Gut microbiota composition reflects disease severity and dysfunctional immune responses in patients with COVID-19

OBJECTIVE

Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus.

METHODS

In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma.

RESULTS

Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase.

CONCLUSION

Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.

Molecular diagnosis in clinical parasitology: When and why?

Microscopic detection and morphological identification of parasites from clinical specimens are the gold standards for the laboratory diagnosis of parasitic infections. The limitations of such diagnostic assays include insufficient sensitivity and operator dependence. Immunoassays for parasitic antigens are not available for most parasitic infections and have not significantly improved the sensitivity of laboratory detection. Advances in molecular detection by nucleic acid amplification may improve the detection in asymptomatic infections with low parasitic burden. Rapidly accumulating genomic data on parasites allow the design of polymerase chain reaction (PCR) primers directed towards multi-copy gene targets, such as the ribosomal and mitochondrial genes, which further improve the sensitivity. Parasitic cell or its free circulating parasitic DNA can be shed from parasites into blood and excreta which may allow its detection without the whole parasite being present within the portion of clinical sample used for DNA extraction. Multiplex nucleic acid amplification technology allows the simultaneous detection of many parasitic species within a single clinical specimen. In addition to improved sensitivity, nucleic acid amplification with sequencing can help to differentiate different parasitic species at different stages with similar morphology, detect and speciate parasites from fixed histopathological sections and identify anti-parasitic drug resistance. The use of consensus primer and PCR sequencing may even help to identify novel parasitic species. The key limitation of molecular detection is the technological expertise and expense which are usually lacking in the field setting at highly endemic areas. However, such tests can be useful for screening important parasitic infections in asymptomatic patients, donors or recipients coming from endemic areas in the settings of transfusion service or tertiary institutions with transplantation service. Such tests can also be used for monitoring these recipients or highly immunosuppressed patients, so that early preemptive treatment can be given for reactivated parasitic infections while the parasitic burden is still low.

The first nocturnal home haemodialysis patient in Hong Kong

We report our experience of the first use of nocturnal home haemodialysis in Hong Kong. The patient, a 40-year-old man with end-stage renal failure, was recruited into the Nocturnal Home Haemodialysis Programme at Princess Margaret Hospital in 2006. He received haemodialysis at home on alternate nights (3.5 sessions per week) for 5.5 to 6 hours per session. After 1 year of nocturnal home haemodialysis, his recombinant human erythropoietin requirement had been reduced by more than 50%. His serum phosphate level decreased by 35% and calcium phosphate product by 34%. After nocturnal home haemodialysis, his blood pressure control has been excellent and he was able to cease taking anti-hypertensive medications soon after commencing nocturnal home haemodialysis. Regression of his left ventricular hypertrophy has also been noted, with a 39% decrease in his left ventricular mass index. The haemodialysis adequacy index, weekly single-pool Kt/V, increased by 59% after switching to nocturnal home haemodialysis and his quality-of-life indices also showed significant improvement. Nocturnal home haemodialysis holds promise as an alternative dialytic therapy for patients on chronic haemodialysis in Hong Kong.

Minimal change disease following exposure to mercury-containing skin lightening cream

A 34-year-old woman developed nephrotic syndrome after using a skin lightening cream that contained an extremely high level of mercury. Blood and urine mercury levels were elevated and a renal biopsy revealed minimal change disease. Membranous nephropathy was excluded using immunofluorescence and electron microscopy. Her proteinuria remitted 9 months after she stopped using the cosmetic cream. This is the first reported case in the English literature of proven minimal change disease secondary to mercury exposure. It is important that mercury poisoning due to cosmetic cream is considered in the differential diagnoses for any woman who presents with nephrotic syndrome.

Sodium ramping reduces hypotension and symptoms during haemodialysis

OBJECTIVES

To evaluate the effectiveness of sodium ramping (profiling) in reducing hypotensive episodes and symptoms during haemodialysis.

DESIGN

Prospective study.

SETTING

Regional hospital, Hong Kong.

PATIENTS

Thirteen patients who experienced frequent episodes of hypotension and/or symptoms such as cramps, dizziness, chest pain, nausea, vomiting, and headache during haemodialysis in the preceding 4 weeks.

INTERVENTIONS

Each patient was switched from standard haemodialysis with a constant dialysate sodium concentration of 135 to 140 mmol/L to a ramped sodium haemodialysis for a period of 4 weeks. During this time the dialysate sodium concentration was ramped linearly downwards from 150 mmol/L at the beginning of dialysis to 140 mmol/L at the end of dialysis.

