Mechanisms of Bacterial Colonization of the Respiratory Tract

Mucosal colonization of Mannheimia haemolytica capsular and adhesin mutants in cattle

Mannheimia haemolytica (Mh) is a normal inhabitant of the upper respiratory tract of ruminants and is associated with bovine respiratory disease. Polysaccharide capsule and surface adhesins are suggested to function in adherence and colonization of M. haemolytica to the mucosa of the upper respiratory tract. M. haemolytica serotype 1 mutant strains containing deletions of either the capsule biosynthetic gene cluster (∆cap) or putative adhesin genes (∆adh123) were created using a temperature-sensitive plasmid and tested for colonization in a calf challenge model. Two treatment groups were used in the study: Sham-Mh-BHV-1 (SMB; intranasal administration of uninfected cell culture lysate/supernatant [sham; S] 4 days before intranasal M. haemolytica inoculation, and intranasal inoculation of bovine-herpesvirus-1 [BHV-1] 20 days post-Mh) and BHV-1-Mh-Sham (BMS; intranasal inoculation of BHV-1 4 days before intranasal Mh inoculation and intranasal sham administration 20 days post-Mh). A mixture of wild-type M. haemolytica parent strain, ∆cap, and ∆adh123 mutants was included in the Mh inoculum. Animals were observed for clinical signs and nasal colonization for approximately 7 weeks. The ∆adh123 mutant and parent strain colonized the nasopharynx, whereas the ∆cap mutant was not detected after 1 day post-inoculation. The ∆adh123 mutant colonized the nasopharynx at significantly higher levels (P < 0.0001) compared to wild type. Higher colonization of ∆adh123 was also found in palatine tonsils. These findings suggest a requirement of capsule in long-term colonization and an advantage for ∆adh123 in colonization over the parent strain.IMPORTANCEUnderstanding the colonization dynamics of Mannheimia haemolytica is crucial for developing effective prevention and treatment strategies for bovine respiratory disease (BRD), a significant cause of economic loss in the cattle industry. This study highlights the role of capsular polysaccharide and surface adhesins in nasopharyngeal colonization. These findings demonstrate that the deletion of putative surface adhesins leads to enhanced colonization compared to the wild-type strain, while mutants containing a deletion of the capsule biosynthetic gene cluster failed to establish long-term colonization. These results suggest that targeting bacterial adhesion mechanisms could influence bacterial persistence and immune response, offering potential avenues for controlling BRD.

Deep-Tissue In Vivo Imaging Using Bioluminescence in a Mouse Infection Model and the Path to High Sensitivity With Near-Infrared Luminescence

The analysis of bacterial infections using animal models has primarily relied on the average evaluation of many individuals at specific time points. Consequently, tracking temporal changes in an infection within the same individual is challenging. InVivo imaging techniques enable the longitudinal assessment of infection in the same individual while reducing the number of animals required. Understanding the dynamics of bacterial infections over time is crucial for elucidating disease mechanisms and developing effective treatment strategies. In this review, we summarize the In Vivo imaging techniques used to detect bacterial colonization in deep tissues in animal models of bacterial infection, along with efforts to enhance their sensitivity. In particular, we introduce a recently developed In Vivo imaging system that employs near-infrared luminescence to achieve high sensitivity and versatility. Furthermore, we discuss strategies for further improving its sensitivity.

Transmission of the human respiratory microbiome and antibiotic resistance genes in healthy populations

BACKGROUND

The human microbiome is transmissible between individuals, including pathogens and commensals with metabolic and immune-modulating effects, which could influence susceptibility, severity, and outcomes of both infection and non-infection diseases. However, limited studies of respiratory microbiome transmission within populations have been conducted. Herein, we performed species- and strain-level metagenomic analyses on oropharyngeal (OP) swabs from 1046 healthy urban dwellers across 13 districts, including 111 households with at least two cohabitants, to elucidate the transmission dynamics of the respiratory microbiome within households and communities.

RESULTS

We found that geographic districts accounted for the greatest variation in the OP microbiome, with unrelated individuals from the same district showing greater microbiome similarity and higher strain-sharing rates than those from different districts. Cohabitants, especially spouses and siblings, exhibited similar microbial abundances and shared more strains, with 16.7% (IQR 0.0-33.3%) of strains shared among cohabitants, compared to 0.0% (IQR 0.0-11.1%) in non-cohabiting pairs (p < 0.05). Both respiratory commensals and opportunistic pathogens were shared among cohabitants. In contrast, no evidence of vertical transmission was detected between mother-offspring pairs. Additionally, the OP microbiome contained diverse antibiotic resistance genes (ARGs), with 15.0% linked to mobile genetic elements (MGEs) or plasmids; the flanking sequences of these ARGs were more conserved across species than those of non-MGE-associated ARGs, suggesting horizontal transfer of ARGs among respiratory microorganisms.

CONCLUSIONS

In summary, we characterized the transmissible nature of the OP microbiome and the risk of ARG dissemination among respiratory microorganisms. These findings underscore the role of respiratory microbes and ARGs exchange in shaping the microbiome of healthy populations and emphasize their relevance to public health strategies for respiratory health management. Video Abstract.

Hospitalization due to pneumonia in Australia, England, and Wales: An ecological cross-sectional study

Pneumonia and other lower respiratory tract diseases rank as the fourth leading cause of death worldwide. The objective of this study was to examine pneumonia hospitalization patterns, and trends in total pneumonia hospitalization stratified by age group, by type of hospitalization, and by age group in Australia, England, Wales. This study utilized 3 databases to obtain hospital admissions data: the National Hospital Morbidity Database for Australian hospital admissions data, the Hospital Episode Statistics database (HES) for England hospital admissions data, and the Patient Episode Database for Wales. Pneumonia hospitalization data were extracted utilizing J12 to J18 codes. From 2013 to 2020, there were 4,514,444 cases of pneumonia hospitalizations reported in Australia (646,515 [14.32%]), England (3,668,106 [81.25%]), and Wales (199,823 [4.43%]). The most common type of pneumonia hospitalization in Australia, England, and Wales was "pneumonia, organism unspecified," accounting for 77.12%, 95.49%, and 95.75% of the total number of pneumonia hospitalizations in each country, respectively. The most common subtype of pneumonia hospitalization in Australia was "pneumonia, unspecified," accounting for 72.98% of the total number of pneumonia hospitalizations in the country. The most common type of pneumonia hospitalization in England and Wales was "lobar pneumonia, unspecified," accounting for 59.00% and 56.73% of the total number of pneumonia hospitalizations in each country, respectively. Most pneumonia hospitalizations in Australia, England, and Wales were non-same-day hospitalizations, accounting for 90.78%, 99.91%, and 99.95%, respectively. Pneumonia hospitalizations in Australia, England, and Wales were directly related to age. Males accounted for most pneumonia hospitalizations in Australia, England, and Wales. This study highlighted that hospitalization rate for pneumonia increased during the past decade in Australia, England, and Wales. The age and male gender were clearly contributing factors that affected pneumonia hospitalizations rate. Educational campaign aiming to increase public knowledge of pneumonia, its risk factors, and lifestyle modification should be prioritized to decrease pneumonia episodes.

Modulating oxidative stress: a reliable strategy for coping with community-acquired pneumonia in older adults

Community-acquired pneumonia (CAP) remains one of the leading respiratory diseases worldwide. With the aging of the global population, the morbidity, criticality and mortality rates of CAP in older adults remain high every year. Modulating the signaling pathways that cause the inflammatory response and improve the immune function of patients has become the focus of reducing inflammatory damage in the lungs, especially CAP in older adults. As an important factor that causes the inflammatory response of CAP and affects the immune status of the body, oxidative stress plays an important role in the occurrence, development and treatment of CAP. Furthermore, in older adults with CAP, oxidative stress is closely associated with immune senescence, sarcopenia, frailty, aging, multimorbidity, and polypharmacy. Therefore, multiple perspectives combined with the disease characteristics of older adults with CAP were reviewed to clarify the research progress and application value of modulating oxidative stress in older adults with CAP. Clearly, there is no doubt that targeted modulation of oxidative stress benefits CAP in older adults. However, many challenges and unknowns concerning how to modulate oxidative stress for further practical clinical applications exist, and more targeted research is needed. Moreover, the limitations and challenges of modulating oxidative stress are analyzed with the aim of providing references and ideas for future clinical treatment or further research in older adults with CAP.

