SARS-CoV-2 Viral Replication Persists in the Human Lung for Several Weeks after Symptom Onset.

Rationale: In the upper respiratory tract, replicating (culturable) severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recoverable for ∼4-8 days after symptom onset, but there is a paucity of data about the frequency and duration of replicating virus in the lower respiratory tract (i.e., the human lung).Objectives: We undertook lung tissue sampling (needle biopsy) shortly after death in 42 mechanically ventilated decedents during the Beta and Delta waves. An independent group of 18 ambulatory patients served as a control group.Methods: Lung biopsy cores from decedents underwent viral culture, histopathological analysis, electron microscopy, transcriptomic profiling, and immunohistochemistry.Measurements and Main Results: Thirty-eight percent (16 of 42) of mechanically ventilated decedents had culturable virus in the lung for a median of 15 days (persisting for up to 4 wk) after symptom onset. Lung viral culture positivity was not associated with comorbidities or steroid use. Delta but not Beta variant lung culture positivity was associated with accelerated death and secondary bacterial infection (P < 0.05). Nasopharyngeal culture was negative in 23.1% (6 of 26) of decedents despite lung culture positivity. This hitherto undescribed biophenotype of lung-specific persisting viral replication was associated with an enhanced transcriptomic pulmonary proinflammatory response but with concurrent viral culture positivity.Conclusions: Concurrent rather than sequential active viral replication continues to drive a heightened proinflammatory response in the human lung beyond the second week of illness and was associated with variant-specific increased mortality and morbidity. These findings have potential implications for the design of interventional strategies and clinical management of patients with severe coronavirus disease (COVID-19).

A retrospective descriptive analysis of non-physician-performed prehospital endotracheal intubation practices and performance in South Africa.

INTRODUCTION: Prehospital advanced airway management, including endotracheal intubation (ETI), is one of the most commonly performed advanced life support skills. In South Africa, prehospital ETI is performed by non-physician prehospital providers. This practice has recently come under scrutiny due to lower first pass (FPS) and overall success rates, a high incidence of adverse events (AEs), and limited evidence regarding the impact of ETI on mortality. The aim of this study was to describe non-physician ETI in a South African national sample in terms of patient demographics, indications for intubation, means of intubation and success rates. A secondary aim was to determine what factors were predictive of first pass success. METHODS: This study was a retrospective chart review of prehospital ETIs performed by non-physician prehospital providers, between 01 January 2017 and 31 December 2017. Two national private Emergency Medical Services (EMS) and one provincial public EMS were sampled. Data were analysed descriptively and summarised. Logistic regression was performed to evaluate factors that affect the likelihood of FPS. RESULTS: A total of 926 cases were included. The majority of cases were adults (n = 781, 84.3%) and male (n = 553, 57.6%). The most common pathologies requiring emergency treatment were head injury, including traumatic brain injury (n = 328, 35.4%), followed by cardiac arrest (n = 204, 22.0%). The mean time on scene was 46 minutes (SD = 28.3). The most cited indication for intubation was decreased level of consciousness (n = 515, 55.6%), followed by cardiac arrest (n = 242, 26.9%) and ineffective ventilation (n = 96, 10.4%). Rapid sequence intubation (RSI, n = 344, 37.2%) was the most common approach. The FPS rate was 75.3%, with an overall success rate of 95.7%. Intubation failed in 33 (3.6%) patients. The need for ventilation was inversely associated with FPS (OR = 0.42, 95% CI: 0.20-0.88, p = 0.02); while deep sedation (OR = 0.56, 95% CI: 0.36-0.88, p = 0.13) and no drugs (OR = 0.47, 95% CI: 0.25-0.90, p = 0.02) compared to RSI was less likely to result in FPS. Increased scene time (OR = 0.99, 95% CI: 0.985-0.997, p < 0.01) was inversely associated FPS. CONCLUSION: This is one of the first and largest studies evaluating prehospital ETI in Africa. In this sample of ground-based EMS non-physician ETI, we found success rates similar to those reported in the literature. More research is needed to determine AE rates and the impact of ETI on patient outcome. There is an urgent need to standardise prehospital ETI reporting in South Africa to facilitate future research.

