Pathogens Of Respiratory Infections Research Articles

Country data on AMR in Pakistan in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome.

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review the current situation with respect to AMR in Pakistan and initiatives addressing it. Identifying areas where more information is required will provide a call to action to minimize any further rises in AMR and improve patient outcomes.MethodsNational AMR initiatives, antibiotic use and prescribing in Pakistan, and availability of susceptibility data, in particular for the key community-acquired respiratory tract infection (CA-RTI) pathogens (Streptococcus pneumoniae and Haemophilus influenzae) were identified. National and international antibiotic prescribing guidelines for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) commonly used locally were also reviewed, plus local antibiotic availability. Insights from a local clinician and clinical microbiologist were sought to contextualize this information.ConclusionsPakistan is active in developing initiatives to address AMR such as compiling a National Action Plan. However, antibiotic consumption is high and although there is legislation in place prohibiting over-the-counter purchase of antibiotics, this is still possible. Healthcare professionals use local and international antibiotic prescribing guidelines for CA-RTIs when managing patients. As highlighted by the clinical microbiologist’s expert comments, surveillance of AMR in locally prevalent microorganisms is lacking. A more standardized inclusive approach in developing local guidelines, using up-to-date local surveillance data of isolates from community-acquired infections, could make management guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve clinical outcomes for patients.

Country data on AMR in Kuwait in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome.

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review AMR in Kuwait and initiatives underway addressing it. Identifying any areas where more information is required will provide a call to action to minimize any further rise in AMR within Kuwait and to improve patient outcomes.MethodsNational initiatives to address AMR, antibiotic use and prescribing, and availability of susceptibility data, particularly for the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used locally for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) were also reviewed, plus local antibiotic availability. Insights from a clinician in Kuwait were sought to contextualize this information.ConclusionsIn Kuwait there have been some initiatives addressing AMR such as annual campaigns for proper use of antibiotics. Antibiotic use is high but there appears to be a low understanding in the general public about their appropriate use. However, there is legislation in place prohibiting over-the-counter purchase of antibiotics. Only international guidelines for CA-RTIs are used. A more standardized inclusive approach in developing local guidelines, using up-to-date surveillance data of isolates from community-acquired infections in Kuwait, could make management guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve clinical patient outcomes.

Country data on AMR in Mexico in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review AMR in Mexico and initiatives addressing it. Identifying any areas where more information is required will provide a call to action to minimize any further rises in AMR and to improve patient outcomes.MethodsNational AMR initiatives in Mexico, antibiotic use and prescribing, and availability of susceptibility data, particularly the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used in Mexico for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) were also reviewed, along with local antibiotic availability. Insights from a local clinician were sought to contextualize this information.ConclusionsThe Mexican national AMR strategy was published in 2018. This comprised similar objectives to the Global Action Plan from the World Health Assembly (2015) and was compulsory, requiring full compliance from members of the National Health System. Historically, antibiotic consumption in Mexico has been high, however, between 2000 and 2015, consumption fell, in sharp contrast to the majority of countries. Mexico lacks a national surveillance network for AMR, however there are several ongoing global surveillance studies providing local antibiotic susceptibility data. International and local antibiotic prescribing guidelines for CA-RTIs are used. A more standardized inclusive approach in developing local guidelines, using up-to-date local surveillance data of isolates from community-acquired infections, could make guideline use more locally relevant. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development in Mexico and improve patient outcomes.

Country data on AMR in Vietnam in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicines and clinical outcome.