MAIN OUTCOME MEASURES

Intradialytic hypotensive episodes, intradialytic symptoms, nursing interventions, systolic and diastolic blood pressures, and interdialytic weight gain.

RESULTS

A total of 248 haemodialysis sessions undertaken by 13 patients were analysed. Switching from constant sodium haemodialysis to ramped sodium haemodialysis resulted in a significant reduction in the number of intradialytic hypotensive episodes from 5.8 (standard deviation, 6.4) to 2.2 (3.3) [P<0.05], the total number of intradialytic symptoms from 7.1 (3.4) to 0.9 (1.3) [P<0.01], and nursing interventions from 11.3 (6.3) to 1.7 (3.9) [P<0.01]. Post-dialysis systolic and diastolic blood pressures were higher during ramped sodium haemodialysis compared with constant sodium haemodialysis (systolic blood pressure, 139 [standard deviation, 23] vs 133 [22] mm Hg, P<0.001; diastolic blood pressure, 77 [11] vs 74 [13] mm Hg, P<0.01), and there was a trend towards a smaller drop in blood pressure after dialysis. The interdialytic weight gain with sodium ramping haemodialysis was greater compared with constant sodium haemodialysis (3.1 [standard deviation, 1.0] vs 2.7 [1.1] kg, P<0.001).

CONCLUSION

Sodium ramping during haemodialysis effectively reduces hypotensive episodes and intradialytic symptoms. Post-dialysis blood pressure is better maintained. A side-effect of sodium ramping is a greater interdialytic weight gain.

In vitro activity and post-antibiotic effect of quinupristin/dalfopristin (Synercid)

The in vitro activities of quinupristin/dalfopristin (Synercid), ampicillin, erythromycin, clarithromycin, vancomycin, teicoplanin, ciprofloxacin and tetracycline were examined and compared against 526 gram-positive bacteria. The minimal inhibitory concentrations (MICs) for quinupristin/dalfopristin against Staphylococcus aureus, including methicillin-resistant strains, were low (MIC(90) = 0.5 mg/l), and were comparable with those of vancomycin and teicoplanin. This compound was superior to the macrolides and highly active against Streptococcus pneumoniae (both penicillin-sensitive and penicillin-resistant strains), with MIC(90) = 2 mg/l. It was also active against other streptococci, with MIC(90) = 4 mg/l. However, this agent is less active against enterococci (MIC(90) = 32 mg/l). Quinupristin/dalfopristin showed high activity against gram-positive anaerobes, including Clostridium spp., Peptococcus spp. and Peptostreptococcus spp., with MIC(90) < or = 2 mg/l. Quinupristin/dalfopristin was also investigated for its post-antibiotic effect (PAE) and bactericidal kinetics against nine strains of gram-positive organisms, including staphylococci, enterococci and pneumococci. Exponentially growing (log phase) cultures were exposed to quinupristin/dalfopristin at 2 x MIC. Growth kinetics was evaluated using viable counting. The drug was uniformly bactericidal against pneumococci and staphylococci within 2 and 8 h of exposure, respectively. The killing activity against enterococci was weak; there was little or no reduction in bacterial count over 24 h of incubation. PAEs ranging from 2.13 to 3.28 h, 0.92 to 3.02 h and 1.89 to 7.07 h were produced on the tested pneumococci, staphylococci and enterococci, respectively. This study showed that quinupristin/dalfopristin is a promising agent active against gram-positive bacteria. The prolonged PAEs also suggest that the drug could be used intermittently at more widely spaced dosing intervals against gram-positive organisms.

Effect of low molecular weight heparin on bone metabolism and hyperlipidemia in patients on maintenance hemodialysis

The effect of low molecular weight heparin (LMWH) on serum lipid profile in hemodialysis remains controversial and its effect on bone metabolism has not been studied. A crossover study was conducted in 40 patients on stable hemodialysis using unfractionated heparin (UFH) for more than 24 months. These patients were then treated with a LMWH (nadroparin-Ca) for 8 months during hemodialysis and subsequently switched back to UFH for 12 months. Serum lipid profile, biochemical markers for bone metabolism, and bone densitometry (BMD) were monitored at four-month intervals while all medications remained unchanged. Cholesterol (TC), triglyceride (TG), low-density lipoprotein-cholesterol (LDL-C), lipoprotein(a) (Lp(a)), apolipoprotein B (Apo B) were raised in 35%, 29%, 12%, 24% and 24% of patients respectively. High-density lipoprotein-cholesterol (HDL-C) and apolipoprotein A1 (Apo A-1) were reduced in 47% and 9% of patients. Bone-specific alkaline phosphatase (BALP) and intact osteocalcin (OSC), both reflecting osteoblastic activity, were raised in 65% and 94% of patients. Tartrate-resistant acid phosphatase (TRACP) reflecting osteoclastic activity and parathyroid hormone (PTH) were elevated in 35% and 88% of patients. Following LMWH treatment, TC, Tg, Lp(a) and Apo B were reduced by 7%, 30%, 21% and 10% respectively (p<0.05 or <0.01) while Apo A-1 were raised by 7% (p<0.01). Simultaneously, TRACP was reduced by 13% (p<0.05). These biochemical changes were detected soon after 4 months of LMWH administration. Although BMD values in our patients were lower than those of age-matched normal subjects, significant changes were not observed with LMWH treatment. After switching back to UFH for hemodialysis, these biochemical indices reverted to previous values during UFH treatment with a significant higher level in TC and Apo B while serum Apo A-1 remained elevated. Our study suggests LMWH may partially alleviate hyperlipidemia and, perhaps, osteoporosis associated with UFH administration in patients on maintenance hemodialysis.