Intensive Care Unit Sluice Room Sinks as Reservoirs and Sources of Potential Transmission of Carbapenem-Resistant Bacteria in a South African Tertiary Care Hospital.

Purpose: Carbapenem-resistant bacteria (CRB) pose a major health risk to patients in intensive care units (ICU) across African hospitals. There are hardly any data about the role of hospital sinks as reservoirs of CRB in resource-poor African settings. Furthermore, the specific within-sink location of the highest concentration of pathogens and the role of splash back as a transmission mechanism remains poorly clarified. Methods: We swabbed ICU sluice room sinks in a tertiary hospital in Cape Town, South Africa. Swabs were taken from four different parts of the sluice room sinks (tap-opening, trap, below the trap, and u-bend). Dilutions were prepared and plated on carbapenem-infused agar. Colonies were identified and drug resistance profiles were determined using a biochemical analyser. To evaluate the potential transmission from the sink, similar plates were placed at fixed distances from the sink when the tap was turned on and off. Results: CRB were isolated from the trap, water interface below the trap, and the u-bend (the latter harboured the highest density of CRB species). Five CRB, resistant to at least 7 antibiotic classes, were isolated including Pseudomonas, Klebsiella, Citrobacter, Serratia, and Providencia. CRB could be cultured from droplets that fell on agar-containing plates placed at a varying distance from the trap. Conclusion: There is a higher density of CRB in the u-bend of ICU sluice room sinks which can act as a potential source of transmission. The data inform targeted CRB transmission-interruption strategies in resource-poor settings.

The impact of enteral feeding and therapeutic monitoring of rifampicin with dose escalation in critically ill patients with tuberculosis.

OBJECTIVES: Critically ill patients with tuberculosis (TB) face a high mortality risk and require effective treatment. There is a paucity of data on rifampicin pharmacokinetics, the impact of continuous enteral feeding on drug absorption, and the potential of therapeutic drug monitoring (TDM) to optimize drug exposure in these patients. METHODS: We performed a sequential pharmacokinetic study to determine the impact of feeding and TDM with rifampicin dose escalation in critically ill patients with TB. Noncompartmental pharmacokinetic analysis was performed. RESULTS: Among 20 critically ill patients (40% were HIV-infected), median rifampicin Cmax (maximum serum concentration) in the fasted and fed states were 5.1 µg/ml versus 3.3 µg/ml, respectively (P <0.0001; geometric mean ratio 1.95; 90% confidence interval 1.46-2.60). The proportion of patients with low rifampicin concentrations in the fasted and fed states was 80% vs 100% (P-value = 0.1336). Optimized dosing led to a per-patient median rifampicin dosing of 24.6 mg/kg and a median Cmax increase from 2.4 µg/ml to 17.8 µg/ml (P-value = 0.0005; geometric mean ratio 8.29; 90% confidence interval 3.88-17.74). TDM-guided dose escalation increased the proportion of patients achieving the suggested target rifampicin concentration compared with standard dosing (83% vs 0%, P-value = 0.004). CONCLUSION: We found low rifampicin concentrations in all patients receiving continuous enteral feeding. TDM-guided dose escalation provided an effective strategy to achieve target drug exposure in these critically ill patients with TB.

Visual mapping of team dynamics and communication patterns on surgical ward rounds: an ethnographic study.