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review the current situation with respect to AMR in Vietnam and initiatives addressing it. Identifying areas where more information is required will provide a call to action to minimize any further rises in AMR within Vietnam and improve patient outcomes.MethodsNational initiatives to address AMR in Vietnam, antibiotic use and prescribing, and availability of susceptibility data, in particular for the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines for CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) commonly used locally were also reviewed, plus local antibiotic availability. Insights from clinicians in Vietnam were sought to contextualize this information.ConclusionsIn Vietnam there have been some initiatives addressing AMR; Vietnam was the first country in the Western Pacific Region to develop a national action plan to combat AMR, which according to the WHO is being implemented. Vietnam also has one of the highest rates of AMR in Asia due, in part, to the overuse of antimicrobial drugs, both in the animal health sector and in humans in both hospitals and the community. In addition, despite a 2005 law requiring antibiotic prescription, there is unrestricted access to over-the-counter antibiotics. Several global surveillance studies provide antibiotic susceptibility data for CA-RTI pathogens in Vietnam including Survey of Antibiotic Resistance (SOAR) and SENTRY (small isolate numbers only). For management of the common CA-RTIs in Vietnam there are several country-specific local antibiotic prescribing guidelines and in addition, there is a range of international guidelines referred to, but these may have been created based on pathogen resistance patterns that might be very different to those in Vietnam. Expert clinician opinion confirms the high resistance rates among common respiratory pathogens. A more standardized inclusive approach in developing local guidelines, using up-to-date surveillance data of isolates from community-acquired infections in Vietnam, could make management guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve clinical outcomes for patients.

Country data on AMR in Türkiye in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome.

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review AMR in Türkiye and initiatives addressing it. Identifying any areas where more information is required will provide a call to action to minimize any further rise in AMR within Türkiye and to improve patient outcomes.MethodsNational AMR initiatives, antibiotic use and prescribing, and availability of susceptibility data, particularly for the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used locally for specific CA-RTIs (community-acquired pneumonia, acute otitis media, acute bacterial rhinosinusitis) were also reviewed, plus local antibiotic availability. Insights from both a local clinician and local clinical microbiologist were sought to contextualize this information.ConclusionsTürkiye developed an antibiotic stewardship programme, The Rational Drug Use National Action Plan 2014–2017, prioritizing appropriate antibiotic prescription in the community. Public campaigns discouraging inappropriate antibiotic use were also initiated. Türkiye has a high level of antibiotic resistance and a high level of consumption, however, in 2015 over-the-counter antibiotic sales were prohibited, resulting in a declining trend in overall consumption. There is still a need for physician education on current developments in antibiotic use. Several ongoing global surveillance studies provide antibiotic susceptibility data in Türkiye. Clinicians in Türkiye use several country-specific guidelines for common CA-RTIs plus a range of international guidelines. A more standardized inclusive approach in developing local guidelines, using up-to-date surveillance data on isolates from community-acquired infections in Türkiye, could make guideline use more relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve patient outcome.

Country data on AMR in Saudi Arabia in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome.

BackgroundAntimicrobial resistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review AMR in Saudi Arabia and initiatives addressing it. Identifying areas where more information is required will provide a call to action to minimize a further rise in AMR within Saudi Arabia and improve patient outcomes.MethodsNational AMR initiatives, antibiotic use and prescribing, and availability of susceptibility data, particularly for the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used locally for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) were also reviewed, plus local antibiotic availability. Insights from a clinician in Saudi Arabia were sought to contextualize this information.ConclusionsVarious initiatives are underway in Saudi Arabia, including a National Action Plan for AMR, which was published in 2017. However, AMR is rising and knowledge about appropriate antibiotic use seems to be lacking among physicians and the general public. Various international guidelines are utilized by clinicians in Saudi Arabia, but a more standardized inclusive approach in developing local guidelines, using up-to-date surveillance data of isolates from community-acquired infections in Saudi Arabia could make management guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve patient outcomes.

Country data on AMR in Russia in the context of community-acquired respiratory tract infections: links between antibiotic susceptibility, local and international antibiotic prescribing guidelines, access to medicine and clinical outcome.