Comparing sputum, nasopharyngeal swabs, and combined samples for respiratory bacterial detection using multiplex PCR

Respiratory tract infections are major global health issues that require rapid and accurate diagnostic methods. Multiplex quantitative PCR (qPCR) is commonly used for pathogen detection in respiratory samples. However, the optimal specimen selection for detecting bacterial pathogens is not well-explored. We evaluated the detection rates of respiratory bacteria from nasopharyngeal swabs (NPS), sputum, and combined NPS and sputum samples using multiplex qPCR (Allplex PneumoBacter Assay, Seegene). Paired NPS and sputum samples from 219 patients with acute respiratory symptoms admitted to Korea University Anam Hospital were analyzed. qPCR was performed to detect seven respiratory bacteria: Bordetella parapertussis, Bordetella pertussis, Chlamydophila pneumoniae, Haemophilus influenzae, Legionella pneumophila, Mycoplasma pneumoniae, and Streptococcus pneumoniae. Combined NPS and sputum samples (n = 92) were created from 46 pairs of positive and 46 pairs of negative signals for NPS-alone and sputum-alone samples. Sputum samples (44.3%; 97/219) had a significantly higher positivity rate compared to NPS samples (21.0%; 46/219) (P < 0.001). The 92 combined samples identified a total of 65 bacterial nucleic acids. The detection rate for the combined samples was 86.2% (56/65), which was comparable to that of sputum alone (89.2%; 58/65) and higher than that of NPS samples (50.8%; 33/65). Combining NPS and sputum samples for PCR testing may offer an alternative for bacterial pathogen detection, providing rates comparable to those of sputum alone and greater sensitivity than that of NPS alone. This combined approach could be a cost-effective method to maximize diagnostic yield, reduce the need for multiple tests, and improve the management of respiratory infections.

IMPORTANCE

This study offers important insights into refining diagnostic strategies for respiratory bacterial infections using multiplex PCR. This study finds that combining sputum and nasopharyngeal swabs into a single tube could serve as an effective alternative for detecting respiratory bacteria in adults with acute respiratory illness.

Correlation between admission hyperglycemia and postoperative pneumonia after hip fracture surgery: A propensity score-matched study

The association between admission hyperglycemia and postoperative pneumonia is unclear in hip fracture patients. We investigated the relationship between admission hyperglycemia and postoperative pneumonia after hip fracture surgery. This retrospective study analyzed data from 1,267 geriatric patients admitted for hip fractures. Patients were categorized into normoglycemic (< 6.10 mmol/L) and hyperglycemic (≥ 6.10 mmol/L) groups based on admission blood glucose levels. Multivariable logistic regression and propensity score matching (PSM) were used to control for potential confounding variables and estimate adjusted odds ratios and 95% confidence intervals for postoperative pneumonia (POP). We also examined the dose-dependent link between admission blood glucose and the likelihood of developing POP. Further analyses evaluated whether admission hyperglycemia has differing impacts on POP outcomes among hip fracture patients without diabetes (NDM) versus those with diabetes (DM). Additionally, subgroup analyses were conducted to assess the influence of other factors on the relationship between admission blood glucose and POP occurrence. Patients with admission hyperglycemia had significantly higher rates of POP compared to normoglycemic patients, both before (13.2% vs. 4.8%) and after (10.1% vs. 5.8%) PSM. Admission hyperglycemia is an independent risk factor of POP (OR = 2.64, 95% CI: 1.42-4.92, p = 0.002). The association persisted after PSM(OR = 2.90, 95% CI: 1.35-3.86, p = 0.016). Additionally, higher blood glucose levels correlated with a greater likelihood of developing POP. A dose-response relationship was observed between blood glucose levels and the risk of POP. Non-diabetic group patients with hyperglycemia were at higher risk of POP than diabetic group patients with hyperglycemia. Finally, the relationship between hyperglycemia and increased POP risk is modulated and influenced by the ASA classification of the patient. Admission hyperglycemia is an independent risk factor for POP after hip fracture surgery in the elderly. There is a dose-response relationship between admission blood glucose and the occurrence of POP, which is more significant in non-diabetic patients than diabetic patients.

Comprehensive human respiratory genome catalogue underlies the high resolution and precision of the respiratory microbiome

The human respiratory microbiome plays a crucial role in respiratory health, but there is no comprehensive respiratory genome catalogue (RGC) for studying the microbiome. In this study, we collected whole-metagenome shotgun sequencing data from 4067 samples and sequenced long reads of 124 samples, yielding 9.08 and 0.42 Tbp of short- and long-read data, respectively. By submitting these data with a novel assembly algorithm, we obtained a comprehensive human RGC. This high-quality RGC contains 190,443 contigs over 1 kbps and an N50 length exceeding 13 kbps; it comprises 159 high-quality and 393 medium-quality genomes, including 117 previously uncharacterized respiratory bacteria. Moreover, the RGC contains 209 respiratory-specific species not captured by the unified human gastrointestinal genome. Using the RGC, we revisited a study on a pediatric pneumonia dataset and identified 17 pneumonia-specific respiratory pathogens, reversing an inaccurate etiological conclusion due to the previous incomplete reference. Furthermore, we applied the RGC to the data of 62 participants with a clinical diagnosis of infection. Compared to the Nucleotide database, the RGC yielded greater specificity (0 versus 0.444, respectively) and sensitivity (0.852 versus 0.881, respectively), suggesting that the RGC provides superior sensitivity and specificity for the clinical diagnosis of respiratory diseases.

Beta-hemolytic Streptococci in respiratory illness

Beta-hemolytic Streptococci are associated with various respiratory illnesses, such as pharyngitis, scarlet fever and pneumonia, highlighting the need for enhanced diagnostic, therapeutic and preventive strategies. Advances in immunology and molecular biology have provided insights into the etiology and host immune responses to these infections, but many questions remain unanswered. Further research is needed to develop advanced diagnostics, explore vaccine candidates, understand immune responses and address antibiotic resistance. Epidemiological studies are crucial to improving our understanding of these infections and their public health impact. A multidisciplinary approach integrating epidemiology, microbiology, immunology and clinical medicine is essential to reduce the burden of beta-hemolytic streptococcal infections and improve overall treatment and prevention efforts.

Near-infrared in vivo imaging system for dynamic visualization of lung-colonizing bacteria in mouse pneumonia

In vivo imaging of bacterial infection models enables noninvasive and temporal analysis of individuals, enhancing our understanding of infectious disease pathogenesis. Conventional in vivo imaging methods for bacterial infection models involve the insertion of the bacterial luciferase LuxCDABE into the bacterial genome, followed by imaging using an expensive ultrasensitive charge-coupled device (CCD) camera. However, issues such as limited light penetration into the body and lack of versatility have been encountered. We focused on near-infrared (NIR) light, which penetrates the body effectively, and attempted to establish an in vivo imaging method to evaluate the number of lung-colonizing bacteria during the course of bacterial pneumonia. This was achieved by employing a novel versatile system that combines plasmid-expressing firefly luciferase bacteria, NIR substrate, and an inexpensive, scientific complementary metal-oxide semiconductor (sCMOS) camera. The D-luciferin derivative "TokeOni," capable of emitting NIR bioluminescence, was utilized in a mouse lung infection model of Acinetobacter baumannii, an opportunistic pathogen that causes pneumonia and is a concern due to drug resistance. TokeOni exhibited the highest sensitivity in detecting bacteria colonizing the mouse lungs compared with other detection systems such as LuxCDABE, enabling the monitoring of changes in bacterial numbers over time and the assessment of antimicrobial agent efficacy. Additionally, it was effective in detecting A. baumannii clinical isolates and Klebsiella pneumoniae. The results of this study are expected to be used in the analysis of animal models of infectious diseases for assessing the efficacy of therapeutic agents and understanding disease pathogenesis.

IMPORTANCE

Conventional animal models of infectious diseases have traditionally relied upon average assessments involving numerous individuals, meaning they do not directly reflect changes in the pathology of an individual. Moreover, in recent years, ethical concerns have resulted in the demand to reduce the number of animals used in such models. Although in vivo imaging offers an effective approach for longitudinally evaluating the pathogenesis of infectious diseases in individual animals, a standardized method has not yet been established. To our knowledge, this study is the first to develop a highly versatile in vivo pulmonary bacterial quantification system utilizing near-infrared luminescence, plasmid-mediated expression of firefly luciferase in bacteria, and a scientific complementary metal-oxide semiconductor camera. Our research holds promise as a useful tool for assessing the efficacy of therapeutic drugs and pathogenesis of infectious diseases.

Decolonization strategies for ESBL-producing or carbapenem-resistant Enterobacterales carriage: a systematic review and meta-analysis

The prevalence of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) and carbapenem-resistant Enterobacterales (CRE) has become a global public health problem. ESBL-E/CRE colonization can increase the risk of infection in patients and lead to poor disease prognosis. We conducted a systematic review and meta-analysis to evaluate current decolonization strategies regarding ESBL-E/CRE and their efficacy. A literature search was conducted until August 2023 on the five databases to review decolonization strategies associated with ESBL-E/CRE. A meta-analysis was conducted using RevMan 5.4 to compare differences in the decolonization strategy with placebo controls. The primary outcome was decolonization rates, with secondary outcomes of attributable death and adverse events. Quality of identified studies was determined using the Newcastle-Ottawa scale and cochrane risk assessment tool. Random and fixed effects meta-analyses were performed to calculate pooled value. A total of 25 studies were included. In five randomized controlled trial (RCT) studies, the decolonization effect of selective digestive decontamination(SDD) on ESBL-E/CRE at the end of treatment was significantly better in the experimental group than the controls [risk radio (RR): 3.30; 95% CI 1.78-6.14]. In three n-RCT studies, the decolonization effect in the experimental group was still better than the controls one month after SDD therapy [odds ratio (OR): 4.01; 95% CI 1.88-8.56]. The combined decolonization rates reported by six single-arm trial studies of SDD therapy ranged from 53.8 to 68.0%. Additionally, TSA analysis confirmed the effectiveness of SDD therapy. In studies on Faecal microbiota transplantation (FMT) therapy, the decolonization effect of the experimental group was significantly better than the controls 1 month after treatment (OR: 2.57; 95% CI 1.07-6.16). In studies without a control group and with varying follow-up times, the decolonization rates varied widely but indicated the effectiveness trend of FMT therapy (61.3-81.2%). Currently, research on the decolonization effect of probiotic therapy on ESBL-E/CRE is insufficient, and only a systematic review was conducted. SDD and FMT strategies have short-term benefits for ESBL-E/CRE decolonization, but long-term effects are unclear. The effect of probiotic therapy on ESBL-E/CRE decolonization is an interesting topic that still requires further investigation.

