Epidemiological characteristics of mycoplasma pneumoniae in hospitalized children before, during, and after COVID-19 pandemic restrictions in Chongqing, China.

Background: Mycoplasma pneumoniae (MP) is a significant cause of community-acquired pneumonia with high macrolide resistance rates. Various COVID-19 pandemic restrictions have impacted the prevalence of MP. Objective: To assess the changes in the pattern of MP infections among children before, during, and after the COVID-19 pandemic. Methods: A total of 36685 enrolled patients, aged 0-18 years, diagnosed with pneumonia and admitted to Children's Hospital of Chongqing Medical University from January 2019 to December 2023, were retrospectively reviewed in this study. The epidemiological characteristics of pediatric MP infection were analyzed. Results: Among 36685 patients, 7610 (20.74%) tested positive for MP. The highest positive rate was observed among children aged over 6 years (55.06%). There was no gender disparity in MP infection across the three phases of the COVID-19 pandemic. Hospital stays were longest for children during the COVID-19 pandemic (P <0.001). MP infection was most prevalent in the summer (29.64%). The lowest positive rate was observed during the pandemic, with the highest rate found after easing the measures across all age groups (P <0.001). There was a surge in the positive rate of MP in the third year after the COVID-19 pandemic. Regression analyses demonstrated a shift in the age range susceptible to MP infection, with children aged 3.8 to 13.5 years post-pandemic compared to the pre-pandemic range of 5.3 to 15.5 years old. Additionally, the average macrolide resistance rate was 79.84%. We observed a higher resistance rate during the pandemic than in the pre- and post-pandemic phases (P <0.001). Conclusion: The restrictive measures implemented during the COVID-19 pandemic have influenced the spread of MP to some extent and altered demographic and clinical characteristics, such as age, age group, season, length of stay, and macrolide resistance. We recommend continuous surveillance of the evolving epidemiological characteristics of MP infection in the post-pandemic period when restrictions are no longer necessary.

Hypermucoviscous Klebsiella Pneumoniae Caused Community-Acquired Pneumonia in Gondar, Northwest Ethiopia.

BACKGROUND: The incidence of hypermucoviscous Klebsiella pneumoniae (hmvKp), which complicates community-acquired pneumonia, has been increasing recently. This study aimed to detect hypermucoviscous K. pneumoniae and determine its antimicrobial susceptibility pattern in adult patients with community-acquired pneumonia in Northwest Ethiopia. METHODS: This cross-sectional study included 39 K. pneumoniae isolates identified by using Gram stain, culture, and biochemical tests from 312 adult patients with community-acquired pneumonia at the University of Gondar Comprehensive Specialized Referral Hospital from April to June 2021. The hypermucoviscous strains were identified by using the string test. Antimicrobial susceptibility testing was performed by using the Kirby-Bauer disk dif-fusion method. Data were entered by using EPI data version 4.6 and were analyzed by using SPSS version 20. A p-value ≤ 0.05 at a 95% confidence interval was considered statistically significant. RESULTS: Overall, 35.9% (n = 14) of the 39 K. pneumoniae isolates were hypermucoviscous phenotype. The mean age of the hmvKp group was lower than of the cKp group (36.93 ± 12.573 vs. 53.52 ± 19.556 years, p = 0.007). All hmvKp isolates were resistant to amoxicillin-clavulanic acid and trimethoprim-sulfamethoxazole. Azithromycin resistance in the hmvKp strains was significantly higher than in the cKp group (p = 0.012). CONCLUSIONS: This study demonstrates that the hmvKp phenotype causes community-acquired pneumonia and a full resistance to amoxicillin-clavulanic acid and trimethoprim-sulfamethoxazole. Antimicrobial resistance was higher in the hmvKp strain than in the classic strains. Further detection of resistance genes, capsular serotypes, hypermucoviscosity-related genes, and virulence genes is necessary.

Serum metabolomics profile identifies patients with community-acquired pneumonia infected by bacteria, fungi, and viruses.

