Sepsis in tropical regions: Report from the task force on tropical diseases by the World Federation of Societies of Intensive and Critical Care Medicine

Diagnosis of pathogens causing bacterial meningitis using Nanopore sequencing in a resource-limited setting

Aim

The aim of the present study is to compare the performance of 16S rRNA Nanopore sequencing and conventional culture in detecting infectious pathogens in patients with suspected meningitis in a resource-limited setting without extensive bioinformatics expertise.

Methods

DNA was isolated from the cerebrospinal fluid (CSF) of 30 patients with suspected bacterial meningitis. The isolated DNA was subjected to 16S sequencing using MinION™. The data were analysed in real time via the EPI2ME cloud platform. The Nanopore sequencing was done in parallel to routine microbiological diagnostics.

Results

Nanopore sequencing detected bacterial pathogens to species level in 13 of 30 (43%) samples. CSF culture showed 40% (12/30) positivity. In 21 of 30 patients (70%) with suspected bacterial meningitis, both methods yielded concordant results. About nine of 30 samples showed discordant results, of these five were false positive and four were false negative. In five of the culture negative results, nanopore sequencing was able to detect pathogen genome, due to the higher sensitivity of the molecular diagnostics. In two other samples, the CSF culture revealed Cryptococcus neoformans and Streptococcus pneumoniae, which were not detected by Nanopore sequencing. Overall, using both the cultures and 16S Nanopore sequencing, positivity rate increased from 40% (12/30) to 57% (17/30).

Conclusion

Next-generation sequencing could detect pathogens within six hours and could become an important tool for both pathogen screening and surveillance in low- and middle-income countries (LMICs) that do not have direct access to extensive bioinformatics expertise.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12941-022-00530-6.

Clinical and microbiological characterization of sepsis and evaluation of sepsis scores

Background

Despite the necessity of early recognition for an optimal outcome, sepsis often remains unrecognized. Available tools for early recognition are rarely evaluated in low- and middle-income countries. In this study, we analyzed the spectrum, treatment and outcome of sepsis at an Ethiopian tertiary hospital and evaluated recommended sepsis scores.

Methods

Patients with an infection and ≥2 SIRS criteria were screened for sepsis by SOFA scoring. From septic patients, socioeconomic and clinical data as well as blood cultures were collected and they were followed until discharge or death; 28-day mortality was determined.

Results

In 170 patients with sepsis, the overall mortality rate was 29.4%. The recognition rate by treating physicians after initial clinical assessment was low (12.4%). Increased risk of mortality was significantly associated with level of SOFA and qSOFA score, Gram-negative bacteremia (in comparison to Gram-positive bacteremia; 42.9 versus 16.7%), and antimicrobial regimen including ceftriaxone (35.7% versus 19.2%) or metronidazole (43.8% versus 25.0%), but not with an increased respiratory rate (≥22/min) or decreased systolic blood pressure (≤100mmHg). In Gram-negative isolates, extended antimicrobial resistance with expression of extended-spectrum beta-lactamase and carbapenemase genes was common. Among adult patients, sensitivity and specificity of qSOFA score for detection of sepsis were 54.3% and 66.7%, respectively.

Conclusion

Sepsis is commonly unrecognized and associated with high mortality, showing the need for reliable and easy-applicable tools to support early recognition. The established sepsis scores were either of limited applicability (SOFA) or, as in the case of qSOFA, were significantly impaired in their sensitivity and specificity, demonstrating the need for further evaluation and adaptation to local settings. Regional factors like malaria endemicity and HIV prevalence might influence the performance of different scores. Ineffective empirical treatment due to antimicrobial resistance is common and associated with mortality. Local antimicrobial resistance statistics are needed for guidance of calculated antimicrobial therapy to support reduction of sepsis mortality.

Effectiveness of a sepsis programme in a resource-limited setting: a retrospective analysis of data of a prospective observational study (Ubon-sepsis)

OBJECTIVE

To evaluate the effectiveness of a Sepsis Fast Track (SFT) programme initiated at a regional referral hospital in Thailand in January 2015.

DESIGN

A retrospective analysis using the data of a prospective observational study (Ubon-sepsis) from March 2013 to January 2017.

SETTING

General medical wards and medical intensive care units (ICUs) of a study hospital.

PARTICIPANTS

Patients with community-acquired sepsis observed under the Ubon-sepsis cohort. Sepsis was defined as modified Sequential Organ Failure Assessment (SOFA) Score ≥2.

MAIN EXPOSURE

The SFT programme was a protocol to identify and initiate sepsis care on hospital admission, implemented at the study hospital in 2015. Patients in the SFT programme were admitted directly to the ICUs when available. The non-exposed group comprised of patients who received standard of care.

MAIN OUTCOME

The primary outcome was 28-day mortality. The secondary outcomes were measured sepsis management interventions.

RESULTS

Of 3806 sepsis patients, 903 (24%) were detected and enrolled in the SFT programme of the study hospital (SFT group) and 2903 received standard of care (non-exposed group). Patients in the SFT group had more organ dysfunction, were more likely to receive measured sepsis management and to be admitted directly to the ICU (19% vs 4%). Patients in the SFT group were more likely to survive (adjusted HR 0.72, 95% CI 0.58 to 0.88, p=0.001) adjusted for admission year, gender, age, comorbidities, modified SOFA Score and direct admission to the ICUs.