A Longitudinal Study of Escherichia coli Clinical Isolates from the Tracheal Aspirates of a Paediatric Patient-Strain Type Similar to Pandemic ST131

Escherichia coli is a Gram-negative bacterium and part of the intestinal microbiota. However, it can cause various diarrhoeal illnesses, i.e., traveller's diarrhoea, dysentery, and extraintestinal infections when the bacteria are translocated from the intestine to other organs, such as urinary tract infections, abdominal and pelvic infections, pneumonia, bacteraemia, and meningitis. It is also an important pathogen in intensive care units where cross-infection may cause intrahospital spread with serious consequences. Within this study, four E. coli isolates from the tracheal aspirates of a tracheotomised paediatric patient on chronic respiratory support were analysed and compared for antibiotic resistance and virulence potential. Genomes of all four isolates (5381a, 5381b, 5681, 5848) were sequenced using Oxford Nanopore Technology. According to PFGE analysis, the clones of isolates 5681 and 5848 were highly similar, and differ from 5381a and 5381b which were isolated first chronologically. All four E. coli isolates belonged to an unknown sequence type, related to the E. coli ST131, a pandemic clone that is evolving rapidly with increasing levels of antimicrobial resistance. All four E. coli isolates in this study exhibited a multidrug-resistant phenotype as, according to MIC data, they were resistant to ceftriaxone, ciprofloxacin, doxycycline, minocycline, and tetracycline. In addition, principal component analyses revealed that isolates 5681 and 5848, which were recovered later than 5381a and 5381b (two weeks and three weeks, respectively) possessed more complex antibiotic resistance genes and virulence profiles, which is concerning considering the short time period during which the strains were isolated.

Serotypes and Genotypes of Streptococcus pneumoniae in an Unvaccinated Population in Suzhou, China

Background

Streptococcus pneumoniae is a significant etiological agent of infection and commonly inhabits the human nasopharynx, alongside other potentially pathogenic bacteria. In this study, S. pneumoniae strains were obtained from a community population and subjected to investigation of their phenotypes, genotypes, and vaccine coverage.

Methods

S. pneumoniae was isolated from nasopharyngeal swab samples of a healthy population in the Guangfu Community. Capsular serotypes and genotypes were identified using Quellung reaction and multilocus sequence typing (MLST), respectively. The antimicrobial susceptibility was tested using minimum inhibitory concentrations.

Results

In total, 500 unvaccinated people were sampled. Ninety-four S. pneumoniae strains were identified. Common serotypes were 19F, 6A, and 9V. The strain coverages of PCV13 and PPV23 were 61.7% and 58.5%, respectively. About 27.6% isolates were non-susceptible to penicillin, and over 80% were resistant to erythromycin and doxycycline. Among 27 novel sequence types (STs) identified in all strains, the most common STs were ST236 (6/94, 6.4%) and ST12669 (6/94, 6.4%). Nearly half of the strains were grouped into four clone complexes (CC12665, CC271, CC6011, and CC180), of which CC271 showed the highest resistance to PEN.

Conclusion

In our study, various drug-resistant clone complexes of Streptococcus pneumoniae were found in the healthy population, the elderly, and children. Consequently, pneumococcal vaccines should be included in the national immunization schedule to prevent disease spread.

The nasopharyngeal microbiome in South African children with lower respiratory tract infection: a nested case-control study of the Drakenstein Child Health Study

Background

Lower respiratory tract infection (LRTI) is a leading cause of infant morbidity and mortality globally. LRTI may be caused by viral or bacterial infections, individually or in combination. We investigated associations between LRTI and infant nasopharyngeal (NP) viruses and bacteria in a South African birth cohort.

Methods

In a case-control study of infants enrolled in the Drakenstein Child Health Study (DCHS), LRTI cases were identified prospectively and age-matched with controls from the cohort. NP swabs were tested using quantitative real-time polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing. We calculated adjusted Conditional Odds Ratios (aORs) for qPCR targets and used mixed effects models to identify differentially abundant taxa between LRTI cases and controls and explore viral-bacterial interactions.

Results

Respiratory Syncytial Virus (RSV) [aOR: 5.69, 95% CI: 3.03-10.69], human rhinovirus (HRV) [1.47, 1.03-2.09], parainfluenza virus [3.46, 1.64-7.26], adenovirus [1.99, 1.08-3.68], enterovirus [2.32, 1.20-4.46], Haemophilus influenzae [1.72, 1.25-2.37], Klebsiella pneumoniae [2.66, 1.59-4.46], or high-density (> 6.9 log10 copies/mL) Streptococcus pneumoniae [1.53, 1.01-2.32] were associated with LRTI. Using 16S sequencing, LRTI was associated with increased relative abundance of Haemophilus (q = 0.0003) and decreased relative abundance of Dolosigranulum (q = 0.001), Corynebacterium (q = 0.091) and Neisseria (q = 0.004). In samples positive for RSV, Staphylococcus and Alloprevotella were present at lower relative abundance in cases than controls. In samples positive for parainfluenza virus or HRV, Haemophilus was present at higher relative abundance in cases.

Conclusions

The associations between bacterial taxa and LRTI are strikingly similar to those identified in high-income countries, suggesting a conserved phenotype. RSV was the major virus associated with LRTI. H. influenzae appears to be the major bacterial driver of LRTI, acting synergistically with viruses. The Gram-positive bacteria Dolosigranulum and Corynebacteria may protect against LRTI, while Staphylococcus was associated with reduced risk of RSV-related LRTI.

Funding

National Institutes of Health of the USA, Bill and Melinda Gates Foundation, National Research Foundation South Africa, South African Medical Research Council, L'Oréal-UNESCO For Women in Science South Africa, Australian National Health and Medical Research Council.

Novel Experimental Mouse Model to Study the Pathogenesis and Therapy of Actinobacillus pleuropneumoniae Infection

Actinobacillus pleuropneumoniae (APP) is a major cause of lung infections in pigs. An experimental mouse has the edge over pigs pertaining to the ease of experimental operation, disease study and therapy, abundance of genetic resources, and cost. However, it is a challenge to introduce APP into a mouse lung due to the small respiratory tract of mice and bacterial host tropism. In this study, an effective airborne transmission of APP serovar 1 (APP1) was developed in mice for lung infection. Consequently, APP1 infected BALB/c mice and caused 60% death within three days of infection at the indicated condition. APP1 seemed to enter the lung and, in turn, spread to other organs of the mice over the first 5 days after infection. Accordingly, APP1 damaged the lung as evidenced by its morphological and histological examinations. Furthermore, ampicillin fully protected mice against APP1 as shown by their survival, clinical symptoms, body weight loss, APP1 count, and lung damages. Finally, the virulence of two extra APP strains, APP2 and APP5, in the model was compared based on the survival rate of mice. Collectively, this study successfully established a fast and reliable mouse model of APP which can benefit APP research and therapy. Such a model is a potentially useful model for airway bacterial infections.

Meta-analysis of the human upper respiratory tract microbiome reveals robust taxonomic associations with health and disease

BACKGROUND

The human upper respiratory tract (URT) microbiome, like the gut microbiome, varies across individuals and between health and disease states. However, study-to-study heterogeneity in reported case-control results has made the identification of consistent and generalizable URT-disease associations difficult.

RESULTS

In order to address this issue, we assembled 26 independent 16S rRNA gene amplicon sequencing data sets from case-control URT studies, with approximately 2-3 studies per respiratory condition and ten distinct conditions covering common chronic and acute respiratory diseases. We leveraged the healthy control data across studies to investigate URT associations with age, sex, and geographic location, in order to isolate these associations from health and disease states.

CONCLUSIONS

We found several robust genus-level associations, across multiple independent studies, with either health or disease status. We identified disease associations specific to a particular respiratory condition and associations general to all conditions. Ultimately, we reveal robust associations between the URT microbiome, health, and disease, which hold across multiple studies and can help guide follow-up work on potential URT microbiome diagnostics and therapeutics.

