The clinical utility of Nanopore 16S rRNA gene sequencing for direct bacterial identification in normally sterile body fluids

The prolonged incubation period of traditional culture methods leads to a delay in diagnosing invasive infections. Nanopore 16S rRNA gene sequencing (Nanopore 16S) offers a potential rapid diagnostic approach for directly identifying bacteria in infected body fluids. To evaluate the clinical utility of Nanopore 16S, we conducted a study involving the collection and sequencing of 128 monomicrobial samples, 65 polymicrobial samples, and 20 culture-negative body fluids. To minimize classification bias, taxonomic classification was performed using 3 analysis pipelines: Epi2me, Emu, and NanoCLUST. The result was compared to the culture references. The limit of detection of Nanopore 16S was also determined using simulated bacteremic blood samples. Among the three classifiers, Emu demonstrated the highest concordance with the culture results. It correctly identified the taxon of 125 (97.7%) of the 128 monomicrobial samples, compared to 109 (85.2%) for Epi2me and 102 (79.7%) for NanoCLUST. For the 230 cultured species in the 65 polymicrobial samples, Emu correctly identified 188 (81.7%) cultured species, compared to 174 (75.7%) for Epi2me and 125 (54.3%) for NanoCLUST. Through ROC analysis on the monomicrobial samples, we determined a threshold of relative abundance at 0.058 for distinguishing potential pathogens from background in Nanopore 16S. Applying this threshold resulted in the identification of 107 (83.6%), 117 (91.4%), and 114 (91.2%) correctly detected samples for Epi2me, Emu, and NanoCLUST, respectively, in the monomicrobial samples. Nanopore 16S coupled with Epi2me could provide preliminary results within 6 h. However, the ROC analysis of polymicrobial samples exhibited a random-like performance, making it difficult to establish a threshold. The overall limit of detection for Nanopore 16S was found to be about 90 CFU/ml.

Significantly Lower Case-fatality Ratio of Coronavirus Disease 2019 (COVID-19) than Severe Acute Respiratory Syndrome (SARS) in Hong Kong-A Territory-Wide Cohort Study

BACKGROUND

The case-fatality ratios (CFR) of coronavirus disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS) appeared to differ substantially. We aimed to compare the CFR and its predictors of COVID-19 and SARS patients using a territory-wide cohort in Hong Kong.

METHODS

This was a territory-wide retrospective cohort study using data captured from all public hospitals in Hong Kong. Laboratory-confirmed COVID-19 and SARS patients were identified. The primary endpoint was a composite endpoint of intensive care unit admission, use of mechanical ventilation, and/or death.

RESULTS

We identified 1013 COVID-19 patients (mean age, 38.4 years; 53.9% male) diagnosed from 23 January to 14 April 2020 and 1670 SARS patients (mean age, 44.4 years; 44.0% male) from March to June 2003. Fifty-five (5.4%) COVID-19 patients and 432 (25.9%) SARS patients had reached the primary endpoint in 30 days. By 30 June 2003, 286 SARS patients had died (CFR, 17.1%). By 7 June 2020, 4 COVID-19 patients had died (CFR, 0.4%). After adjusting for demographic and clinical parameters, COVID-19 was associated with a 71% lower risk of primary endpoint compared with SARS (adjusted hazard ratio, 0.29; 95% confidence interval, .21-.40; P < .0001). Age, diabetes mellitus, and laboratory parameters (high lactate dehydrogenase, high C-reactive protein, and low platelet count) were independent predictors of the primary endpoint in COVID-19 patients, whereas use of antiviral treatments was not associated with primary endpoint.

CONCLUSIONS

The CFR of COVID-19 was 0.4%. Age and diabetes were associated with worse outcomes, whereas antiviral treatments were not.

Liver injury is independently associated with adverse clinical outcomes in patients with COVID-19

OBJECTIVE

Data on serial liver biochemistries of patients infected by different human coronaviruses (HCoVs) are lacking. The impact of liver injury on adverse clinical outcomes in coronavirus disease 2019 (COVID-19) patients remains unclear.

