Aetiology of community-acquired pneumonia in hospitalized adult patients in New Caledonia

Epidemiological trends of respiratory tract pathogens detected via mPCR in Australian adult patients before COVID-19

BACKGROUND

Respiratory tract infections (RTIs) are a major global health burden due to their high morbidity and mortality. This retrospective study described the epidemiology of respiratory pathogens in adults over a 5-year period at an Australian tertiary healthcare network.

METHODS

All multiplex reverse transcription polymerase chain reaction respiratory samples taken between the 1st of November 2014 and the 31st of October 2019 were included in this study. Overall prevalence and variations according to seasons, age groups and sex were analysed, as well as factors associated with prolonged hospital and intensive care length of stay.

RESULTS

There were 12,453 pathogens detected amongst the 12,185 positive samples, with coinfection rates of 3.7%. Picornavirus (Rhinovirus), Influenza A and respiratory syncytial virus were the most commonly detected pathogens. Mycoplasma pneumoniae was the most commonly detected atypical bacteria. Significant differences in the prevalence of Chlamydia pneumoniae and Human metapneumovirus infections were found between sexes. Longest median length of intensive care and hospital stay was for Legionella species. Seasonal variations were evident for certain pathogens.

CONCLUSIONS

The high rates of pathogen detection and hospitalisation in this real-world study highlights the significant burden of RTIs, and the urgent need for an improved understanding of the pathogenicity as well as preventative and treatment options of RTIs.

Low Levels of Procalcitonin Are Related to Decreased Antibiotic Use in Children Hospitalized Due to Influenza

Procalcitonin increases in bacterial infections, which are often suspected (though rarely confirmed) in paediatric influenza. We retrospectively verified procalcitonin’s usefulness in antibiotic guidance in children hospitalized due to laboratory-confirmed influenza. The ROC curve analysis evaluated procalcitonin’s performance in terms of antibiotic implementation or continuation in patients who were naive or had been receiving antibiotic treatment prior to hospital admission. We also assessed the procalcitonin’s usefulness to predict lower-respiratory-tract infections (LRTI), the presence of radiologically confirmed pneumonia, an intensive care unit transfer and a fatal outcome. Multiple regression models were built to verify the previously reported procalcitonin cut-off values. The study enrolled 371 children (median age 33 months). The AUC (area under the curve) for antibiotic implementation reached 0.66 (95%CI: 0.58–0.73) and 0.713 (95%CI: 0.6–0.83) for antibiotic continuation; optimal cut-offs (0.4 and 0.23 ng/mL, respectively) resulted in a negative predictive value (NPV) of 79.7% (95%CI: 76.2–82.9%) and 54.6% (95%CI: 45.8–63%), respectively. The use of 0.25 ng/mL as a reference decreased the odds of antibiotic treatment by 67% (95%CI: 43–81%) and 91% (95%CI: 56–98%), respectively. Procalcitonin showed lower AUC for the prediction of LRTI and pneumonia (0.6, 95%CI: 0.53–0.66, and 0.63, 95%CI: 0.56–0.7, respectively), with a moderately high NPV in the latter case (83%, 95%CI: 79.3–86.1%). Procalcitonin use may decrease the antibiotic frequency in hospitalized influenza cases both in terms of antibiotic administration and continuation. Procalcitonin concentrations may suggest bacterial suprainfections at lower concentrations than in adults, and a focus on its rule-out value is of special interest.

Radiological, epidemiological and clinical patterns of pulmonary viral infections

Respiratory viruses are the most common causes of acute respiratory infections. However, identification of the underlying viral pathogen may not always be easy. Clinical presentations of respiratory viral infections usually overlap and may mimic those of diseases caused by bacteria. However, certain imaging morphologic patterns may suggest a particular viral pathogen as the cause of the infection. Although definitive diagnosis cannot be made on the basis of clinical or imaging features alone, the use of a combination of clinical and radiographic findings can substantially improve the accuracy of diagnosis. The purpose of this review is to present the clinical, epidemiological and radiological patterns of lower respiratory tract viral pathogens providing a comprehensive approach for their diagnosis and identification in hospitals and community outbreaks.

Respiratory virus detection and co-infection in children and adults in a large Australian hospital in 2009-2015

AIM

This hospital network-based retrospective observational study aimed to describe the prevalence and seasonality of paediatric and adult viral respiratory pathogens and their rates of co-infections, following the introduction of a rapid multiplex molecular diagnostic assay.

METHODS

All nasopharyngeal samples tested in patients presenting to Monash Health, Melbourne, Australia, from August 2009 to July 2015 by means of multiplex tandem polymerase chain reaction using the Respiratory Pathogen 12Plex kit (AusDiagnostics) were included in the analysis.