Contribution of Particulates to Airborne Disease Transmission and Severity: A Review

The emergence of coronavirus disease 2019 (COVID-19) has catalyzed great interest in the spread of airborne pathogens. Airborne infectious diseases are classified into viral, bacterial, and fungal infections. Environmental factors can elevate their transmission and lethality. Air pollution has been reported as the leading environmental cause of disease and premature death worldwide. Notably, ambient particulates of various components and sizes are harmful pollutants. There are two prominent health effects of particles in the atmosphere: (1) particulate matter (PM) penetrates the respiratory tract and adversely affects health, such as heart and respiratory diseases; and (2) bioaerosols of particles act as a medium for the spread of pathogens in the air. Particulates contribute to the occurrence of infectious diseases by increasing vulnerability to infection through inhalation and spreading disease through interactions with airborne pathogens. Here, we focus on the synergistic effects of airborne particulates on infectious disease. We outline the concepts and characteristics of bioaerosols, from their generation to transformation and circulation on Earth. Considering that microorganisms coexist with other particulates as bioaerosols, we investigate studies examining respiratory infections associated with airborne PM. Furthermore, we discuss four factors (meteorological, biological, physical, and chemical) that may impact the influence of PM on the survival of contagious pathogens in the atmosphere. Our review highlights the significant role of particulates in supporting the transmission of infectious aerosols and emphasizes the need for further research in this area.

Incidence and risk factors for subsequent infections among rectal carriers with carbapenem-resistant Klebsiella pneumoniae: a systematic review and meta-analysis

BACKGROUND

Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a major pathogen causing nosocomial infections with a high mortality and poor prognosis. Gastrointestinal carriage has been acknowledged as the primary reservoir of CRKp infections.

AIM

To explore the incidence and risk factors associated with CRKp infection following colonization.

METHODS

The PubMed, Web of Science, and Cochrane Library databases were searched for relevant articles published between December 1998 and June 2023. Pooled estimates with a 95% confidence interval (CI) were calculated for the incidence rate, whereas pooled odds ratios (ORs) were calculated for the risk factors for which the OR was reported in three or more studies.

FINDINGS

Fourteen studies were included in the review with 5483 patients for the assessment of incidence, whereas seven of these studies with 2170 patients were included for the analysis of risk factors. In the meta-analysis, the incidence of CRKp infections after colonization was 23.2% (17.9-28.5). Additionally, three independent risk factors for subsequent CRKp infections were identified as admission to the intensive care unit (ICU) (2.59; 95% CI: 1.64-4.11), invasive procedures (2.53; 95% CI: 1.59-4.03), and multi-site colonization (6.24; 95% CI: 2.38-16.33).

CONCLUSION

This review reveals the incidence of CRKp infections in rectal carriers in different countries, emphasizing the role of rectal colonization with CRKp as an important source of nosocomial infections. Significantly, the risk factors indicated in this review can assist clinicians in identifying CRKp carriers with an elevated risk of subsequent infections, thereby enabling further measures to be taken to prevent nosocomial infections.

Diagnostic value of systematic bronchial aspirate on postoperative pneumonia after pulmonary resection surgery for lung cancer: a monocentre retrospective study

OBJECTIVES

Intraoperative bacterial airway colonization seems to be associated with an increased risk of postoperative pneumonia (POP). It can be easily assessed by performing a bronchial aspirate (BA). The objective of this study is to assess the diagnostic performance of the BA to predict POP.

METHODS

We conducted a single-centre retrospective observational study over a period of 10 years, from 1 January 2011 to 30 December 2020. The population study included patients admitted for a scheduled pulmonary resection surgery for lung cancer. Patients were classified into 2 populations depending on whether or not they developed a POP. Uni- and multivariable analyses were performed to identify risk factors for developing POP. The diagnostic performance of BA was represented by its sensitivity, specificity and positive and negative predictive values.

RESULTS

A total of 1006 patients were included in the study. Uni- and multivariable analyses found that a positive BA was independently associated with a greater risk of developing POP with an odds ratio of 6.57 [4.165-10.865]; P < 0.001. Its specificity was 95%, sensitivity was 31%, positive predictive value was 66% and negative predictive value was 81%.

CONCLUSIONS

A positive intraoperative BA is an independent risk factor for POP after lung cancer surgery. Further trials are required to validate the systematic implementation of BA as an early diagnostic tool for POP.

Co-culturing with Streptococcus anginosus alters Staphylococcus aureus transcriptome when exposed to tonsillar cells

Introduction

Improved understanding of Staphylococcus aureus throat colonization in the presence of other co-existing microbes is important for mapping S. aureus adaptation to the human throat, and recurrence of infection. Here, we explore the responses triggered by the encounter between two common throat bacteria, S. aureus and Streptococcus anginosus, to identify genes in S. aureus that are important for colonization in the presence of human tonsillar epithelial cells and S. anginosus, and further compare this transcriptome with the genes expressed in S. aureus as only bacterium.

Methods

We performed an in vitro co-culture experiment followed by RNA sequencing to identify interaction-induced transcriptional alterations and differentially expressed genes (DEGs), followed by gene enrichment analysis.

Results and discussion

A total of 332 and 279 significantly differentially expressed genes with p-value < 0.05 and log2 FoldChange (log2FC) ≥ |2| were identified in S. aureus after 1 h and 3 h co-culturing, respectively. Alterations in expression of various S. aureus survival factors were observed when co-cultured with S. anginosus and tonsillar cells. The serine-aspartate repeat-containing protein D (sdrD) involved in adhesion, was for example highly upregulated in S. aureus during co-culturing with S. anginosus compared to S. aureus grown in the absence of S. anginosus, especially at 3 h. Several virulence genes encoding secreted proteins were also highly upregulated only when S. aureus was co-cultured with S. anginosus and tonsillar cells, and iron does not appear to be a limiting factor in this environment. These findings may be useful for the development of interventions against S. aureus throat colonization and could be further investigated to decipher the roles of the identified genes in the host immune response in context of a throat commensal landscape.

Necroptosis in Pneumonia: Therapeutic Strategies and Future Perspectives

Pneumonia remains a major global health challenge, necessitating the development of effective therapeutic approaches. Recently, necroptosis, a regulated form of cell death, has garnered attention in the fields of pharmacology and immunology for its role in the pathogenesis of pneumonia. Characterized by cell death and inflammatory responses, necroptosis is a key mechanism contributing to tissue damage and immune dysregulation in various diseases, including pneumonia. This review comprehensively analyzes the role of necroptosis in pneumonia and explores potential pharmacological interventions targeting this cell death pathway. Moreover, we highlight the intricate interplay between necroptosis and immune responses in pneumonia, revealing a bidirectional relationship between necrotic cell death and inflammatory signaling. Importantly, we assess current therapeutic strategies modulating necroptosis, encompassing synthetic inhibitors, natural products, and other drugs targeting key components of the programmed necrosis pathway. The article also discusses challenges and future directions in targeting programmed necrosis for pneumonia treatment, proposing novel therapeutic strategies that combine antibiotics with necroptosis inhibitors. This review underscores the importance of understanding necroptosis in pneumonia and highlights the potential of pharmacological interventions to mitigate tissue damage and restore immune homeostasis in this devastating respiratory infection.

Lambda-free light chain: A serum marker of dengue disease via NS3 protease-mediated antibody cleavage

Dengue poses a significant global public health threat, with diverse clinical manifestations due to complex interactions between the host and the pathogen. Recent reports have highlighted elevated serum-free light chain (FLC) levels in viral infectious diseases. Hence, our study aimed to investigate serum FLC levels in dengue patients. The findings revealed elevated serum λ FLCs, which were associated with the severity of dengue. Receiver operating characteristic curve (ROC) analysis demonstrated that λ FLCs may serve as a serum marker for identifying dengue disease (AUC: 0.7825, sensitivity: 80, specificity: 71.43) and classifying severe dengue (AUC: 0.8102, sensitivity: 75, specificity: 79.52). The viral protease, Dengue virus (DENV) nonstructural protein 3 (NS3), acts as a protease that cleaves viral polyproteins as well as host substrates. Therefore, we proposed that antibodies might be potential targets of NS3 protease, leading to an increase in FLCs. LC/MS-MS analysis confirmed that λ FLCs were the predominant products after antibody degradation by NS3 protease. Additionally, purified NS3 protease cleaved both human IgG and DENV2-neutralizing antibodies, resulting in the presence of λ FLCs. Moreover, NS3 protease administration in vitro led to a reduction in the neutralizing efficacy of DENV2-neutralizing antibodies. In summary, the elevated serum λ FLC levels effectively differentiate dengue patients from healthy individuals and identify severe dengue. Furthermore, the elevation of serum λ FLCs is, at least in part, mediated through NS3 protease-mediated antibody cleavage. These findings provide new insights for developing diagnostic tools and understanding the pathogenesis of DENV infection.

Eco-evolutionary dynamics of experimental Pseudomonas aeruginosa populations under oxidative stress

Within-host environments are likely to present a challenging and stressful environment for opportunistic pathogenic bacteria colonizing from the external environment. How populations of pathogenic bacteria respond to such environmental challenges and how this varies between strains is not well understood. Oxidative stress is one of the defences adopted by the human immune system to confront invading bacteria. In this study, we show that strains of the opportunistic pathogenic bacterium Pseudomonas aeruginosa vary in their eco-evolutionary responses to hydrogen peroxide stress. By quantifying their 24 h growth kinetics across hydrogen peroxide gradients we show that a transmissible epidemic strain isolated from a chronic airway infection of a cystic fibrosis patient, LESB58, is much more susceptible to hydrogen peroxide than either of the reference strains, PA14 or PAO1, with PAO1 showing the lowest susceptibility. Using a 12 day serial passaging experiment combined with a mathematical model, we then show that short-term susceptibility controls the longer-term survival of populations exposed to subinhibitory levels of hydrogen peroxide, but that phenotypic evolutionary responses can delay population extinction. Our model further suggests that hydrogen peroxide driven extinctions are more likely with higher rates of population turnover. Together, these findings suggest that hydrogen peroxide is likely to be an effective defence in host niches where there is high population turnover, which may explain the counter-intuitively high susceptibility of a strain isolated from chronic lung infection, where such ecological dynamics may be slower.