BackgroundAntimicrobial reistance (AMR) is one of the biggest threats to global public health. Selection of resistant bacteria is driven by inappropriate use of antibiotics, amongst other factors. COVID-19 may have exacerbated AMR due to unnecessary antibiotic prescribing. Country-level knowledge is needed to understand options for action.ObjectivesTo review AMR in Russia and any initiatives addressing it. Identifying any areas where more information is required will provide a call to action to minimize any further rise in AMR within Russia and to improve patient outcomes.MethodsNational AMR initiatives, antibiotic use and prescribing, and availability of susceptibility data, in particular for the key community-acquired respiratory tract infection (CA-RTI) pathogens Streptococcus pneumoniae and Haemophilus influenzae, were identified. National and international antibiotic prescribing guidelines commonly used locally for specific CA-RTIs (community-acquired pneumonia, acute otitis media and acute bacterial rhinosinusitis) were also reviewed, plus local antibiotic availability. Insights from both a local clinician and a local clinical microbiologist were sought to contextualize this information.ConclusionsRussia launched a national strategy in 2017 to prevent the spread of AMR and the WHO reports that as of 2020–21, it is being implemented and actively monitored. Reports suggest outpatient antibiotic use of antibiotics is high and that non-prescription access and self-medication are very common. Antibiotic susceptibility studies in Russia include PeHASus, a multicentre epidemiological study focusing on susceptibilities of community-acquired respiratory pathogens and international studies such as Survey of Antibiotic Resistance (SOAR), Antimicrobial Testing Leadership and Surveillance (ATLAS) and SENTRY Antimicrobial Surveillance Program. International guidelines are used to support the development of local guidelines in Russia, and for the common CA-RTIs Russian clinicians use of several country-specific local antibiotic prescribing guidelines. A standardized inclusive approach in developing local guidelines, using up-to-date surveillance data of isolates from community-acquired infections in Russia, could make guideline use more locally relevant for clinicians. This would pave the way for a higher level of appropriate antibiotic prescribing and improved adherence. This would, in turn, potentially limit AMR development and improve patient outcomes.

Human adenovirus (HAdV) infection in children with acute respiratory tract infections in Guangzhou, China, 2010–2021: a molecular epidemiology study

BackgroundHuman adenovirus (HAdV) infection can cause a variety of diseases. It is a major pathogen of pediatric acute respiratory tract infections (ARIs) and can be life-threatening in younger children. We described the epidemiology and subtypes shifting of HAdV among children with ARI in Guangzhou, China.MethodsWe conducted a retrospective study of 161,079 children diagnosed with acute respiratory illness at the Guangzhou Women and Children’s Medical Center between 2010 and 2021. HAdV specimens were detected by real-time PCR and the hexon gene was used for phylogenetic analysis.ResultsBefore the COVID-19 outbreak in Guangzhou, the annual frequency of adenovirus infection detected during this period ranged from 3.92% to 13.58%, with an epidemic peak every four to five years. HAdV demonstrated a clear seasonal distribution, with the lowest positivity in March and peaking during summer (July or August) every year. A significant increase in HAdV cases was recorded for 2018 and 2019, which coincided with a shift in the dominant HAdV subtype from HAdV-3 to HAdV-7. The latter was associated with a more severe disease compared to HAdV-3. The average mortality proportion for children infected with HAdV from 2016 to 2019 was 0.38% but increased to 20% in severe cases. After COVID-19 emerged, HAdV cases dropped to 2.68%, suggesting that non-pharmaceutical interventions probably reduced the transmission of HAdV in the community.ConclusionOur study provides the foundation for the understanding of the epidemiology of HAdV and its associated risks in children in Southern China.

Frequency, Etiology, Mortality, Cost, and Prevention of Respiratory Tract Infections-Prospective, One Center Study.

Background: Ventilator-associated pneumonia (VAP) is the most monitored form of respiratory tract infections (RTIs). A small number of epidemiological studies have monitored community-acquired pneumonia (CAP), non-ventilator hospital-acquired pneumonia (NV-HAP) and ventilator-associated tracheobronchitis (VAT) in intensive care units (ICUs). The objective of this study was to assess the frequency, etiology, mortality, and additional costs of RTIs. Methods: One-year prospective RTI surveillance at a 30-bed ICU. The study assessed the rates and microbiological profiles of CAP, VAP, NV-HAP, VAT, and VAP prevention factors, the impact of VAP and NV-HAP on the length of ICU stays, and the additional costs of RTI treatment and mortality. Results: Among 578 patients, RTIs were found in 30%. The CAP, NV-HAP, VAP, and VAT rates/100 admissions were 5.9, 9.0, 8.65, and 6.05, respectively. The VAP incidence density/1000 MV-days was 10.8. The most common pathogen of RTI was Acinetobacter baumannii MDR. ICU stays were extended by VAP and NV-HAP for 17.8 and 3.7 days, respectively, and these RTIs increased the cost of therapy by 13,029 and 2708 EUR per patient, respectively. The mortality rate was higher by 11.55% in patients with VAP than those without device-associated and healthcare-associated infections (p = 0.0861). Conclusions: RTIs are a serious epidemiological problem in patients who are admitted and treated in ICU, as they may affect one-third of patients. Hospital-acquired RTIs extend hospitalization time, increase the cost of treatment, and worsen outcomes.