DESIGN

This was a retrospective cohort study using data from a territory-wide database in Hong Kong. COVID-19, severe acute respiratory syndrome (SARS) and other HCoV patients were identified by diagnosis codes and/or virological results. Alanine aminotransferase (ALT)/aspartate aminotransferase (AST) elevation was defined as ALT/AST ≥2 × upper limit of normal (ie, 80 U/L). The primary end point was a composite of intensive care unit (ICU) admission, use of invasive mechanical ventilation and/or death.

RESULTS

We identified 1040 COVID-19 patients (mean age 38 years, 54% men), 1670 SARS patients (mean age 44 years, 44% men) and 675 other HCoV patients (mean age 20 years, 57% men). ALT/AST elevation occurred in 50.3% SARS patients, 22.5% COVID-19 patients and 36.0% other HCoV patients. For COVID-19 patients, 53 (5.1%) were admitted to ICU, 22 (2.1%) received invasive mechanical ventilation and 4 (0.4%) died. ALT/AST elevation was independently associated with primary end point (adjusted OR (aOR) 7.92, 95% CI 4.14 to 15.14, p<0.001) after adjusted for albumin, diabetes and hypertension. Use of lopinavir-ritonavir ±ribavirin + interferon beta (aOR 1.94, 95% CI 1.20 to 3.13, p=0.006) and corticosteroids (aOR 3.92, 95% CI 2.14 to 7.16, p<0.001) was independently associated with ALT/AST elevation.

CONCLUSION

ALT/AST elevation was common and independently associated with adverse clinical outcomes in COVID-19 patients. Use of lopinavir-ritonavir, with or without ribavirin, interferon beta and/or corticosteroids was independently associated with ALT/AST elevation.

Risks of AKI and Major Adverse Clinical Outcomes in Patients with Severe Acute Respiratory Syndrome or Coronavirus Disease 2019

BACKGROUND

Severe acute respiratory syndrome (SARS) and coronavirus disease 2019 (COVID-19) are closely related. The effect of AKI on the clinical outcomes of these two conditions is unclear.

METHODS

This retrospective, territory-wide cohort study used an electronic public healthcare database in Hong Kong to identify patients with SARS or COVID-19 by diagnosis codes, virologic results, or both. The primary endpoint was a composite of intensive care unit admission, use of invasive mechanical ventilation, and/or death.

RESULTS

We identified 1670 patients with SARS and 1040 patients with COVID-19 (median ages, 41 versus 35 years, respectively). Among patients with SARS, 26% met the primary endpoint versus 5.3% of those with COVID-19. Diabetes mellitus, abnormal liver function, and AKI were factors significantly associated with the primary endpoint among patients with either SARS or COVID-19. Among patients with SARS, 7.9%, 2.1%, and 3.7% developed stage 1, stage 2, and stage 3 AKI, respectively; among those with COVID-19, 6.6%, 0.4%, and 1.1% developed stage 1, stage 2, and stage 3 AKI, respectively. In both groups, factors significantly associated with AKI included diabetes mellitus and hypertension. Among patients with AKI, those with COVID-19 had a lower rate of major adverse clinical outcomes versus patients with SARS. Renal function recovery usually occurred within 30 days after an initial AKI event.

CONCLUSIONS

AKI rates were higher among patients with SARS than those with COVID-19. AKI was associated with major adverse clinical outcomes for both diseases. Patients with diabetes mellitus and abnormal liver function were also at risk of developing severe consequences after SARS and COVID-19 infection.