Leptospiral cell wall hydrolase (LIC_10271) binding peptidoglycan, lipopolysaccharide, and laminin and the protein show LysM and M23 domains are co-existing in pathogenic species

Leptospirosis, a global reemerging zoonosis caused by the spirochete Leptospira, has severe human and veterinary implications. Cell wall hydrolase (LIC_10271) with LytM (peptidase M23) and LysM domains are found to be associated with various pathogenic bacteria. These domains regulate effects on extracellular matrix and biofilm components, which promote cell wall remodeling and pathogen dissemination in the host. In this study, we present the cloning, expression, purification, and characterization of LIC_10271. To determine the localization of LIC_10271 within the inner membrane of Leptospira, Triton X-114 subcellular fractionation and immunoblot studies were performed. Furthermore, r-LIC_10271 binds with peptidoglycan, lipopolysaccharide, and laminin in a dose-dependent manner. Analysis of the signal peptide, M23, and LysM domains revealed conservation primarily within the P1 group of Leptospira, which encompasses the most pathogenic species. Moreover, the presence of native-LIC_10271 in the inner membrane and the distribution of M23 and LysM domains across pathogenic strains indicates their potential involvement in the interaction between the host and Leptospira.

Streptococcus pneumoniae and other bacterial nasopharyngeal colonization seven years post-introduction of 13-valent pneumococcal conjugate vaccine in South African children

OBJECTIVES

Pneumococcal conjugate vaccines (PCVs) reduce pneumococcal-associated disease by reducing vaccine-serotype (VT) acquisition in vaccinated children, thereby interrupting VT transmission. The 7-valent-PCV was introduced in the South African immunization program in 2009 (13-valent-PCV since 2011) using a 2+1 schedule (at 6, 14, and 40 weeks of age). We aimed to evaluate temporal changes in VT and non-vaccine-serotype (NVT) colonization after 9 years of childhood PCV immunization in South Africa.

METHODS

Nasopharyngeal swabs were collected from healthy children <60-month-old (n = 571) in 2018 (period-2) and compared with samples (n = 1135) collected during early PCV7-introduction (period-1, 2010-11) in an urban low-income setting (Soweto). Pneumococci were tested for using a multiplex quantitative-polymerase chain reaction serotyping reaction-set.

RESULTS

Overall pneumococcal colonization in period-2 (49.4%; 282/571) was 27.5% lower than period-1 (68.1%; 773/1135; adjusted odds ratio [aOR]: 0.66; 95% confidence interval [CI]: 0.54-0.88). Colonization by VT was reduced by 54.5% in period-2 (18.6%; 106/571) compared with period-1 (40.9%; 465/1135; aOR: 0.41; 95% CI: 0.3-0.56). Nevertheless, serotype 19F carriage prevalence was higher (8.1%; 46/571) in period-2 compared with period-1 (6.6%; 75/1135; aOR: 2.0; 95% CI: 1.09-3.56). NVT colonization prevalence was similar in period-2 and period-1 (37.8%; 216/571 and 42.4%; 481/1135).

CONCLUSION

There remains a high residual prevalence of VT, particularly 19F, colonization nine years post-introduction of PCV in the South African childhood immunization program.

Association between admission hyperglycemia and postoperative pneumonia in geriatric patients with hip fractures

BACKGROUND

Admission hyperglycemia is a common phenomenon in the early stages of injury. This study aimed to determine the relationship between admission hyperglycemia and postoperative pneumonia in geriatric patients with hip fractures.

METHODS

A total of 600 geriatric patients admitted to Dandong Central Hospital with hip fractures were included. Patients were divided into four groups based on quartiles of admission blood glucose levels: Q1- Q4. Multivariable logistic regression and propensity score-matched analyses were conducted to calculate adjusted odds ratios (ORs) and 95% confidence intervals (CIs) for postoperative pneumonia. Receiver operating characteristic (ROC) curves were used to determine the cut-off value of admission hyperglycemia for predicting postoperative pneumonia.

RESULTS

The incidence of postoperative pneumonia was significantly higher among hyperglycemic patients than those with normal glucose levels (OR = 2.090, 95% CI: 1.135-3.846, p = 0.016). Admission hyperglycemia showed moderate predictive power, with an area under the ROC curve of 0.803. Furthermore, propensity score-matched analyses demonstrated that patients in the Q3 (OR = 4.250, 95% CI: 1.361-13.272, p = 0.013) and Q4 (OR = 4.667, 95% CI: 1.251-17.405, p = 0.022) quartiles had a significantly higher risk of postoperative pneumonia compared to patients in the Q1 quartile.

CONCLUSIONS

Admission hyperglycemia in elderly hip fracture patients increases the risk of postoperative pneumonia. This biomarker can aid clinical assessment and perioperative management.

Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome

BACKGROUND

Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens.

RESULTS

This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People's Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS.

CONCLUSIONS

In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.

Revisiting ESKAPE Pathogens: virulence, resistance, and combating strategies focusing on quorum sensing

The human-bacterial association is long-known and well-established in terms of both augmentations of human health and attenuation. However, the growing incidents of nosocomial infections caused by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) call for a much deeper understanding of these organisms. Adopting a holistic approach that includes the science of infection and the recent advancements in preventing and treating infections is imperative in designing novel intervention strategies against ESKAPE pathogens. In this regard, this review captures the ingenious strategies commissioned by these master players, which are teamed up against the defenses of the human team, that are equally, if not more, versatile and potent through an analogy. We have taken a basketball match as our analogy, dividing the human and bacterial species into two teams playing with the ball of health. Through this analogy, we make the concept of infectious biology more accessible.

Amino Acid Starvation-Induced Glutamine Accumulation Enhances Pneumococcal Survival

Bacteria are known to cope with amino acid starvation by the stringent response signaling system, which is mediated by the accumulation of the (p)ppGpp alarmones when uncharged tRNAs stall at the ribosomal A site. While a number of metabolic processes have been shown to be regulatory targets of the stringent response in many bacteria, the global impact of amino acid starvation on bacterial metabolism remains obscure. This work reports the metabolomic profiling of the human pathogen Streptococcus pneumoniae under methionine starvation. Methionine limitation led to the massive overhaul of the pneumococcal metabolome. In particular, methionine-starved pneumococci showed a massive accumulation of many metabolites such as glutamine, glutamic acid, lactate, and cyclic AMP (cAMP). In the meantime, methionine-starved pneumococci showed a lower intracellular pH and prolonged survival. Isotope tracing revealed that pneumococci depend predominantly on amino acid uptake to replenish intracellular glutamine but cannot convert glutamine to methionine. Further genetic and biochemical analyses strongly suggested that glutamine is involved in the formation of a "prosurvival" metabolic state by maintaining an appropriate intracellular pH, which is accomplished by the enzymatic release of ammonia from glutamine. Methionine starvation-induced intracellular pH reduction and glutamine accumulation also occurred to various extents under the limitation of other amino acids. These findings have uncovered a new metabolic mechanism of bacterial adaptation to amino acid limitation and perhaps other stresses, which may be used as a potential therapeutic target for infection control. IMPORTANCE Bacteria are known to cope with amino acid starvation by halting growth and prolonging survival via the stringent response signaling system. Previous investigations have allowed us to understand how the stringent response regulates many aspects of macromolecule synthesis and catabolism, but how amino acid starvation promotes bacterial survival at the metabolic level remains largely unclear. This paper reports our systematic profiling of the methionine starvation-induced metabolome in S. pneumoniae. To the best of our knowledge, this represents the first reported bacterial metabolome under amino acid starvation. These data have revealed that the significant accumulation of glutamine and lactate enables S. pneumoniae to form a "prosurvival" metabolic state with a lower intracellular pH, which inhibits bacterial growth for prolonged survival. Our findings have provided insightful information on the metabolic mechanisms of pneumococcal adaptation to nutrient limitation during the colonization of the human upper airway.

Influence of bacterial and alveolar cell co-culture on microbial VOC production using HS-GC/MS

Volatile organic compounds (VOCs) found in exhaled breath continue to garner interest as an alternative diagnostic tool in pulmonary infections yet, their clinical integration remains a challenge with difficulties in translating identified biomarkers. Alterations in bacterial metabolism secondary to host nutritional availability may explain this but is often inadequately modelled in vitro. The influence of more clinically relevant nutrients on VOC production for two common respiratory pathogens was investigated. VOCs from Staphylococcus aureus (S.aureus) and Pseudomonas aeruginosa (P.aeruginosa) cultured with and without human alveolar A549 epithelial cells were analyzed using headspace extraction coupled with gas chromatography-mass spectrometry. Untargeted and targeted analyses were performed, volatile molecules identified from published data, and the differences in VOC production evaluated. Principal component analysis (PCA) could differentiate alveolar cells from either S. aureus or P. aeruginosa when cultured in isolation based on PC1 (p = 0.0017 and 0.0498, respectively). However, this separation was lost for S. aureus (p = 0.31) but not for P. aeruginosa (p = 0.028) when they were cultured with alveolar cells. S. aureus cultured with alveolar cells led to higher concentrations of two candidate biomarkers, 3-methyl-1-butanol (p = 0.001) and 3-methylbutanal (p = 0.002) when compared to S. aureus, alone. P. aeruginosa metabolism resulted in less generation of pathogen-associated VOCs when co-cultured with alveolar cells compared to culturing in isolation. VOC biomarkers previously considered indicative of bacterial presence are influenced by the local nutritional environment and this should be considered when evaluating their biochemical origin.