Vydovyi spektr bakteriinykh chynnykiv shpytalnykh infektsii dykhalnykh shliakhiv u likarnianykh ustanovakh m. Lvova ta poshyrenist sered nykh antybiotykorezystentnosty

Introduction. Healthcare-associated infections (HAIs) are a pressing problem in the health care system. Respiratory tract infections (RTI) are the second most common group of HAIs. One of the determining factors in the development of nosocomial pneumonia, which is predominantly bacterial in origin, is the properties and level of virulence of microbial factors. Early nosocomial pneumonia occurs when the upper respiratory tract microbiota infects the respiratory tract. Late nosocomial pneumonia is caused by nosocomial strains of microorganisms, characterized by multidrug resistance to antibiotics and disinfectants high levels of virulence, which include P. aeruginosa, Acinetobacter spp., Enterobacteriaceae family, MRSA. Unfortunately, in Ukraine, the structure and prevalence of HAIs and the antimicrobial resistance of pathogens are extremely poorly studied. The aim of the study. Therefore, the study investigates the species spectrum and antimicrobial resistance of the main causative agents of respiratory tract infections. Materials and methods. A study of microbial factors of nosocomial respiratory tract infections in 4 hospitals in Lviv. 205 patients of intensive care units diagnosed with RTI (36.6 %) were examined. Statistical analysis of the results was performed using the standard package of the program “Microsoft Excel 2010”. Microbiological diagnostics were performed following current regulations in the specialty “Bacteriology and Virology” and “Guidelines for Clinical Microbiology” of the 12th revision of the American Association for Microbiology. Microbiological diagnostics is performed in the research laboratory of the Department of Microbiology of Danylo Halytsky Lviv National Medical University. Results. The species profile of the detected pathogens of RTI indicates that among 14 representatives of different taxa, the gram-positive microbiota predominates, but the quantitative level of seeding per gram-negative microbiota accounts for 70.17 %. Among the isolates – factors of HAIs, multidrug-resistant (MDR) share accounted for 62.8 %. 3 strains are classified as pan drug resistant (PDR): 2 – P. putida and 1 – P. aeruginosa. Of the gram-positive microbiota, Enterococcus spp., represented mainly by E. faecalis and E. faecium, was most often detected in clinical material. E. faecalis was most often detected in the clinical material of the gram-positive microbiota. E. faecalis isolates were characterized by pronounced resistance to penicillins (including oxacillin), cephalosporins, fluoroquinolones, erythromycin and azithromycin, clindamycin with preserved sensitivity to vancomycin and linezolid. Pseudomonas aeruginosa isolates showed absolute sensitivity to colistin. Among other antibiotics, the most effective in terms of the number of sensitive strains were carbapenems – imipenem (57.5 %) and meronem (55.0 %). Only 37.5 % of the cultures were sensitive to tobramycin and tegicillin, an inhibitor of the protected cephalosporin antibiotic, sulfperazone. The genus Staphylococcus was among the causative agents of pneumonia other than Staph. aureus subsp. aureus, will Staph. haemolyticus, Staph. lugdunensis. Moreover, only one strain of methicillin-resistant Staphylococcus was detected. Most cases of RTI (57.4%) of patients in intensive care units occurred within 48 hours after the installation of a tracheostomy or intubation tube. Conclusions. According to the results of microbiological diagnostics, it has been established that the main etiological factors of nosocomial pneumonia associated with medical care are opportunistic microorganisms – Pseudomonas aeruginosa and enterococci. 62.8 % of strains were MDR. Furthermore, the results of monitoring the antibiotic resistance of hospital strains of microorganisms show their differences in different institutions of Lviv and the connection exclusively with the hospital environment. Therefore, optimization of antimicrobial treatment of nosocomial pneumonia is possible only based on the broader use of microbiological research results, constant monitoring of the microbiological status of patients in intensive care units, hospitality (distribution and properties of pathogens in hospitals).