BACKGROUND: The effect of team dynamics on infection management and antimicrobial stewardship (AMS) behaviours is not well understood. Using innovative visual mapping, alongside traditional qualitative methods, we studied how surgical team dynamics and communication patterns influence infection-related decision making. MATERIALS/METHODS: Between May and November 2019, data were gathered through direct observations of ward rounds and face-to-face interviews with ward round participants in three high infection risk surgical specialties at a tertiary hospital in South Africa. Sociograms, a visual mapping method, mapped content and flow of communication and the social links between participants. Data were analysed using a grounded theory approach. RESULTS: Data were gathered from 70 hours of ward round observations, including 1024 individual patient discussions, 60 sociograms and face-to-face interviews with 61 healthcare professionals. AMS and infection-related discussions on ward rounds vary across specialties and are affected by the content and structure of the clinical update provided, consultant leadership styles and competing priorities at the bedside. Registrars and consultants dominate the discussions, limiting the input of other team members with recognised roles in AMS and infection management. Team hierarchies also manifest where staff position themselves, and this influences their contribution to active participation in patient care. Leadership styles affect ward-round dynamics, determining whether nurses and patients are actively engaged in discussions on infection management and antibiotic therapy and whether actions are assigned to identified persons. CONCLUSIONS: The surgical bedside ward round remains a medium of communication between registrars and consultants, with little interaction with the patient or other healthcare professionals. A team-focused and inclusive approach could result in more effective decision making about infection management and AMS.

Critical care admission of South African (SA) surgical patients: Results of the SA Surgical Outcomes Study.

BACKGROUND: Appropriate critical care admissions are an important component of surgical care. However, there are few data describing postoperative critical care admission in resource-limited low- and middle-income countries. OBJECTIVE: To describe the demographics, organ failures, organ support and outcomes of non-cardiac surgical patients admitted to critical care units in South Africa (SA). METHODS: The SA Surgical Outcomes Study (SASOS) was a 7-day national, multicentre, prospective, observational cohort study of all patients ≥16 years of age undergoing inpatient non-cardiac surgery between 19 and 26 May 2014 at 50 government-funded hospitals. All patients admitted to critical care units during this study were included for analysis. RESULTS: Of the 3 927 SASOS patients, 255 (6.5%) were admitted to critical care units; of these admissions, 144 (56.5%) were planned, and 111 (43.5%) unplanned. The incidence of confirmed or strongly suspected infection at the time of admission was 35.4%, with a significantly higher incidence in unplanned admissions (49.1 v. 24.8%, p<0.001). Unplanned admission cases were more frequently hypovolaemic, had septic shock, and required significantly more inotropic, ventilatory and renal support in the first 48 hours after admission. Overall mortality was 22.4%, with unplanned admissions having a significantly longer critical care length of stay and overall mortality (33.3 v. 13.9%, p<0.001). CONCLUSION: The outcome of patients admitted to public sector critical care units in SA is strongly associated with unplanned admissions. Adequate 'high care-dependency units' for postoperative care of elective surgical patients could potentially decrease the burden on critical care resources in SA by 23%. This study was registered on ClinicalTrials.gov (NCT02141867).

Burden of tuberculosis in intensive care units in Cape Town, South Africa, and assessment of the accuracy and effect on patient outcomes of the Xpert MTB/RIF test on tracheal aspirate samples for diagnosis of pulmonary tuberculosis: a prospective burden of disease study with a nested randomised controlled trial.