Rothia from the Human Nose Inhibit Moraxella catarrhalis Colonization with a Secreted Peptidoglycan Endopeptidase

Moraxella catarrhalis is found almost exclusively within the human respiratory tract. This pathobiont is associated with ear infections and the development of respiratory illnesses, including allergies and asthma. Given the limited ecological distribution of M. catarrhalis, we hypothesized that we could leverage the nasal microbiomes of healthy children without M. catarrhalis to identify bacteria that may represent potential sources of therapeutics. Rothia was more abundant in the noses of healthy children compared to children with cold symptoms and M. catarrhalis. We cultured Rothia from nasal samples and determined that most isolates of Rothia dentocariosa and "Rothia similmucilaginosa" were able to fully inhibit the growth of M. catarrhalis in vitro, whereas isolates of Rothia aeria varied in their ability to inhibit M. catarrhalis. Using comparative genomics and proteomics, we identified a putative peptidoglycan hydrolase called secreted antigen A (SagA). This protein was present at higher relative abundance in the secreted proteomes of R. dentocariosa and R. similmucilaginosa than in those from non-inhibitory R. aeria, suggesting that it may be involved in M. catarrhalis inhibition. We produced SagA from R. similmucilaginosa in Escherichia coli and confirmed its ability to degrade M. catarrhalis peptidoglycan and inhibit its growth. We then demonstrated that R. aeria and R. similmucilaginosa reduced M. catarrhalis levels in an air-liquid interface culture model of the respiratory epithelium. Together, our results suggest that Rothia restricts M. catarrhalis colonization of the human respiratory tract in vivo. IMPORTANCE Moraxella catarrhalis is a pathobiont of the respiratory tract, responsible for ear infections in children and wheezing illnesses in children and adults with chronic respiratory diseases. Detection of M. catarrhalis during wheezing episodes in early life is associated with the development of persistent asthma. There are currently no effective vaccines for M. catarrhalis, and most clinical isolates are resistant to the commonly prescribed antibiotics amoxicillin and penicillin. Given the limited niche of M. catarrhalis, we hypothesized that other nasal bacteria have evolved mechanisms to compete against M. catarrhalis. We found that Rothia are associated with the nasal microbiomes of healthy children without Moraxella. Next, we demonstrated that Rothia inhibit M. catarrhalis in vitro and on airway cells. We identified an enzyme produced by Rothia called SagA that degrades M. catarrhalis peptidoglycan and inhibits its growth. We suggest that Rothia or SagA could be developed as highly specific therapeutics against M. catarrhalis.

Molecular basis of Klebsiella pneumoniae colonization in host

Klebsiella pneumoniae (K. pneumoniae) is a common cause of nosocomial infection, which causing disseminated infections such as cystitis, pneumonia and sepsis. K. pneumoniae is intrinsic resistant to penicillin, and members of the population usually have acquired resistance to a variety of antibiotics, which makes it a major threat to clinical and public health. Bacteria can colonize on or within the hosts, accompanied by growth and reproduction of the organisms, but no clinical symptoms are presented. As the "first step" of bacterial infection, colonization in the hosts is of great importance. Colonization of bacteria can last from days to years, with resolution influenced by immune response to the organism, competition at the site from other organisms and, sometimes, use of antimicrobials. Colonized pathogenic bacteria cause healthcare-associated infections at times of reduced host immunity, which is an important cause of clinical occurrence of postoperative complications and increased mortality in ICU patients. Though, K. pneumoniae is one of the most common conditional pathogens of hospital-acquired infections, the mechanisms of K. pneumoniae colonization in humans are not completely clear. In this review, we made a brief summary of the molecular basis of K. pneumoniae colonization in the upper respiratory tract and intestinal niche, and provided new insights for understanding the pathogenesis of K. pneumoniae.

Analysing sinonasal microbiota of fungal rhinosinusitis by next-generation sequencing

OBJECTIVES

Fungal rhinosinusitis is an inflammatory disease of the nose that may lead to life-threatening complications. This study compared the bacterial and fungal microbiomes between patients with invasive fungal rhinosinusitis (IFRS) and non-IFRS (NIFRS).

DESIGN

This was a prospective study including 18 IFRS and NIFRS patients. Fungal and bacterial microbiomes from surgical specimens were sequenced from amplicons of the internal transcribed spacer 1 (ITS1) region and the V3-V4 region of the 16S locus, respectively. Microbiomes were generated using the Illumina MiSeq System 2 x 301 base pair chemistry with a paired-end protocol.

SETTING

Tertiary medical centre.

RESULTS

Targeted metagenomics identified Aspergillus spp. as the predominant fungus in both IFRS and NIFRS patients. Based on phylum and genera level diversity, and abundance differences, significant differences of operational taxonomic units (OTUs) (Fusobacterium, Prevotella, Pseudomonas, Neisseria and Streptococcus) were more abundant in NIFRS compared with IFRS patients.

CONCLUSIONS

This is the first study to analyse bacterial and fungal microbiomes in patients with IFRS and NIFRS via ITS1 and 16S genomics sequencing. Bacterial microbiomes from patients with IFRS demonstrated dysbiosis (alterations in diversity and abundance) compared to those from patients with NIFRS.

Structure and mechanism of a tripartite ATP-independent periplasmic TRAP transporter

In bacteria and archaea, tripartite ATP-independent periplasmic (TRAP) transporters uptake essential nutrients. TRAP transporters receive their substrates via a secreted soluble substrate-binding protein. How a sodium ion-driven secondary active transporter is strictly coupled to a substrate-binding protein is poorly understood. Here we report the cryo-EM structure of the sialic acid TRAP transporter SiaQM from Photobacterium profundum at 2.97 Å resolution. SiaM comprises a "transport" domain and a "scaffold" domain, with the transport domain consisting of helical hairpins as seen in the sodium ion-coupled elevator transporter VcINDY. The SiaQ protein forms intimate contacts with SiaM to extend the size of the scaffold domain, suggesting that TRAP transporters may operate as monomers, rather than the typically observed oligomers for elevator-type transporters. We identify the Na⁺ and sialic acid binding sites in SiaM and demonstrate a strict dependence on the substrate-binding protein SiaP for uptake. We report the SiaP crystal structure that, together with docking studies, suggest the molecular basis for how sialic acid is delivered to the SiaQM transporter complex. We thus propose a model for substrate transport by TRAP proteins, which we describe herein as an 'elevator-with-an-operator' mechanism.

Multidrug resistant bacterial infections in severely ill COVID-19 patients admitted in a national referral and teaching hospital, Kenya

BACKGROUND

Bacterial infections are a common complication in patients with seasonal viral respiratory tract infections and are associated with poor prognosis, increased risk of intensive care unit admission and 29-55% mortality. Yet, there is limited data on the burden of bacterial infections among COVID-19 patients in Africa, where underdeveloped healthcare systems are likely to play a pertinent role in the epidemiology of the COVID-19 pandemic. Here, we evaluated the etiologies, antimicrobial resistance profiles, risk factors, and outcomes of bacterial infections in severely ill COVID-19 patients.

METHODS

A descriptive cross-sectional study design was adopted in severely ill COVID-19 patients at Kenyatta National Hospital, Kenya, from October to December 2021. We used a structured questionnaire and case report forms to collect sociodemographics, clinical presentation, and hospitalization outcome data. Blood, nasal/oropharyngeal swabs and tracheal aspirate samples were collected based on the patient's clinical presentation and transported to the Kenyatta National Hospital microbiology laboratory for immediate processing following the standard bacteriological procedures.

RESULTS

We found at least one bacterial infection in 44.2% (53/120) of the patients sampled, with a 31.7% mortality rate. Pathogens were mainly from the upper respiratory tract (62.7%, 42/67), with gram-negative bacteria dominating (73.1%, 49/67). Males were about three times more likely to acquire bacterial infection (p = 0.015). Those aged 25 to 44 years (p = 0.009), immunized against SARS-CoV-2 (p = 0.027), and admitted to the infectious disease unit ward (p = 0.031) for a short length of stay (0-5 days, p < 0.001) were more likely to have a positive outcome. Multidrug-resistant isolates were the majority (64.3%, 46/67), mainly gram-negative bacteria (69.6%, 32/46). The predominant multidrug-resistant phenotypes were in Enterococcus cloacae (42.9%, 3/7), Klebsiella pneumonia (25%, 4/16), and Escherichia coli (40%, 2/5).