Multiplex detection of five common respiratory pathogens from bronchoalveolar lavages using high resolution melting curve analysis

BackgroundThe study describes the application of the multiplex high-resolution melting curve (MHRM) assay for the simultaneous detection of five common bacterial pathogens (Pseudomonas aeruginosa, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli) directly from bronchoalveolar lavage samples.ResultsOur MHRM assay successfully identified all five respiratory pathogens in less than 5 h, with five separate melting curves with specific melt peak temperatures (Tm). The different Tm were characterized by peaks of 78.1 ± 0.4 °C for S. aureus, 83.3 ± 0.1 °C for A. baumannii, 86.7 ± 0.2 °C for E. coli, 90.5 ± 0.1 °C for K. pneumoniae, 94.5 ± 0.2 °C for P. aeruginosa. The overall sensitivity and specificity of MHRM were 100% and 88.8–100%, respectively.ConclusionsOur MHRM assay offers a simple and fast alternative to culture approach for simultaneous detection of five major bacterial lower respiratory tract infection pathogens. Utilization of this assay can help clinicians initiate prompt and appropriate antimicrobial treatment, towards reducing the morbidity and mortality of severe respiratory infections.

A Retrospective Cohort Study on Infant Respiratory Tract Infection Hospitalizations and Recurrent Wheeze and Asthma Risk: Impact of Respiratory Syncytial Virus.

Infant respiratory syncytial virus infection (RSV) has been associated with asthma later in life. We explored the risk of recurrent wheeze or asthma in children with infant RSV-associated hospitalization compared to other respiratory infections. We performed a retrospective cohort study using Danish national hospital discharge registers. Infants younger than 6 months, born between January 1995 and October 2018, and with a RSV hospital admission were compared to infants hospitalized for injuries, non-RSV acute upper respiratory tract infection (AURTI), pneumonia and other respiratory pathogens, nonpathogen-coded lower respiratory tract infections (LRTI), pertussis, or nonspecific respiratory infections. Infants were followed until recurrent wheeze or asthma diagnosis, death, migration, age 10 years, or study end. We estimated cumulative incidence rate ratios (CIRR) and hazard ratios (HR) adjusted for sex, age at inclusion, hospital length of stay (LOS), maternal smoking, 5-minute APGAR score (APGAR5), prematurity, and congenital risk factors (CRF). We included 68 130 infants, of whom 20 920 (30.7%) had RSV hospitalization. The cumulative incidence rate of recurrent wheeze or asthma was 16.6 per 1000 person-years after RSV hospitalization, higher than after injury (CIRR, 2.69; 95% confidence interval [CI], 2.48-2.92), AURTI (CIRR, 1.48; 95% CI, 1.34-1.58), or pertussis (CIRR, 2.32; 95% CI, 1.85-2.91), similar to pneumonia and other respiratory pathogens (CIRR, 1.15; 95% CI, .99-1.34) and LRTI (CIRR, 0.79; 95% CI, .60-1.04), but lower than nonspecific respiratory infections (CIRR, 0.79; 95% CI, .73-.87). Adjusted HRs for recurrent wheeze or asthma after RSV hospitalization compared to injuries decreased from 2.37 (95% CI, 2.08-2.70) for 0 to <1 year to 1.23 (95% CI, .88-1.73) for 6 to <10 years for term-born children, and from 1.48 (95% CI, 1.09-2.00) to 0.60 (95% CI, .25-1.43) for preterm-born children. Sex, maternal smoking, LOS, CRF, and APGAR5 were independent risk factors. Infant RSV hospitalization is associated with recurrent wheeze and asthma hospitalization, predominantly at preschool age. If causal, RSV prophylaxis, including vaccines, may significantly reduce disease burden of wheeze and asthma.