BACKGROUND: There are few prospective data about the incidence and mortality associated with pulmonary tuberculosis in intensive care units (ICUs), and none on the accuracy and clinical effect of the Xpert-MTB/RIF assay in this setting. We aimed to measure the frequency of culture-positive tuberculosis in ICUs in Cape Town, South Africa and to assess the performance and effect on patient outcomes of Xpert MTB/RIF versus smear microscopy for diagnosis of tuberculosis. METHODS: We did a prospective burden of disease study with a randomised controlled substudy at the ICUs of four hospitals in Cape Town. Mechanically ventilated adults (≥18 years) with suspected pulmonary tuberculosis admitted between Aug 1, 2010, and July 31, 2013 (irrespective of the reason for admission), were prospectively investigated by culture, and by Xpert-MTB/RIF testing or smear microscopy, of tracheal aspirate samples. In the substudy, patients were randomly assigned (1:1), via a computer-generated allocation list, to smear microscopy or Xpert MTB/RIF. Participants, caregivers, and outcome assessors were not masked to group assignment. Only the laboratory staff were blinded to the clinical details of the participants. In November, 2012, Xpert MTB/RIF was adopted as the initial diagnostic test for respiratory samples in Western Cape province. Thereafter, patients received Xpert MTB/MIF and culture as standard of care. For the whole study cohort, the primary outcome was the frequency of bacteriologically confirmed tuberculosis. The primary endpoint of the randomised substudy was the proportion of culture-positive patients on treatment at 48 h after enrolment. The randomised substudy is registered with ClinicalTrials.gov, number NCT01530568. FINDINGS: We investigated 341 patients for suspected pulmonary tuberculosis out of a total of 2309 ICU admissions. 46 (15%) of 317 patients included in the final analysis had a positive test for tuberculosis (Xpert MTB/RIF or culture). Culture-positive patients who failed to initiate treatment (adjusted HR 4·49, 95% CI 1·45-13·89) or who received inotropes (4·33, 1·49-12·60) were more likely to die. However, tuberculosis status was not associated with 28-day or 90-day mortality. In the substudy, we randomly assigned 115 patients to smear microscopy and 111 to Xpert MTB/RIF. Smear microscopy detected six (43%) of 14 culture-positive patients, and Xpert MTB/RIF detected 11 (100%) of 11 culture-positive patients (p=0·002). The proportion of culture-positive patients on treatment at 48 h was higher in the Xpert MTB/RIF group than in the smear microscopy group (11 [92%] of 12 vs nine [53%] of 17; p=0·043), although use of Xpert MTB/RIF had no effect on mortality or other patient outcomes. INTERPRETATION: Tuberculosis is fairly common in ICUs in high-burden settings, and clinicians should screen and test patients for tuberculosis with Xpert MTB/RIF where available. This test improves diagnostic yield and rates of treatment initiation, and reduces unnecessary treatment, but might not increase the total number of patients on treatment when empirical treatment is widely used. A suspected diagnosis of pulmonary tuberculosis should not exclude patients from ICU care in resource-limited settings because mortality is unaffected by the presence of this disease. FUNDING: European and Developing Countries Clinical Trials Partnership, South African Medical Research Council, and the Discovery Foundation.

ICU-associated Acinetobacter baumannii colonisation/infection in a high HIV-prevalence resource-poor setting.

BACKGROUND: There are hardly any data about the incidence, risk factors and outcomes of ICU-associated A.baumannii colonisation/infection in HIV-infected and uninfected persons from resource-poor settings like Africa. METHODS: We reviewed the case records of patients with A.baumannii colonisation/infection admitted into the adult respiratory and surgical ICUs in Cape Town, South Africa, from January 1 to December 31 2008. In contrast to colonisation, infection was defined as isolation of A.baumannii from any biological site in conjunction with a compatible clinical picture warranting treatment with antibiotics effective against A.baumannii. RESULTS: The incidence of A.baumannii colonisation/infection in 268 patients was 15 per 100 person-years, with an in-ICU mortality of 26.5 per 100 person-years. The average length of stay in ICU was 15 days (range 1-150). A.baumannii was most commonly isolated from the respiratory tract followed by the bloodstream. Independent predictors of mortality included older age (p = 0.02), low CD4 count if HIV-infected (p = 0.038), surgical intervention (p = 0.047), co-morbid Gram-negative sepsis (p = 0.01), high APACHE-II score (p = 0.001), multi-organ dysfunction syndrome (p = 0.012), and a positive blood culture for A.baumannii (p = 0.017). Of 21 A.baumannii colonised/infected HIV-positive persons those with clinical AIDS (CD4<200 cells/mm(3)) had significantly higher in-ICU mortality and were more likely to have a positive blood culture. Conclusion In this resource-poor setting A.baumannii infection in critically ill patients is common and associated with high mortality. HIV co-infected patients with advanced immunosuppression are at higher risk of death.

Antimicrobial susceptibility of gram-negative pathogens isolated from patients with complicated intra-abdominal infections in South African hospitals (SMART Study 2004-2009): impact of the new carbapenem breakpoints.