Randomised controlled study of oral erythromycin for treatment of gastrointestinal dysmotility in preterm infants

AIM

To evaluate the effectiveness of oral erythromycin as a prokinetic agent for the treatment of moderately severe gastrointestinal dysmotility in preterm very low birthweight infants.

METHODS

A prospective, double blind, randomised, placebo controlled study in a tertiary referral centre of a university teaching hospital was conducted on 56 preterm infants (< 1500 g) consecutively admitted to the neonatal unit. The infants were randomly allocated by minimisation to receive oral erythromycin (12.5 mg/kg, every six hours for 14 days) or an equivalent volume of placebo solution (normal saline) if they received less than half the total daily fluid intake or less than 75 ml/kg/day of milk feeds by the enteral route on day 14 of life. The times taken to establish half, three quarters, and full enteral feeding after the drug treatment were compared between the two groups. Potential adverse effects of oral erythromycin and complications associated with parenteral nutrition were assessed as secondary outcomes.

RESULTS

Twenty seven and 29 infants received oral erythromycin and placebo solution respectively. The times taken to establish half, three quarters, and full enteral feeding after the drug treatment were significantly shorter in the group receiving oral erythromycin than in those receiving the placebo (p < 0.05, p < 0.05 and p < 0.0001 respectively). There was also a trend suggesting that more infants with prolonged feed intolerance developed cholestatic jaundice in the placebo than in the oral erythromycin group (10 v 5 infants). None of the infants receiving oral erythromycin developed cardiac dysrhythmia, pyloric stenosis, or septicaemia caused by multiresistant organisms.

CONCLUSIONS

Oral erythromycin is effective in facilitating enteral feeding in preterm very low birthweight infants with moderately severe gastrointestinal dysmotility. Treated infants can achieve full enteral feeding 10 days earlier, and this may result in a substantial saving on hyperalimentation. However, until the safety of erythromycin has been confirmed in preterm infants, this treatment modality should remain experimental. Prophylactic or routine use of this medication for treatment of mild cases of gastrointestinal dysmotility is probably not warranted at this stage.

Epidemiology of respiratory syncytial virus infection among paediatric patients in Hong Kong: seasonality and disease impact

In a 5-year retrospective survey of respiratory syncytial virus (RSV) infections among hospitalized children, 1340 cases were identified of which, 98.4% were children < 5 years old with a male:female ratio of 1.5: 1. Most cases occurred from April to September showing a significant positive correlation with temperature and relative humidity. Community-acquired infections accounted for 92.5% of the cases with a mean hospital stay of 5 days. The estimated annual incidence of RSV infection requiring hospitalization was 2.5/1000 children < 5 years old with a mortality of 0.15% among hospitalized cases. On average, 248 children were admitted each year to the 1400-bed acute regional hospital accounting for an expenditure of HK S1.94 ((approximately US +/-0.25) million for hospitalization costs which equates to an annual cost in excess of HK $6.67 (approximately US $0.86) million for the whole of Hong Kong. An RSV vaccine should be a priority.