CONCLUSIONS

The SFT programme is associated with improved sepsis care and lower risk of death in sepsis patients in rural Thailand, where some critical care resources are limited. The survival benefit is observed even when all patients enrolled in the programme could not be admitted directly into the ICUs.

TRIAL REGISTRATION NUMBER

NCT02217592.

The comparative ability of commonly used disease severity scores to predict death or a requirement for ICU care in patients hospitalised with possible sepsis in Yangon, Myanmar

OBJECTIVES

To determine the comparative prognostic utility of commonly used disease prediction scores in adults with presumed community-acquired sepsis in a resource-limited tropical setting.

METHODS

This prospective, observational study was performed on the medical ward of a tertiary-referral hospital in Yangon, Myanmar. The ability of the National Early Warning Score 2 (NEWS2), quick NEWS (qNEWS), quick Sequential Organ Failure Assessment (qSOFA) score, Universal Vital Assessment (UVA) and Sequential Organ Failure Assessment (SOFA) scores to predict a complicated inpatient course (death or requirement for intensive care unit (ICU) support) in patients with two or more systemic inflammatory response syndrome criteria was determined.

RESULTS

Among the 509 patients, 30 (6%) were HIV-seropositive. The most commonly confirmed diagnoses were tuberculosis (30/509, 5.9%) and measles (26/509, 5.1%). Overall, 75/509 (14.7%) died or required ICU support. All the scores except the qSOFA score, which was inferior, had a similar ability to predict a complicated inpatient course.

CONCLUSIONS

In this resource-limited tropical setting, disease severity scores calculated at presentation using only vital signs-such as the NEWS2 score-identified high-risk sepsis patient as well as the SOFA score, which is calculated at 24 h and which also requires laboratory data. Use of these simple clinical scores can be used to facilitate recognition of the high-risk patient and to optimise the use of finite resources.

The clinical characteristics of patients with sepsis in a tertiary referral hospital in Yangon, Myanmar

Background

The clinical characteristics and course of patients hospitalised with sepsis in Myanmar and the responsible pathogens remain poorly defined.

Methods

We performed an observational study of adults admitted from the community to a tertiary referral hospital in Yangon with fever and dysfunction of at least two organ systems.

Results

The 120 patients had a median age of 47 y (interquartile range 28-63); 11 (9%) were human immunodeficiency virus positive. Limited laboratory support meant that a microbiological diagnosis was possible in only 35 (29%) patients, but 18 (13%) had pathogens in blood cultures, including 9 (50%) organisms that were multidrug resistant (4 Escherichia coli, 4 Pseudomonas aeruginosa, 1 Burkholderia pseudomallei). Tuberculosis was confirmed in six patients, with two being rifampicin resistant, and dengue infection was confirmed in five patients. Without access to comprehensive intensive care support, 34 (28%) patients died. An admission National Early Warning Score ≥7 (odds ratio [OR] 8.6 [95% confidence interval {CI} 2.6 to 28.2], p=0.001) and quick sequential (sepsis-related) organ failure assessment score ≥2 (OR 3.2 [95% CI 1.3 to 8.0], p=0.02) were helpful in predicting death.

Conclusions

Tropical pathogens are a common cause of sepsis in Myanmar. The frequent identification of multidrug-resistant organisms and limited diagnostic and intensive care support hinder patient care significantly. However, simple clinical assessment on admission has prognostic utility.

Critical care outcomes in resource-limited settings

PURPOSE OF REVIEW

The burden of critical illness in low-income and middle-income countries (LMICs) is substantial. A better understanding of critical care outcomes is essential for improving critical care delivery in resource-limited settings. In this review, we provide an overview of recent literature reporting on critical care outcomes in LMICs. We discuss several barriers and potential solutions for a better understanding of critical care outcomes in LMICs.

RECENT FINDINGS

Epidemiologic studies show higher in-hospital mortality rates for critically ill patients in LMICs as compared with patients in high-income countries (HICs). Recent findings suggest that critical care interventions that are effective in HICs may not be effective and may even be harmful in LMICs. Little data on long-term and morbidity outcomes exist. Better outcomes measurement is beginning to emerge in LMICs through decision support tools that report process outcome measures, studies employing mobile health technologies with community health workers and the development of context-specific severity of illness scores.

SUMMARY

Outcomes from HICs cannot be reliably extrapolated to LMICs, so it is important to study outcomes for critically ill patients in LMICs. Specific challenges to achieving meaningful outcomes studies in LMICs include defining the critically ill population when few ICU beds exist, the resource-intensiveness of long-term follow-up, and the need for reliable severity of illness scores to interpret outcomes. Although much work remains to be done, examples of studies overcoming these challenges are beginning to emerge.

Chromobacterium violaceum in Northern Australia: A Sheep in Wolf's Clothing?

In many parts of the world, the case-fatality rate of Chromobacterium violaceum infection approaches 60%. To evaluate the spectrum of disease associated with C. violaceum in Far North Queensland (FNQ), Australia, we reviewed all culture-confirmed isolates from 1997 to 2017. There were 28 isolates, 15 represented infection, 11 were contaminants, and two charts were destroyed preventing detailed evaluation of these cases. The most common sites of infection were the skin and soft tissue and the urinary tract; there were two cases of bacteremia without focus. There were no deaths attributable to C. violaceum during the study period and only two cases required intensive care unit support, although in both patients this was not for the C. violaceum infection, but for the management of other health issues. Globally, C. violaceum has a reputation as a deadly pathogen, but in FNQ, Australia, infections usually follow a relatively benign course.