Deep throat saliva as an alternative diagnostic specimen type for the detection of SARS-CoV-2

Nasopharyngeal swabs (NPS) are widely accepted as specimens for the detection of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) in the current pandemic of coronavirus disease 2019. However, the collection procedures for NPS specimens causes sneezing and coughing in most patients, which generate droplets or aerosol particles that are hazardous to the healthcare workers collecting these specimens. In this study, 95 patient‐matched paired deep throat saliva (DTS) and NPS specimens from 62 patients were analyzed. Samples were tested for SARS‐CoV‐2 by reverse‐transcription polymerase chain reaction (RT‐PCR). The rates of detection for DTS (53.7%) and NPS (47.4%) samples were comparable (P = .13). It is important to note that the patients should be clearly instructed or supervised during DTS collection. In conclusion, SARS‐CoV‐2 detection by RT‐PCR was equivalent in DTS and NPS specimens.

This study aimed to assess the comparability of deep throat saliva (DTS) to nasopharyngeal swab (NPS) for the detection of SARS‐CoV‐2 by RT‐PCR.

The results showed that SARS‐CoV‐2 detection by RT‐PCR was equivalent in DTS and NPS specimens.

Continuous ambulatory peritoneal dialysis peritonitis: broth inoculation culture versus water lysis method

BACKGROUND/AIM

In the setting of empiric antibiotic treatment of peritoneal-dialysis-related peritonitis complications, the speed with which a bacteriological diagnosis can be achieved is of importance. We compare the clinical performance of two culture methods to diagnose the causative microorganisms as suggested by the International Society for Peritoneal Dialysis and the United Kingdom Health Protection Agency.

METHODS

We prospectively evaluated microbiological cultures of peritoneal fluid samples by the direct broth culture versus water lysis. Samples from 17 consecutive patients with dialysis-associated peritonitis were examined.

RESULTS

Of the 17 dialysates cultured, 14 (82.4%) were positive by one of the two methods. The final culture results agreed in 16 of 17 specimens (94.1%). The preliminary organism identification rate by Gram staining with the broth culture method was 70.6%, which was significantly greater than 17.6% by the water lysis method (p = 0.0019). In particular, the broth culture technique demonstrated superior Gram stain performance to identify Gram-positive organisms. Among the 13 dialysate samples positive by both methods, the broth culture method detected organisms faster than the water lysis method (1.3 +/- 0.7 vs. 2.6 +/- 1.6 days, p = 0.005).

CONCLUSIONS

Our results support the routine use of the broth culture technique using BacT/Alert blood culture bottles in order to facilitate early streamlining of empiric antibiotic therapy. Gram staining of sediments after centrifugation is associated with low diagnostic yield. Whether the lysis-centrifugation technique could provide additional value in case of peritonitis with a high likelihood of culture-negative results needs to be evaluated.

Rhodococcus equi peritonitis in continuous ambulatory peritoneal dialysis

The human Rhodococcus equi (R. equi) infection is now emerging, although extrapulmonary manifestation and isolation from patients without human immunodeficiency virus (HIV) infection remains unusual. Considerable effort is required to correctly identify and diagnose this facultative pathogen in patients with peritonitis in end-stage renal failure (ESRF) on continuous ambulatory peritoneal dialysis (CAPD). In the six cases of R. equi CAPD peritonitis reported in this series, diagnoses were made, on average, after 15 days and prolonged antibiotic therapy with morbidity in two patients. A diagnosis of R. equi should be considered in patients with suspected diphtheroid or Nocardia CAPD peritonitis, even with no history of animal contact. This study is the largest series on R. equi CAPD peritonitis and highlights the impact of this disease.

Indication for peritoneal biopsy in tuberculous peritonitis

BACKGROUND

With the introduction of effective antituberculous chemotherapy, the clinical outcome of tuberculous peritonitis depends much on the diagnostic accuracy of this disease entity. This review summarizes the current state-of-the-art thinking regarding the protean manifestation and diagnostic modalities of this major infectious disease.

DATA SOURCES

This review was compiled after an extensive search of the current and historical literature, comprising 1,070 cases of tuberculous peritonitis. A number of important areas were highlighted, with emphasis on the diagnostic value and clinical impact of peritoneal biopsy.

CONCLUSIONS

We believe an aggressive diagnostic approach, particularly with peritoneal biopsy, is warranted for the diagnosis and timely treatment of tuberculous peritonitis.