Corynebacterium pseudodiphtheriticum as a Pathogen in Bacterial Co-Infection in COVID-19 Patients on Mechanical Ventilation.

Many studies have been conducted on ventilator-associated complications (VACs) in patients with coronavirus 2019 (COVID-19). However, in these studies, the causative organisms were similar, and there were no reports on VAC corresponding with Corynebacteria. Coryneforms are frequently cultured in cases of polymicrobial infections and are usually considered contaminants in respiratory specimens. However, Corynebacterium pseudodiphtheriticum or C. striatum is known to be a pathogen in lower respiratory tract infections. We report three cases of VAC, probably due to C. pseudodiphtheriticum, in patients with COVID-19. If purulent lower respiratory tract specimens showed coryneform predominantly upon Gram staining, empirical therapy should be started. Furthermore, species identification and drug susceptibility testing should be performed.

Study genetic polymorphisms IL-1β, IL-28 and susceptibility to antibiotics of Staphylococcus aureus in children with recurrent respiratory infections

IntroductionRecurrent Respiratory Infections (RRI) are especially common in young children. In developing countries, they are a leading cause of childhood mortality while in developed countries nearly 50% of pediatric consultations are caused by them. Many factors were known as critical in RRI including causing pathogens, its susceptibility to treatment, immunological reactions, and genetic expression, which recently showed an important effect on inflammatory and immunological reactions. Staphylococcus aureus (S. aureus) is responsible for a small proportion of RRI, but with virulent nature. On the other hand, among inflammation and immunity associated genes, cytokines are with special importance since proinflammatory cytokines such as interleukin-1β (IL-1β), produced by activated macrophages, are involved in inflammatory reactions up-regulation while other cytokines, interleukin-28B (IL-28B), for example, are associated with innate immunological responses. This study aimed to investigate the association of two cytokines genes polymorphisms (IL-1β, IL-28В) with Staphylococcus aureus nasopharyngeal carriage in RRI children and the antibiotics susceptibility of this pathogen in RRI. MethodsS. aureus detection were conducted in 507 RRI children (1–14 years old) pharyngeal and nasal swabs. Antibiotics susceptibility test was performed in S. aureus positive samples using disc diffusion technique. 146 RRI children (aged 2–12 years) was genotyped for targeted polymorphisms. Differences in genetic distribution were assessed by χ2-test and considered as statistically significant if p < 0.05 then intergenic interactions were investigated using Multifactor Dimensionality Reduction (MDR) algorithm. ResultsThe prevalence of carriage of S. aureus among children with RRI was 30.8%. S. aureus carriers showed high dergree of resistance to many antibiotics: Clarithromycin (16%), Erythromycin, Amoxicillin (about 26%), Ampicillin (31.3%) and Amoxiclav (42.2%). No significant associations were found between carriers and noncarriers of S. aureus regarding IL-1β rs1143627 and IL-28B rs8099917 genotypes and allele frequencies. ConclusionStudying antibiotics susceptibility for RRI pathogens is very important to improve therapy and minimize outcomes. The targeted polymorphisms have no significant associations with S. aureus carriage in RRI children, but further studies are needed to find other possible genetic markers for this pathogen.

Next-generation sequencing as an advanced supplementary tool for the diagnosis of pathogens in lower respiratory tract infections: An observational trial in Xi'an, China.

The application of next-generation sequencing (NGS) in routine clinical analysis is still limited. The significance of NGS in the identification of pathogens of lower respiratory tract infection should be assessed as part of routine clinical bacterial examinations and chest imaging results. In the present study, the alveolar lavage fluid samples of 30 patients (25 males and 5 females, aged 19-92 years old, with a median age of 62) were examined by routine bacterial culture and NGS, and the results of pathogen detection and identification were compared. Chest imaging showed consolidation in all 30 patients (100%), and pleural effusion in 13 of the 30 patients (43.33%). The routine bacterial culture of the lavage solution was only positive in 14 of the 30 patients (46.6%), and negative in 16 patients (53.33%). However, the positive rate of NGS test results of the lavage fluid was 100%. A total of 12 cases (40%) were completely consistent with the routine bacterial culture test, with 56 other pathogens of mixed infection detected, accounting for the short comings of the routine bacterial examination. Although NGS cannot distinguish between live and dead bacteria, it is still a useful detection technology for accurate diagnosis of clinical infectious diseases. It is worthy of adaptation in the clinic for more effective clinical management and treatment of the lower respiratory airway infection in addition to the routine bacterial culture testing.