RESULTS

There were 28 729 patient samples analysed after duplicate samples were excluded. Positive results were twice as likely in paediatrics, 7573/11 491 (65.9%), compared to adults, 5410/17 238 (31.4%). Co-infection was more frequent in paediatrics, 1642/7573 (21.7% of positives), compared to adults 299/5410 (5.5%). Adenovirus had a high prevalence as a co-infection, 639/990 (64.5%), in paediatrics. Testing frequency increased by 179% in the paediatric group and by 949% for adults over the 6 years of observation.

CONCLUSIONS

This study demonstrated a significant difference in the positive detection rate of pathogens and co-infections between the population groups. Adenovirus had a surprisingly high prevalence as a co-infection, especially in paediatric patients. Over the study period, rapid uptake of the test was observed, especially in adults. This raises concerns about how we can ensure that testing remains rational and is able to be provided in a cost-effective manner in the future.

Comparison of viral infection in healthcare-associated pneumonia (HCAP) and community-acquired pneumonia (CAP)

Background

Although viruses are known to be the second most common etiological factor in community-acquired pneumonia (CAP), the respiratory viral profile of the patients with healthcare-associated pneumonia (HCAP) has not yet been elucidated. We investigated the prevalence and the clinical impact of respiratory virus infection in adult patients with HCAP.

Methods

Patients admitted with HCAP or CAP, between January and December 2016, to a tertiary referral hospital in Korea, were prospectively enrolled, and virus identification was performed using reverse-transcription polymerase chain reaction (RT-PCR).

Results

Among 452 enrolled patients (224 with HCAP, 228 with CAP), samples for respiratory viruses were collected from sputum or endotracheal aspirate in 430 (95.1%) patients and from nasopharyngeal specimens in 22 (4.9%) patients. Eighty-seven (19.2%) patients had a viral infection, and the proportion of those with viral infection was significantly lower in the HCAP than in the CAP group (13.8% vs 24.6%, p = 0.004). In both the HCAP and CAP groups, influenza A was the most common respiratory virus, followed by entero-rhinovirus. The seasonal distributions of respiratory viruses were also similar in both groups. In the HCAP group, the viral infection resulted in a similar length of hospital stay and in-hospital mortality as viral–bacterial coinfection and bacterial infection, and the CAP group showed similar results.

Conclusions

The prevalence of viral infection in patients with HCAP was lower than that in patients with CAP, and resulted in a similar prognosis as viral–bacterial coinfection or bacterial infection.

Viral infection in community-acquired pneumonia: a systematic review and meta-analysis

The advent of PCR has improved the identification of viruses in patients with community-acquired pneumonia (CAP). Several studies have used PCR to establish the importance of viruses in the aetiology of CAP.We performed a systematic review and meta-analysis of the studies that reported the proportion of viral infection detected via PCR in patients with CAP. We excluded studies with paediatric populations. The primary outcome was the proportion of patients with viral infection. The secondary outcome was short-term mortality.Our review included 31 studies. Most obtained PCR via nasopharyngeal or oropharyngeal swab. The pooled proportion of patients with viral infection was 24.5% (95% CI 21.5-27.5%). In studies that obtained lower respiratory samples in >50% of patients, the proportion was 44.2% (95% CI 35.1-53.3%). The odds of death were higher in patients with dual bacterial and viral infection (OR 2.1, 95% CI 1.32-3.31).Viral infection is present in a high proportion of patients with CAP. The true proportion of viral infection is probably underestimated because of negative test results from nasopharyngeal or oropharyngeal swab PCR. There is increased mortality in patients with dual bacterial and viral infection.

The frequency of influenza and bacterial coinfection: a systematic review and meta-analysis

Aim

Coinfecting bacterial pathogens are a major cause of morbidity and mortality in influenza. However, there remains a paucity of literature on the magnitude of coinfection in influenza patients.

Method

A systematic search of MeSH, Cochrane Library, Web of Science, SCOPUS, EMBASE, and PubMed was performed. Studies of humans in which all individuals had laboratory confirmed influenza, and all individuals were tested for an array of common bacterial species, met inclusion criteria.

Results

Twenty‐seven studies including 3215 participants met all inclusion criteria. Common etiologies were defined from a subset of eight articles. There was high heterogeneity in the results (I² = 95%), with reported coinfection rates ranging from 2% to 65%. Although only a subset of papers were responsible for observed heterogeneity, subanalyses and meta‐regression analysis found no study characteristic that was significantly associated with coinfection. The most common coinfecting species were Streptococcus pneumoniae and Staphylococcus aureus, which accounted for 35% (95% CI, 14%–56%) and 28% (95% CI, 16%–40%) of infections, respectively; a wide range of other pathogens caused the remaining infections. An assessment of bias suggested that lack of small‐study publications may have biased the results.