Comparison of double-bag and Y-set disconnect systems in continuous ambulatory peritoneal dialysis: a randomized prospective multicenter study

We performed a multicenter, single-blinded, prospective randomized study on the use of a double-bag disconnect system (B) versus a Y-set disconnect system (Y). The peritonitis rate, exit site infection, clinical outcome, and patients' acceptance to the procedure were assessed. A total of 120 new end-stage renal failure patients of three regional hospitals were randomized: 60 each to the B and the Y systems. The results of 60 patients on the B system and 51 on the Y system were analyzable. They were followed up for a median of 16 months. Peritonitis rates for the B and the Y systems were 33.5 and 29.4 patient-months per episode, respectively. Exit site infection rates for the B and Y systems were 17.4 and 16.0 patient-months per episode, respectively. Four catheters were removed in each group. Patients on the B system were hospitalized for 2.1 days per patient per year related to peritonitis and exit site infection, and those on the Y system were hospitalized for 1.2 days. There was no significant difference between the B and Y systems in the incidences of peritonitis (all causes and those due to coagulase-negative staphylococci), exit site infection, and in hospitalization days. However, there was a higher percentage of gram-positive infections in the Y system (52%) than in the B system (32%) and a lower percentage of gram-negative infections in the Y system (16%) than in the B system (32%). Patients on the B system had a better acceptance of the procedure than patients on the Y system, as assessed by a six-item, 10-point questionnaire (total score, 43.1 +/- 10.2 v 37.6 +/- 9.4; P < 0.005 at 1 month; 44.6 +/- 9.1 v 39.8 +/- 8.6; P < 0.01 at 6 months). From this study, it is concluded that the B and Y systems are similar in the incidences of peritonitis and exit site infection, although the B system is better accepted by patients. This is probably the first multicenter randomized study comparing the double-bag and Y-set disconnect system using only new patients who had never used other systems of continuous ambulatory peritoneal dialysis.

A tracing evoked potential estimator

The paper presents an adaptive Gaussian radial basis function neural network (RBFNN) for rapid estimation of evoked potential (EP). Usually, a recorded EP is severely contaminated by background ongoing activities of the brain. Many approaches have been reported to enhance the signal-to-noise ratio (SNR) of the recorded signal. However, non-linear methods are seldom explored due to their complexity and the fact that the non-linear characteristics of the signal are generally hard to determine. An RBFNN possesses built-in non-linear activation functions that enable the neural network to learn any function mapping. An RBFNN was carefully designed to model the EP signal. It has the advantage of being linear-in-parameter, thus a conventional adaptive method can efficiently estimate its parameters. The proposed algorithm is simple so that its convergence behaviour and performance in signal-to-noise ratio (SNR) improvement can be mathematically derived. A series of experiments carried out on simulated and human test responses confirmed the superior performance of the method. In a simulation experiment, an RBFNN having 15 hidden nodes was trained to approximate human visual EP (VEP). For detecting human brain stem auditory EP (BAEP), the approach (40 hidden nodes and convergence rate = 0.005) speeded up the estimation remarkably by using only 80 ensembles to achieve a result comparable to that obtained by averaging 1000 ensembles.

Rotavirus infection in Hong Kong: epidemiology and estimates of disease burden

Rotavirus gastroenteritis should soon be a vaccine-preventable disease. In a 10-year survey of rotavirus gastroenteritis conducted at the Prince of Wales Hospital (PWH), 2281 cases were detected of which 2213 (97%) occurred in children < 5 years old. A consistent epidemic occurred each winter during the months of December and January. Of all laboratory-confirmed cases, 78% were community-acquired with a mean hospital stay of 4.7 days. The estimated incidence of rotavirus-attributed hospitalization was 2/1000 children < 5 years old. Over the 10 years, rotavirus was responsible for one death, and contributory to three other deaths. On average each year, 195 children < 5 years old were hospitalized for a total of 917 days in PWH, accounting for an estimated expenditure of HK$2.8 (approximately US$0.4) million on hospitalization costs. The annual financial burden for rotavirus gastroenteritis for the whole of Hong Kong could be in excess of HK$9.6 (approximately US$1.2) million.

Necrotizing fasciitis of the foot caused by an unusual organism, Vibrio vulnificus

In modern medicine, there are very few infectious disease processes occurring in the foot that can cause death within 48 hr. and have an overall mortality rate of 50% despite appropriate antibiotic and surgical treatment. Such a condition must be regarded as being potentially deadly. The authors report a case of necrotizing fasciitis of the left foot resulting from an unusual organism of Vibrio vulnificus.

Rapid emergence of penicillin-resistant pneumococci in Hong Kong

The prevalence of penicillin resistance in Streptococcus pneumoniae isolated at the Prince of Wales Hospital, Hong Kong, rose from 6.6% of sputum isolates in the first quarter of 1993 to 55.8% of isolates in the second quarter of 1995. Most of the isolates were also resistant to co-trimoxazole, tetracycline, choramphenicol and erythromycin. Type 19F was the most common capsular type in 1993-1994, comprising 40.0% of typed isolates in this period. Type 23F emerged in 1995 as the predominant type, making up 62.2% of typed isolates in the first 2 quarters of 1995. A high population density and excessive community use of antibiotics are likely to be factors promoting the rapid emergence of multiply-resistant pneumococci in Hong Kong.

