS (Illumina MiSeq), or reported as negative, depending on cycle threshold (Ct) value. 2,146 normally sterile tissues or body fluids were tested between August 2020 and March 2021. Clinical sensitivity was assessed in 579 subjects from whom clinical data was available.

RESULTS

Compared to Sanger sequencing alone (400 positive tests), positivity increased by 87% by adding NGS (347 added positive tests). Clinical sensitivity of the assay incorporating NGS was 53%, higher than culture (42%, p<0.001), with an impact on clinical decision-making in 14% of infected cases. Clinical sensitivity in the subgroup receiving antibiotics at sampling was 41% for culture and 63% for the sequencing assay (p<0.001).

CONCLUSION

Adding NGS to Sanger sequencing of the PCR-amplified 16S rRNA gene substantially improved test positivity. In the patient population studied, the assay was more sensitive than culture, and especially so in patients who had received antibiotic therapy.

Role of 16S Ribosomal RNA Analysis in Identification of Microorganisms in Febrile Urinary Tract Infection of Infants

OBJECTIVES

To assess the role of 16S ribosomal RNA analysis in microbial identification in febrile infants under six months of age diagnosed with UTI, and compare it with the conventional culture results.

METHODS

Young infants under 6 mo of age who were suspected UTI from May 2018 to April 2019 had been enrolled. Uropathogens were analyzed by the traditional microbiologic culture system and the 16S rRNA analysis. The 16S rRNA analysis included 16S rRNA amplicon band confirmation and bacterial identification through the sequencing analysis.

RESULTS

A total of 57 infants with the febrile UTI were enrolled, and the median age was 3 mo. Uropathogens were identified in 43 patients (75.4%) in a conventional culture method: Escherichia coli in 38 patients (88.4%), Klebsiella pneumoniae in 3 (7.0%), Enterobacter cloacae in 1 (2.3%), and Pseudomonas aeruginosa in 1 (2.3%). Fifty urine samples (87.8%) had positive 16S rRNA amplicon band on electrophoresis. Among the 16S rRNA-positive urines, 40 samples were available for the sequence analysis of 16S rRNA, and the identification of bacteria were as follows: E. fergusonii in 36, K. pneumoniae in 3, and Shigella flexneri in 1. The sensitivity of 16S rRNA sequencing was 81.4% [95% confidence interval (CI), 67.4-90.3%] and the specificity was 64.3% (95% CI, 38.8-83.7%).

CONCLUSION

Uropathogen identification using 16S rRNA analysis could be applied to manage the febrile UTI in young infants clinically in combination with the conventional culture.

Reproductive outcomes and reproductive tract microbiota shift in women with moderate-to-severe intrauterine adhesions following 30-day post-hysteroscopic placement of balloon stents or intrauterine contraceptive devices: A randomized controlled trial

BACKGROUND

Intrauterine adhesions (IUA) develop in up to 20% of women with a history of abortion. After hysteroscopic adhesiolysis, balloon stents are usually placed for seven days to prevent recurrence. The efficacy of prolonged use (30 days) of balloon stents has not been determined.

METHODS

The trial was conducted from June 2019 to March 2021. Ninety-one patients who underwent hysteroscopic adhesiolysis for moderate or severe IUA were randomized to receive a 30-day placement of a balloon stent (n = 44) or an intrauterine device (IUD) (n = 47). The primary outcomes were the ongoing pregnancy and miscarriage rates assessed at 15-19 months. The secondary outcomes were the recurrence of IUA and the American Fertility Society (AFS) intrauterine adhesion scores at the first and second hysteroscopies, the diagnosis of new chronic endometritis at the second-look hysteroscopy, and the vaginal/uterine microbiome assessed using 16S rRNA sequencing. The trial was registered at Chinese Clinical Trial Registry (ChiCTR1900023306).

FINDINGS

The ongoing pregnancy rates (balloon 56·4% versus IUD 57·1%) and miscarriage rates (balloon 10·3% versus IUD 22·9%) were not significantly different between the groups. No differences in the recurrence of IUA, reduction of AFS scores, or new endometritis rates were detected. The bacterial load in the uterus and vagina increased in the IUD group but not in the balloon group.

INTERPRETATION

Balloon placement has a similar effect on ongoing pregnancy rates as intrauterine device (IUD) placement. Patients who underwent balloon placement had a lower miscarriage rate, although the difference was not significant. There were no differences in the recurrence rate of IUA, reduction of American Fertility Society scores, or rate of new chronic endometritis. The balloon stent has less effects on the uterine microbiota.

FUNDING

National Natural Science Foundation of China (81802593).

Diagnostic Value of 16S Ribosomal RNA Gene Polymerase Chain Reaction/Sanger Sequencing in Clinical Practice

BACKGROUND

Accurate microbiologic diagnosis is important for appropriate management of infectious diseases. Sequencing-based molecular diagnostics are increasingly used for precision diagnosis of infections. However, their clinical utility is unclear.

METHODS

We conducted a retrospective analysis of specimens that underwent 16S ribosomal RNA (rRNA) gene polymerase chain reaction (PCR) followed by Sanger sequencing at our institution from April 2017 through March 2019.

RESULTS

A total of 566 specimens obtained from 460 patients were studied. Patients were considered clinically infected or noninfected based on final diagnosis and management. In 17% of patients, 16S rRNA PCR/sequencing was positive and in 5% of patients, this test led to an impact on clinical care. In comparison, bacterial cultures were positive in 21% of patients. Specimens with a positive Gram stain had 12 times greater odds of having a positive molecular result than those with a negative Gram stain (95% confidence interval for odds ratio, 5.2-31.4). Overall, PCR positivity was higher in cardiovascular specimens (37%) obtained from clinically infected patients, with bacterial cultures being more likely to be positive for musculoskeletal specimens (P < .001). 16S rRNA PCR/sequencing identified a probable pathogen in 10% culture-negative specimens.

CONCLUSION

16S rRNA PCR/sequencing can play a role in the diagnostic evaluation of patients with culture-negative infections, especially those with cardiovascular infections.

Fast label-free identification of bacteria by synchronous fluorescence of amino acids

Fast identification of pathogenic bacteria is an essential need for patient's diagnostic in hospitals and environmental monitoring of water and air quality. Bacterial cells consist of a very high amount of biological molecules whose content changes in response to different environmental conditions. The similarity between the molecular compositions of different bacterial cells limits the possibility to find unique markers to enable differentiation among species. Although many biological molecules in the cells absorb at the UV-Vis region, only a few of them can be detected in whole cells by their intrinsic fluorescence. Among these molecules are the amino acids phenylalanine, tyrosine, and tryptophan. In this work, we develop a rapid method for bacterial identification by synchronous fluorescence. We show that we can quantify the concentration for the 3 amino acids without any significant interference from other fluorophores in the cells and that we can differentiate among 6 pathogenic bacterial species by using the concentrations of their amino acids as a bacterial fingerprint. Fluorescent amino acids exist in all living cells. Therefore, this method has the potential to be applicative for the rapid identification of cells from all kinds of organisms.