Conclusions

The frequency of coinfection in the published studies included in this review suggests that although providers should consider possible bacterial coinfection in all patients hospitalized with influenza, they should not assume all patients are coinfected and be sure to properly treat underlying viral processes. Further, high heterogeneity suggests additional large‐scale studies are needed to better understand the etiology of influenza bacterial coinfection.

Incidence of respiratory viral infections detected by PCR and real-time PCR in adult patients with community-acquired pneumonia: a meta-analysis

Background

With the development of more rapid and sensitive detection methods based on PCR techniques, the contributions of respiratory viral infections to community-acquired pneumonia (CAP) in adult patients are being more and more recognized. Yet, up to now, there has been a lack of synthetic data that clearly demonstrates the incidence of respiratory viral infections in adult patients with CAP.

Objectives

We intended to demonstrate the incidence of respiratory viral infections detected by PCR and real-time PCR in adult patients with CAP.

Methods

We searched PubMed and Embase for studies providing the incidence of respiratory viral infections in adult patients with CAP. We investigated potential sources of heterogeneity by a univariant metaregression analysis and calculated the combined incidence of viral infections, viral infections mixed with other pathogens and individual respiratory virus species.

Results

We eventually identified 23 eligible reports with a total number of 6,404 patients. Incidences ranged from 8.6 to 56.2% for overall respiratory viral infections. We noted significant heterogeneity in incidence estimates for the incidence of viral infections (Cochran's χ² = 269.9, p < 0.0001, I² = 91.8%). The combined incidence of viral infections was 22.4% (95% CI = 19.0-25.7). Incidences of viral coinfections with other pathogens ranged from 3 to 28%. A high level of heterogeneity was identified as well during the estimates for incidences of coinfections (χ² = 200.9, p < 0.0001, I² = 91.5%). The combined incidence of viral coinfections with other pathogens was 12.4% (95% CI = 9.7-15.0). Our heterogeneity analyses suggested that a lower respiratory tract sample was associated with higher overall viral incidence. Moreover, the influenza virus, rhinovirus and coronavirus were the 3 most frequently detected viral pathogens in adult patients with CAP according to our study.

Conclusions

Respiratory viruses are probably crucial pathogens of adult patients with CAP, with the influenza virus being the most frequent viral pathogen identified. More than half of the viral infections are characterized as mixed infections with other pathogens.

Sputum bacteriology and antibiotic sensitivity patterns of community-acquired pneumonia in hospitalized adult patients in Nigeria: a 5-year multicentre retrospective study

BACKGROUND

A clear knowledge of the pathogens responsible for community-acquired pneumonia (CAP) in a given region and their antibiotic sensitivity patterns is necessary for optimal treatment. We determined the common bacterial pathogens causing CAP in Nigeria and further reviewed their antibiotic senstivity patterns with a view to providing recommendations to improve antibiotic management of CAP.

METHODS

Case notes of all adult patients who were 18 years or more admitted to four major tertiary hospitals in South East Nigeria with a diagnosis of CAP between 2008 and 2012 were retrospectively studied. To be eligible, patients were required to have sputum culture and sensitivity results available. Socio-demographic, clinical, pre-admission and in-hospital treatment data were also obtained.

RESULTS

Of 400 patients with a radiologically confirmed diagnosis of CAP, 232 fulfilled the study criteria; 122 (52.6%) were women and the mean age was 50.6 ± 18.8 years. Aetiological agents were identified from sputum in 189 (81.5%) patients. Streptococcus pneumoniae (n = 90, 47.6%) was the most frequent isolate followed by Klebsiella pneumoniae (n = 62, 32.8%), Staphylococcus aureus (n = 24, 12.7%) and Streptococcus pyogenes (n = 13, 6.9%). The pathogens were most sensitive to levofloxacin (77%), ceftazidime (75.5%) and ofloxacin (55.8%). The susceptibility of the isolates to antibiotics most frequently presecribed for empirical therapy was low (co-amoxiclav, 47.6%; ciprofloxacin, 45.9% and ceftriaxone, 47.6%) and this was associated with higher mortality and/or longer duration of hospital stay in survivors.

CONCLUSION

Strep. pneumoniae and K. pneumoniae were the most common causes of CAP. The pathogens were most sensitive to levofloxacin and ceftazidime. We suggest that these antibiotics should increasingly be considered as superior options for empirical treatment of CAP in Nigeria.