Self-inflicted bacteraemia and fungaemia in Vietnamese migrants

From early 1993, we received a number of blood cultures, all from Vietnamese inmates of the Whitehead Detention Centre, the biggest detention camp in Hong Kong, which grew unusual organisms. Upon follow-up, the majority of the patients were found to abscond from the hospital a few days after having been admitted with a clinical picture of septic shock. During the period from March 1993 to late 1994, we noted a total of 25 positive blood cultures from 21 previously healthy Vietnamese migrants with this syndrome. The mean age was 27.8 years and 20 were males. The organisms isolated from the blood cultures were of low pathogenicity such as Saccharomyces cerevisiae, Trichosporon spp., Baciflus spp. and Micrococcus spp. Fourteen of the patients complained of abdominal pain and 3 others had apical pneumothoraces. Eighteen had shock requiring resuscitation. Multiple puncture or needle marks were found in 11 patients, mainly involving the lower limbs. One patient admitted inducing illness by self-injection, and it was suspected that all these infections were self-inflicted. The range of hospitalization was 1-13 days (mean 3.05 days). Eighteen of the 21 patients absconded.

Cutaneous protothecosis: report of a case in Hong Kong

We report a patient who presented with recalcitrant ulcerated papules and plaques on both legs. Histopathology revealed protothecosis, and subsequent culture of the lesions grew Prototheca wickerhamii. Gradual resolution of the ulcers occurred on treatment with itraconazole.

Development and validation of a claims based index for adjusting for risk of mortality: the case of acute myocardial infarction

We developed a comorbidity index on a cohort of 162,699 Medicare beneficiaries who had an acute myocardial infarction (AMI) in 1987 and validate it on two national cohorts: (1) a cohort of 164,427 Medicare beneficiaries who had an AMI in 1988 and (2) a cohort of 10,466 patients admitted to Veterans Administration Hospitals (VAH) for AMI in 1988-1991. The impact of each sensitivity was expressed as; (1) the risk of mortality for those with the comorbidity, (2) the adjustment to the log odds for 2 year mortality and (3) the age-based likelihood of 2 year mortality. Models were validated by calculated the area under an ROC curve obtained by fitting a logistic regression model to each validation population. The two year mortality rate for 30-day survivors was approximately 30% in each of the 3 cohorts. The 5 most prevlent comorbidities coded in the developmental cohort were heart failure (34%), chronic angina (27%), minor arrythmias (25%) and uncomplicated hypertension (18%). Cancer was the most powerful predictor of 2 year mortality, impacting mortality the same as a 18.3 year age increase. Saturation (having all secondary diagnoses in the discharge summary filled) resulted in a 9.2 year age increase. Validation in the 1988 Medicare and in the Veterans Administration Hospitals cohorts resulted in areas of 73% and 72% under the respective ROC curves. Our methods can serve as a prototype for others wishing to assess comorbidity in other targeted subgroups.

The antimicrobial activity and beta-lactamase stability of cefpirome, a new fourth-generation cephalosporin in comparison with other agents

The antimicrobial activity of cefpirome was compared with amoxycillin/clavulanic acid, ampicillin/sulbactam, cefuroxime, ceftazidime, gentamicin and amikacin against 743 non-duplicate clinical isolates. MIC50 and MIC90 showed that the antibiotic was active against both Gram-negative and Gram-positive organisms. Cefpirome was highly active against most of the Enterobacteriaceae, including indole-positive Proteus spp., Aeromonas spp. (MIC < or = 1 mg/L) and Salmonella spp. (MIC < or = 0.5 mg/L). Neisseria gonorrhoeae and Haemophilus influenzae (including beta-lactamase producers) were all susceptible, with MIC less than 0.5 and 0.25 mg/L respectively. Cefpirome was more active than cefuroxime and ceftazidime against Campylobacter spp. (MIC < or = 2 mg/L), but less active than ceftazidime against Pseudomonas aeruginosa. Cefpirome was active against Streptococcus pneumoniae. Streptococcus bovis and coagulase-negative staphylococci (MIC < or = 0.5 mg/L) and methicillin-sensitive Staphylococcus aureus (MIC < or = 2 mg/L). Methicillin-resistant S. aureus, Gram-positive and Gram-negative anaerobes were resistant to cefpirome. The stability of cefpirome to TEM-1, TEM-2, PSE-1, SHV-1 and the chromosomal-mediated P99 and K-1 beta-lactamases was comparable to ceftazidime.