BACKGROUND: The Study for Monitoring Antimicrobial Resistance Trends (SMART) follows trends in resistance among aerobic and facultative anaerobic gram-negative bacilli (GNB) isolated from complicated intra-abdominal infections (cIAIs) in patients around the world. METHODS: During 2004-2009, three centralized clinical microbiology laboratories serving 59 private hospitals in three large South African cities collected 1,218 GNB from complicated intra-abdominal infections (cIAIs) and tested them for susceptibility to 12 antibiotics according to the 2011 Clinical Laboratory Standards Institute (CLSI) guidelines. RESULTS: Enterobacteriaceae comprised 83.7% of the isolates. Escherichia coli was the species isolated most commonly (46.4%), and 7.6% of these were extended-spectrum ß-lactamase (ESBL)-positive. The highest ESBL rate was documented for Klebsiella pneumoniae (41.2%). Overall, ertapenem was the antibiotic most active against susceptible species for which it has breakpoints (94.6%) followed by amikacin (91.9%), piperacillin-tazobactam (89.3%), and imipenem-cilastatin (87.1%), whereas rates of resistance to ceftriaxone, cefotaxime, ciprofloxacin, and levofloxacin were documented to be 29.7%, 28.7%, 22.5%, and 21.1%, respectively. Multi-drug resistance (MDR), defined as resistance to three or more antibiotic classes, was significantly more common in K. pneumoniae (27.9%) than in E. coli (4.9%; p<0.0001) or Proteus mirabilis (4.1%; p<0.05). Applying the new CLSI breakpoints for carbapenems, susceptibility to ertapenem was reduced significantly in ESBL-positive E. coli compared with ESBL-negative isolates (91% vs. 98%; p<0.05), but this did not apply to imipenem-cilastatin (95% vs. 99%; p=0.0928). A large disparity between imipenem-cilastatin and ertapenem susceptibility in P. mirabilis and Morganella morganii was documented (24% vs. 96% and 15% vs. 92%, respectively), as most isolates of these two species had imipenem-cilastatin minimum inhibitory concentrations in the 2-4 mcg/mL range, which is no longer regarded as susceptible. CONCLUSIONS: This study documented substantial resistance to standard antimicrobial therapy among GNB commonly isolated from cIAIs in South Africa. With the application of the new CLSI carbapenem breakpoints, discrepancies were noted between ertapenem and imipenem-cilastatin with regard to the changes in their individual susceptibilities. Longitudinal surveillance of susceptibility patterns is useful to guide recommendations for empiric antibiotic use in cIAIs.

Low-dose spinal anaesthesia for caesarean section.

PURPOSE OF REVIEW: The literature on the appropriate dose of local anaesthetic and combinations with opioids for spinal anaesthesia for caesarean section in patients without comorbid conditions is reviewed. The controversial issue of spinal anaesthesia in severe preeclampsia is also addressed. RECENT FINDINGS: Recent comparisons with ropivacaine and levobupivacaine suggest that bupivacaine remains the best agent for spinal anaesthesia for caesarean section. The addition of various combinations of opioids has allowed a reduction in the dose of bupivacaine. Intrathecal diamorphine has been extensively investigated and appears to have a favourable pharmacokinetic and pharmacodynamic profile. In severe preeclampsia, spinal anaesthesia may be associated with less hypotension than in healthy parturients, where similar doses of local anaesthetic are used. SUMMARY: Low-dose spinal anaesthesia has been advocated in the interests of improving cardiovascular stability. However, current sophistication of knowledge concerning spinal anaesthetic technique makes cardiovascular instability easy to prevent. Therefore this review emphasizes the importance of adequate surgical anaesthesia during caesarean section, and makes suggestions as to the optimal pharmacological agents for intraoperative anaesthesia and postoperative analgesia. Spinal anaesthesia is safe in severe preeclampsia, provided there are no contraindications to regional anaesthesia.