Viral Respiratory Infections: New Tools for a Rapid Diagnosis.

Respiratory tract infection is one of the most common diseases in human worldwide. Many viruses are implicated in these infections, including emerging viruses, such as the novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Identification of the causative viral pathogens of respiratory tract infections is important to select a correct management of patients, choose an appropriate treatment, and avoid unnecessary antibiotics use. Different diagnostic approaches present variable performance in terms of accuracy, sensitivity, specificity, and time-to-result, that have to be acknowledged to be able to choose the right diagnostic test at the right time, in the right patient. This review describes currently available rapid diagnostic strategies and syndromic approaches for the detection of viruses commonly responsible for respiratory diseases.

Molecular characterization of bacterial pathogens-causing snuffles in rabbits in terms of prevalence and pathogenicity

Respiratory disease or snuffling is a major problem associated with serious economic losses in the rabbit industry. The disease in rabbit is a polybacterial infection in nature, resulting from co-infection with more than one bacterial pathogen. To determine the involved bacterial pathogens in respiratory infections in terms of prevalence and pathogenicity, different specimens from rabbits with typically respiratory disorders are subjected to the bacteriological examination followed by molecular verification through RT-PCR or PCR followed by sequencing the PCR-product. The results identified Mycoplasma sp. as a major partner in mixed infection with virulent strains of P. multocida or S. aureus, suggesting that, initial infection with Mycoplasma sp creates vulnerability to subsequent infection with P. multocida or S. aureus. Gross and microscopic analysis were also applied to demonstrate lesions accompanied by the detected bacterial pathogens. In conclusion, this study described the prevalence and characteristic of respiratory illness in rabbits domesticated in Al-Sharkia Governorate, Egypt and highlighted for the first time the role of Mycoplasma sp in increasing the severity of rabbit-respiratory infections.

Occurrence and disease burden of respiratory syncytial virus and other respiratory pathogens in adults aged ≥65 years in community: A prospective cohort study in Japan.

BackgroundThe frequency and clinical profile of respiratory syncytial virus (RSV)–acute respiratory disease (ARD) in older adults in Japan has not been well‐characterized.MethodsThis was a multicenter prospective observational cohort study to evaluate the occurrence rate of ARD in 1000 older adult participants (≥65 years) for 52 weeks during the 2019 to 2020 season. A multiplex polymerase chain reaction panel was used for pathogen detection in nasopharyngeal swab from participants diagnosed with ARD. Symptoms and impact of ARD was assessed using the Respiratory Infection Intensity and Impact Questionnaire (RiiQ™). The study was registered at UMIN (https://www.umin.ac.jp/ctr/): UMIN000037891.ResultsRSV–ARD was detected in 24/1000 (2.4%) participants and RSV‐lower respiratory tract disease in 8/1000 (0.8%) participants. The median duration of RSV–ARD was 18 days. All 24 participants had utilized the medical services of outpatient visits and only 1 (4.2%) participant was hospitalized for RSV–ARD. The most common viruses other than RSV that caused ARD (detected in >10 participants) were human rhinovirus/enterovirus, parainfluenza 3, coronavirus OC43, human metapneumovirus, and influenza A/H1. The most frequent symptoms of RSV–ARD were cough, sore throat, nasal congestion, and expectoration.ConclusionsRSV was reported as a major pathogen for respiratory infections in older adults in Japan.