Epidemiology of human respiratory viruses in children with acute respiratory tract infections in Jinan, China

The viral etiologies of UTRIs and LTRIs in children in Jinan city were investigated between July 2009 and June 2010. Nasal and throat swabs were collected from 397 children with URTIs and bronchoalveolar lavage fluid specimens were collected from 323 children with LRTIs. RT-PCR/PCR was used to examine all samples for IFV, PIV, RSV, RV, hMPV, HBoV, CoV, ADV, RSV, and EV. Viral pathogens were detected in 47.10% of URTI samples and 66.57% samples, and the incidence of viral coinfection was 5.29% and 21.05%, respectively. IFV was the most common virus in URTIs, with a detection rate of 19.40%, followed by PIV (10.83%), RV (10.58%), and EV (6.30%). For LRTIs, PIV and RV were both detected in 27% of samples, followed by RSV (9.91%), HBoV (8.36%), IFV (5.57%), and hMPV (5.57%). RSV and HBoV were more prevalent in the youngest children of no more than six months. Meanwhile, RV, PIV, and RSV were the most frequent viruses combined with bacterial pathogens in LRTIs. In conclusion, the spectrum of respiratory virus infections in URTIs and LRTIs differed in terms of the most common pathogens, seasonal distribution, and coinfection rate.

A review of the evidence to support influenza vaccine introduction in countries and areas of WHO's Western Pacific Region

Background

Immunization against influenza is considered an essential public health intervention to control both seasonal epidemics and pandemic influenza. According to the World Health Organization (WHO), there are five key policy and three key programmatic issues that decision-makers should consider before introducing a vaccine. These are (a) public health priority, (b) disease burden, (c) efficacy, quality and safety of the vaccine, (d) other inventions, (e) economic and financial issues, (f) vaccine presentation, (g) supply availability and (h) programmatic strength. We analyzed the body of evidence currently available on these eight issues in the WHO Western Pacific Region.

Methodology/Principal Findings

Studies indexed in PubMed and published in English between 1 January 2000 and 31 December 2010 from the 37 countries and areas of the Western Pacific Region were screened for keywords pertaining to the five policy and three programmatic issues. Studies were grouped according to country income level and vaccine target group. There were 133 articles that met the selection criteria, with most (90%) coming from high-income countries. Disease burden (n = 34), vaccine efficacy, quality and safety (n = 27) and public health priority (n = 27) were most frequently addressed by studies conducted in the Region. Many studies assessed influenza vaccine policy and programmatic issues in the general population (42%), in the elderly (24%) and in children (17%). Few studies (2%) addressed the eight issues relating to pregnant women.

Conclusions/Significance

The evidence for vaccine introduction in countries and areas in this Region remains limited, particularly in low- and middle-income countries that do not currently have influenza vaccination programmes. Surveillance activities and specialized studies can be used to assess the eight issues including disease burden among vaccine target groups and the cost-effectiveness of influenza vaccine. Multi-country studies should be considered to maximize resource utilization for cross-cutting issues such as vaccine presentation and other inventions.

Prospects for molecular point-of-care diagnosis of lower respiratory infections at the hospital’s doorstep

Now that molecular assays have been simplified, they can be performed at the point of care (POC). As we aimed to evaluate POC detection of respiratory viruses, we have collected studies on the molecular detection of viruses in children and adults with a well-characterized diagnosis, made in hospital settings, of community-acquired acute bronchiolitis (AB) or pneumonia (CAP). We then present the epidemiological issues for each disease. The prevalence of 18 virus species and types was determined separately for each disease, virus by virus. Overall, the median detection rate of viruses was 90% (interquartile range [IQR]: 69.25–93.5%) and 71.8% (IQR: 69.25–74.25%) in children with AB and CAP, respectively, and 24.5% (IQR: 20–30%) in adults with CAP. The observations on the relationship between virological findings and severity of disease were conflicting in AB, while those for influenza-related CAP were significantly associated with high morbidity/mortality. There is evidence supporting the suggestion that molecular POC detection of targeted pathogens could optimize bed management in emergency departments, guide anti-infective therapies and prevent nosocomial outbreaks. However, further investigations are required to determine when the detection of a large panel of viruses should be processed in clinical practice.

Lower respiratory infections among hospitalized children in New Caledonia: a pilot study for the Pneumonia Etiology Research for Child Health project

We conducted a prospective pilot study over a 1-year period in New Caledonia in preparation for the Pneumonia Research for Child Health (PERCH) project. The pathogens associated with hospitalized lower respiratory infections in children were identified through the use of culture of induced sputum and blood, urinary antigen detection, polymerase chain reaction (PCR) on respiratory specimens, and serology on paired sera. Respiratory viruses were detected on respiratory specimens by immunofluorescence and PCR, and by serology on paired sera. Pathogens were detected in 87.9% of the 108 hospitalized cases. Viruses represented 81.6% of the 152 pathogens detected. Respiratory syncytial virus and rhinovirus were the most frequent, accounting for 32.2% and 24.3% of the pathogens identified, respectively. Only 26.3% of 99 induced sputum specimens collected were determined to be of good quality, which may be a consequence of the collection method used.