CONCLUSION

Our findings highlight a high prevalence of multidrug-resistant bacterial infections in severely ill COVID-19 patients, with male gender as a risk factor for bacterial infection. Elderly Patients, non-SARS-CoV-2 vaccination, intensive care unit admission, and long length of hospital stay were associated with poor outcomes. There is a need to emphasize strict adherence to infection and prevention at KNH-IDU and antimicrobial stewardship in line with local and global AMR control action plans.

Electrospun-Based Membranes as a Key Tool to Prevent Respiratory Infections

The use of electrospun meshes has been proposed as highly efficient protective equipment to prevent respiratory infections. Those infections can result from the activity of micro-organisms and other small dust particles, such as those resulting from air pollution, that impair the respiratory tract, induce cellular damage and compromise breathing capacity. Therefore, electrospun meshes can contribute to promoting air-breathing quality and controlling the spread of such epidemic-disrupting agents due to their intrinsic characteristics, namely, low pore size, and high porosity and surface area. In this review, the mechanisms behind the pathogenesis of several stressors of the respiratory system are covered as well as the strategies adopted to inhibit their action. The main goal is to discuss the performance of antimicrobial electrospun nanofibers by comparing the results already reported in the literature. Further, the main aspects of the certification of filtering systems are highlighted, and the expected technology developments in the industry are also discussed.

Sex and gender differences in community-acquired pneumonia

Awareness of the influence of sex ands gender on the natural history of several diseases is increasing. Community-acquired pneumonia (CAP) is the most common acute respiratory disease, and it is associated with both morbidity and mortality across all age groups. Although a role for sex- and gender-based differences in the development and associated complications of CAP has been postulated, there is currently high uncertainty on the actual contribution of these factors in the epidemiology and clinical course of CAP. More evidence has been produced on the topic during the last decades, and sex- and gender-based differences have also been extensively studied in COVID-19 patients since the beginning of the SARS-CoV-2 pandemic. This review aims to provide an extensive outlook of the role of sex and gender in the epidemiology, pathogenesis, treatment, and outcomes of patients with CAP, and on the future research scenarios, with also a specific focus on COVID-19.

Tracheal cellular immune response in chickens inoculated with Mycoplasma synoviae vaccine, MS-H or its parent strain 86079/7NS

Mycoplasma synoviae causes respiratory tract disease in chickens characterised by mild to moderate lymphoplasmacytic infiltration of the tracheal mucosa. MS-H (Vaxsafe1 MS, Bioproperties Pty Ltd.) is an effective live attenuated vaccine for M. synoviae, but the immunological basis for its mechanism of protection has not been investigated, and the phenotypes of lymphocytes and associated cytokines involved in the local adaptive immune response have not been described previously. In this study, specific-pathogen-free chickens were inoculated intra-ocularly at 3 weeks of age with either M. synoviae vaccine strain MS-H or vaccine parent strain 86079/7NS (7NS), or remained uninoculated. At 2-, 7- and 21 days post-inoculation (dpi), tracheal mucosal pathology, infiltrating lymphocytes subsets and transcription levels of mRNA encoding 8 cytokines were assessed using light microscopy, indirect immunofluorescent staining and RT-qPCR, respectively. After inoculation, tracheal mucosal thickness, tracheal mucosal lesions, and numbers of infiltrating CD4⁺CD25^- cells, B-cells, and macrophages were greater in MS-H- and 7NS-inoculated chickens compared with non-inoculated. Inoculation with 7NS induced up-regulation of IFN-γ, while vaccination with MS-H induced up-regulation of IL-17A, when compared with non-inoculated birds. Both inoculated groups had a moderate infiltrate of CD4⁺CD25⁺ T cells in the tracheal mucosa. These findings reveal that the tracheal local cellular response after MS-H inoculation is dominated by a Th-17 response, while that of 7NS-inoculated chickens is dominated by a Th-1 type response.

Motility Suppression and Trapping Bacteria by ZnO Nanostructures

Regulating the swimming motility of bacteria near surfaces is essential to suppress or avoid bacterial contamination and infection in catheters and medical devices with wall surfaces. However, the motility of bacteria near walls strongly depends on the combination of the local physicochemical properties of the surfaces. To unravel how nanostructures and their local chemical microenvironment dynamically affect the bacterial motility near surfaces, here, we directly visualize the bacterial swimming and systematically analyze the motility of Escherichia coli swimming on ZnO nanoparticle films and nanowire arrays with further ultraviolet irradiation. The results show that the ZnO nanowire arrays reduce the swimming motility, thus significantly enhancing the trapping ability for motile bacteria. Additionally, thanks to the wide bandgap nature of a ZnO semiconductor, the ultraviolet irradiation rapidly reduces the bacteria locomotion due to the hydroxyl and singlet oxygen produced by the photodynamic effects of ZnO nanowire arrays in an aqueous solution. The findings quantitatively reveal how the combination of geometrical nanostructured surfaces and local tuning of the steric microenvironment are able to regulate the motility of swimming bacteria and suggest the efficient inhibition of bacterial translocation and infection by nanostructured coatings.

Combatting Planktonic and Biofilm Populations of Carbapenem-Resistant Acinetobacter baumannii with Polymyxin-Based Combinations

Carbapenem-resistant Acinetobacter baumannii (CRAB) can cause serious infections that are associated with high mortality rates. During the course of an infection, many CRAB isolates are able to form biofilms, which are recalcitrant to several antibiotics and can be difficult to treat. Polymyxin-based regimens are a first-line treatment option for CRAB infections, but they have not been optimized against both planktonic and biofilm phases of growth. The objective of this study was to identify polymyxin-based combinations that are active against planktonic and biofilm populations of CRAB. Four CRAB isolates (meropenem MICs: 8-256 mg/L) capable of forming biofilms were used in each experiment. The activities of polymyxin B alone and in combination with ampicillin/sulbactam, meropenem, minocycline, and rifampin were assessed using time-kill assays, with the CRAB isolates grown in planktonic and biofilm phases. Viable colony counts were used to detect the bactericidal activity and synergy of the antibiotic combinations. Against the planktonic populations, polymyxin B combined with meropenem, minocycline, ampicillin/sulbactam, and rifampin caused 3.78, -0.15, 4.38, and 3.23 mean log₁₀ CFU/mL reductions against all isolates at 24 h, respectively. Polymyxin B combined with meropenem, ampicillin/sulbactam, or rifampin was synergistic against 75-100% (3/4 or 4/4) of CRAB isolates. Against biofilms, polymyxin B combined with meropenem, minocycline, ampicillin/sulbactam, and rifampin caused 1.86, 1.01, 0.66, and 3.55 mean log₁₀ CFU/mL reductions against all isolates at 24 h, respectively. Only the combination of polymyxin B and rifampin retained bactericidal activity or synergy against any of the isolates when grown as biofilms (50% of isolates). The combination of polymyxin B and rifampin may be promising for CRAB infections that have planktonic and biofilm populations present.

Features and Colonization Strategies of Enterococcus faecalis in the Gut of Bombyx mori

The complex gut microbiome is a malleable microbial community that can undergo remodeling in response to many factors, including the gut environment and microbial properties. Enterococcus has emerged as one of the predominant gut commensal bacterial and plays a fundamental role in the host physiology and health of the major economic agricultural insect, Bombyx mori. Although extensive research on gut structure and microbiome diversity has been carried out, how these microbial consortia are established in multifarious niches within the gut has not been well characterized to date. Here, an Enterococcus species that was stably associated with its host, the model organism B. mori, was identified in the larval gut. GFP–tagged E. faecalis LX10 was constructed as a model bacterium to track the colonization mechanism in the intestine of B. mori. The results revealed that the minimum and optimum colonization results were obtained by feeding at doses of 10⁵ CFU/silkworm and 10⁷ CFU/silkworm, respectively, as confirmed by bioassays and fluorescence-activated cell sorting analyses (FACS). Furthermore, a comprehensive genome-wide exploration of signal sequences provided insight into the relevant colonization properties of E. faecalis LX10. E. faecalis LX10 grew well under alkaline conditions and stably reduced the intestinal pH through lactic acid production. Additionally, the genomic features responsible for lactic acid fermentation were characterized. We further expressed and purified E. faecalis bacteriocin and found that it was particularly effective against other gut bacteria, including Enterococcus casselifavus, Enterococcus mundtii, Serratia marcescens, Bacillus amyloliquefaciens, and Escherichia coli. In addition, the successful colonization of E. faecalis LX10 led to drastically increased expression of all adhesion genes (znuA, lepB, hssA, adhE, EbpA, and Lap), defense genes (cspp, tagF, and esp), regulation gene (BfmRS), secretion gene (prkC) and immune evasion genes (patA and patB), while the expression of iron acquisition genes (ddpD and metN) was largely unchanged or decreased. This work establishes an unprecedented conceptual model for understanding B. mori–gut microbiota interactions in an ecological context. Moreover, these results shed light on the molecular mechanisms of gut microbiota proliferation and colonization in the intestinal tract of this insect.