Analysis of bacterial pathogens and clinical characteristics of children with respiratory tract infections in Tianjin

Objective: To analyze the pathogenic bacteria and epidemiological characteristics in children with respiratory tract infection in Tianjin area. Methods: Retrospective case analysis was performed on 2 392 hospitalized children in the wards of respiratory diseases, intensive care unit and special care ward of Tianjin Children's Hospital from June 2018 to May 2019. Thirteen pathogenic bacteria in deep sputum and bronchoalveolar lavage fluid samples were detected by loop-mediated isothermal amplification. The laboratory data and clinical characteristics of the infected children were analyzed, and the comparison between groups was performed by t test or χ2 test. Results: Among 2 392 cases, 1 407 were males and 985 females. There was no significant difference in the detection rate between males and females (72.5% (1 020/1 407) vs.74.2% (731/985), χ2=0.87, P=0.35). A total of 1 751 strains and 12 kinds of positive respiratory pathogens were detected, with a detection rate of 73.2%. Among them, 913 (38.2%) strains were Mycoplasma pneumoniae (MP), 514 (21.5%) were Streptococcus pneumoniae (Sp), 381 (15.9%) were Methicillin-resistant Staphylococcus aureus (MRSA) and 279 (11.7%) were Hemophilus influenzae (Hi). There was significant difference in the detection rate of pathogens among different age groups (χ²=83.67, P<0.01). The positive rate of alveolar lavage fluid group was higher than that of deep sputum fluid group [81.6% (614/752) vs. 69.3% (1 137/1 640), χ2=39.89, P<0.01]. The length of hospital stay of children infected with different pathogens was significantly different (all P<0.01). There was significant difference in duration of fever among children infected with different pathogens (χ²=228.69,103.56, 3.96, 27.38,24.50,41.66, all P<0.05). There were 63 (7.7%) cases of atelectasis, 260 (31.9%) cases of pleurisy and 120 (14.7%) cases of pleural effusion in MP children. Children with Sma were most likely to involve the heart system (2/9), and children with Eco infection had a higher incidence of complications such as those of blood (3/19), urinary (2/19), digestive systems(4/19), systemic inflammatory response syndrome and sepsis (1/19). Conclusions: The main bacterial pathogens of respiratory tract infection in children in Tianjin were MP, Sp, MRSA and Hi. It is suggested that clinicians should not only pay attention to the respiratory symptoms of children, but also pay attention to the complications caused by bacterial pathogen infection, so as to prevent the deterioration of the disease and improve the prognosis.

Current Trend in the Antibiogram of Bacterial Pathogens of Adult Lower Respiratory Tract Infections in a Nigerian Tertiary Hospital

Background: Lower respiratory tract infections (LRTIs) are among the commonest infectious diseases requiring hospitalization. There is an increasing resistance development of bacterial pathogens of LRTIs to the commonly prescribed antibiotics necessitating regular surveillance for these bacteria and their antibiogram.&#x0D; Aim: To identify bacterial pathogens of adult LRTIs, determine their antibiotic susceptibility pattern, and suggest the best empirical treatment of adult LRTIs in the setting.&#x0D; Study Design: Descriptive cross-sectional study.&#x0D; Methods: A total of 194 respiratory samples from 194 consecutive consenting adult in-patient of a Federal Teaching Hospital were processed. Identification of isolated bacteria and antibiotic susceptibility testing of the isolates were carried out following the standard protocol.&#x0D; Results: Bacteria isolation was seen in 52.1% of all specimens, highest isolation rate was from sputum (55.2%). Isolation was higher in males (54.9%) than females (48.1%) but no significant difference was seen (P=0.36). Gram negative bacteria were predominantly isolated (64.4%) and Klebsilla pneumoniae was the most common (33.7%). Eight extended-spectrum beta-lactamase (ESBL) producers and 3 methicillin-resistant Staphylococcus aureus (MRSA) were also detected. All isolates were sensitive to imipenem and meropenem. All MRSAs were sensitive to vancomycin. There was poor sensitivity pattern seen against most antibiotics tested.&#x0D; Conclusion: Gram negative bacteria were the predominant bacterial pathogen isolated, and isolates were resistant to most antibiotics tested, though, all were sensitive to carbapenems. Levofloxacin plus gentamicin, and carbapenems were the suggested first and second line empirical treatment of choice respectively for adult LRTIs in this and similar settings.