Fungal and Bacterial Co-infection of Supraglottis in an Immunocompetent Patient Secondary to Herbal Medicine

Fungal infections are among the major infections among immunocompromised patients. They are becoming more common with the widespread use of antibiotics, steroid therapy, and the increasing number of immunocompromised patients. However, the incidence of laryngeal fungal and bacterial co-infection has rarely been reported. As same as laryngeal fungal infection, it mimics other types of laryngeal disease such as gastroesophageal reflux disease, granulomatous disease, and malignant lesions. There is a high likelihood of misdiagnosis, leading to delayed treatment and morbidity from fungal and bacterial co-infection of the larynx. A high index of suspicion is required to make the diagnosis and one should look for evidence of immunosuppression and predisposing factors to local mucosal barrier impairment. However, herbal medicine is a rare cause. We present a case of fungal and bacterial co-infection of supraglottis in an immunocompetent patient secondary to herbal medicine.

Risk factors for carriage of antimicrobial-resistant bacteria in community dwelling-children in the Asia-Pacific region: a systematic review and meta-analysis

Background

Antimicrobial resistance is an increasingly important issue in public health as antibiotics are overused. Resistance to antimicrobial agents can pose significant challenges to infection treatment.

Objectives

To evaluate risk factors associated with carriage of antimicrobial-resistant (AMR) bacteria in children in the Asia-Pacific region to consolidate evidence for future implementation of antibiotic prescribing practice.

Methods

Three electronic databases-PubMed, EMBASE and Cochrane Library-were searched. Observational studies that investigated the risk factors for carriage of MRSA, penicillin-resistant Streptococcus pneumoniae, ESBL-producing Escherichia coli and Klebsiella pneumoniae among the paediatric population in community settings in the Asia-Pacific region were considered eligible. Summary statistics from the identified studies were pooled using meta-analyses.

Results

From the 4145 search results, 25 papers were included in this review. Sixteen papers were included in the meta-analysis based on reported risk factors. Young age of 2-6 months compared with children aged 7-60 months (OR 2.74, 95% CI: 1.75-4.29), antibiotic use within the past 3 months (OR 2.65, 95% CI: 1.70-4.12), daycare attendance (OR 1.49, 95% CI: 1.17-1.91) and hospital admission within the past 3 months (OR 3.43, 95% CI: 2.13-5.51) were found to be significant risk factors for AMR bacterial carriage, whilst breastfeeding (OR 0.69, 95% CI: 0.60-0.81) and concurrent colonization of S. pneumoniae (OR 0.59, 95% CI: 0.38-0.91) are protective factors.

Conclusions

The findings support that there are a number of significant risk factors associated with carriage of AMR bacteria in the Asia-Pacific paediatric population. To combat antimicrobial resistance in the future, these risk factors should be considered, and measures taken to mitigate associated carriage.

Identification of a two-component regulatory system involved in antimicrobial peptide resistance in Streptococcus pneumoniae

Two-component regulatory systems (TCS) are among the most widespread mechanisms that bacteria use to sense and respond to environmental changes. In the human pathogen Streptococcus pneumoniae, a total of 13 TCS have been identified and many of them have been linked to pathogenicity. Notably, TCS01 strongly contributes to pneumococcal virulence in several infection models. However, it remains one of the least studied TCS in pneumococci and its functional role is still unclear. In this study, we demonstrate that TCS01 cooperates with a BceAB-type ABC transporter to sense and induce resistance to structurally-unrelated antimicrobial peptides of bacterial origin that all target undecaprenyl-pyrophosphate or lipid II, which are essential precursors of cell wall biosynthesis. Even though tcs01 and bceAB genes do not locate in the same gene cluster, disruption of either of them equally sensitized the bacterium to the same set of antimicrobial peptides. We show that the key function of TCS01 is to upregulate the expression of the transporter, while the latter appears the main actor in resistance. Electrophoretic mobility shift assays further demonstrated that the response regulator of TCS01 binds to the promoter region of the bceAB genes, implying a direct control of these genes. The BceAB transporter was overexpressed and purified from E. coli. After reconstitution in liposomes, it displayed substantial ATPase and GTPase activities that were stimulated by antimicrobial peptides to which it confers resistance to, revealing new functional features of a BceAB-type transporter. Altogether, this inducible defense mechanism likely contributes to the survival of the opportunistic microorganism in the human host, in which competition among commensal microorganisms is a key determinant for effective host colonization and invasive path.

Nasal colonization by potential bacterial pathogens in healthy kindergarten children of Nepal: a prevalence study

INTRODUCTION

In low- and middle-income countries including Nepal, respiratory tract infection (RTI) is considered as one of the most prominent public health problems in children. Multiple carriage of respiratory pathogens is common in children, especially in preschoolers as they are easily transmitted through close contact and poor hygienic condition. Thus, this research is based on the study of prevalence, co-existence, associated factors and antibiogram of nasal isolates among healthy preschoolers.

METHODS

The study was conducted in four randomly selected kindergarten schools (two government run and two private run) of Bhaktapur Municipality. Out of a total 140 students, 136 eligible participants of age group 2-5 years old were involved in the study. Nasal swab was collected for the isolation of five target isolates (Staphylococcus aureus, Streptococcus pneumoniae, Moraxella catarrhalis, Haemophilus influenzae and Haemophilus parainfluenzae) and their antibiotic resistance determination.

RESULTS

Of 136 participants involved, 128 (94.5%) were positive for carriage of at least one of the target bacteria. The most common isolate was M. catarrhalis 62.5% (80/128) followed by S. aureus 43.0% (55/128). There was a significant difference in bacterial carriage with respect to type of school (p value<0.05, OR=0.50, CI=0.20-0.90). Regarding bacterial co-existence, the most common co-existence was of S. aureus and M. catarrhalis & S. pneumoniae and M. catarrhalis 48.8%. Multiple logistic regression analysis showed that S. aureus was negatively associated with S. pneumoniae, M. catarrhalis and H. influenzae and S. pneumoniae was positively associated with M. catarrhalis and H. influenzae. Multidrug resistance was seen in 63 isolates (29.4%).

CONCLUSIONS

Nepalese kindergarten children are at a high risk of respiratory tract infection by multidrug resistant bacteria.

A genome-wide association study in a large community-based cohort identifies multiple loci associated with susceptibility to bacterial and viral infections

There is limited data on host-specific genetic determinants of susceptibility to bacterial and viral infections. Genome-wide association studies using large population cohorts can be a first step towards identifying patients prone to infectious diseases and targets for new therapies. Genetic variants associated with clinically relevant entities of bacterial and viral infections (e.g., abdominal infections, respiratory infections, and sepsis) in 337,484 participants of the UK Biobank cohort were explored by genome-wide association analyses. Cases (n = 81,179) were identified based on ICD-10 diagnosis codes of hospital inpatient and death registries. Functional annotation was performed using gene expression (eQTL) data. Fifty-seven unique genome-wide significant loci were found, many of which are novel in the context of infectious diseases. Some of the detected genetic variants were previously reported associated with infectious, inflammatory, autoimmune, and malignant diseases or key components of the immune system (e.g., white blood cells, cytokines). Fine mapping of the HLA region revealed significant associations with HLA-DQA1, HLA-DRB1, and HLA-DRB4 locus alleles. PPP1R14A showed strong colocalization with abdominal infections and gene expression in sigmoid and transverse colon, suggesting causality. Shared significant loci across infections and non-infectious phenotypes in the UK Biobank cohort were found, suggesting associations for example between SNPs identified for abdominal infections and CRP, rheumatoid arthritis, and diabetes mellitus. We report multiple loci associated with bacterial and viral infections. A better understanding of the genetic determinants of bacterial and viral infections can be useful to identify patients at risk and in the development of new drugs.

Vaping and Lung Inflammation and Injury

The use of electronic (e)-cigarettes was initially considered a beneficial solution to conventional cigarette smoking cessation. However, paradoxically, e-cigarette use is rapidly growing among nonsmokers, including youth and young adults. In 2019, this rapid growth resulted in an epidemic of hospitalizations and deaths of e-cigarette users (vapers) due to acute lung injury; this novel disease was termed e-cigarette or vaping use-associated lung injury (EVALI). Pathophysiologic mechanisms of EVALI likely involve cytotoxicity and neutrophilic inflammation caused by inhaled chemicals, but further details remain unknown. The undiscovered mechanisms of EVALI are a barrier to identifying biomarkers and developing therapeutics. Furthermore, adverse effects of e-cigarette use have been linked to chronic lung diseases and systemic effects on multiple organs. In this comprehensive review, we discuss the diverse spectrum of vaping exposures, epidemiological and clinical reports, and experimental findings to provide a better understanding of EVALI and the adverse health effects of chronic e-cigarette exposure.

The management of delirium in the older adult in advanced nursing practice

Delirium is a term used to describe an array of symptoms that indicate a disruption in cerebral metabolism, a condition that is often under-recognised, leading to delayed interventions. The condition is a common cause of older adults presenting in hospital, with significant morbidity and mortality associated with increased length of stay. A case study is used to illustrate the use of a diagnostic algorithm for older adults presenting with delirium to an advanced nurse practitioner (ANP)-led service. The clinical decision pathway provides four differential diagnoses, using the case study to put the decision-making process in context. The article demonstrates the ability of the ANP to practise at a high level of expertise as an autonomous practitioner and shows how the pathway supports the nurse to reach an accurate diagnosis. It shows that prompt and accurate diagnosis of delirium in older adults is crucial to avoiding the complications and cognitive decline associated with the condition.