PURPOSE: Patients with bacterial, fungal, and viral community-acquired pneumonia (CAP) were studied to determine their metabolic profiles. METHODS: Loop-mediated isothermal amplification technology and nucleic acid sequence-dependent amplification combined with microfluidic chip technology were applied to screen multiple pathogens from respiratory tract samples. Eighteen patients with single bacterial infection (B-CAP), fifteen with single virus infection (V-CAP), twenty with single fungal infection (F-CAP), and twenty controls were enrolled. UHPLC-MS/MS analysis of untargeted serum samples for metabolic profiles. Multiple linear regression and Spearman's rank correlation analysis were used to determine associations between metabolites and clinical parameters. The sensitivity and specificity of the screened metabolites were also examined, along with their area under the curve. RESULTS: The metabolic signatures of patients with CAP infected by bacteria, viruses, and fungi were markedly different from those of controls. The abundances of 45, 56, and 79 metabolites were significantly unbalanced. Among these differential metabolites, 11, 13, and 29 were unique to the B-CAP, V-CAP, and F-CAP groups, respectively. Bacterial infections were the only known causes of disturbances in the pentose and glucuronate and aldarate and ascorbate metabolism interconversions metabolic pathway. CONCLUSIONS: Serum metabolomic techniques based on UHPLC-MS/MS may identify differences between individuals with CAP who have been infected by various pathogens, and they can also build a metabolite signature for early detection of the origin of infection and prompt care.

Diagnosis and management of bacterial meningitis in adult Sudanese patients: a six years hospital based, retrospective, cross-sectional study.

PURPOSE: To evaluate the diagnosis and management of bacterial meningitis in adult Sudanese patients in accordance with the Infectious Diseases Society of America (IDSA) guidelines for bacterial meningitis management. PATIENTS AND METHODS: A cross-sectional, retrospective study design was used to recruit all patients aged > 18 years who were diagnosed with or suspected of having bacterial meningitis and admitted to Wad Medani Teaching Hospital, Gezira State, Sudan, between January 2017 and October 2022. RESULTS: In total, 201 patients were included in the analysis. The mean age of the participants was 44.1 ± 21.4 years, and 107 (53.2%) were male. Community-acquired bacterial meningitis accounted for 193 (96%) of the studied patients, and only 8 (4%) of the patients had healthcare-associated meningitis. Neuroimaging was utilized appropriately in 148 (73.6%) patients, blood cultures were not performed entirely, and lumbar puncture was seldom performed in 1 (0.5%) patient. Corticosteroids were appropriately administered to 65 (32.3%) patients, and antibiotics were administered appropriately to only 5 (2.5%) patients. Ceftriaxone 185 (76.1%) was the most frequently utilized antibiotic, followed by vancomycin 23 (9.5%). In terms of overall adherence, this study demonstrated that the IDSA guidelines were not followed at all in the treatment of patients with suspected bacterial meningitis. CONCLUSION: The results of this study contradict the IDSA guidelines for the standard of care for bacterial meningitis. Antibiotic regimens are often incorrect, corticosteroids are administered appropriately in approximately one-third of patients, and neuroimaging is reasonably utilized. This study raises attention to several important issues regarding the diagnosis of bacterial meningitis, including the lack of confirming microbiological tests and the reliance of the diagnosis primarily on CT and clinical examination.

Clinical presentation and microbiological characteristics of community-acquired Staphylococcus aureus bacteraemia at a tertiary hospital in Costa Rica.

Introduction. Staphylococcus aureus is a leading agent in community-acquired bacteraemia (CAB) and has been linked to elevated mortality rates and methicillin resistance in Costa Rica.Gap statement and aim. To update and enhance previous data obtained in this country, we analysed the clinical manifestations of 54 S. aureus CAB cases in a tertiary hospital and delineated the sequence types (STs), virulome, and resistome of the implicated isolates.Methodology. Clinical information was retrieved from patient files. Antibiotic susceptibility profiles were obtained with disc diffusion and automated phenotypic tests. Genomic data were exploited to type the isolates and for detection of resistance and virulence genes.Results. Primary infections predominantly manifested as bone and joint infections, followed by skin and soft tissue infections. Alarmingly, 70% of patients continued to exhibit positive haemocultures beyond 48 h of treatment modification, with nearly a quarter requiring mechanical ventilation or developing septic shock. The 30-day mortality rate reached an alarming 40%. More than 60% of the patients were found to have received suboptimal or inappropriate antibiotic treatment, and there was an alarming tendency towards the overuse of third-generation cephalosporins as empirical treatment. Laboratory tests indicated elevated creatinine levels, leukocytosis, and bandaemia within the first 24 h of hospitalization. However, most showed improvement after 48 h. The isolates were categorized into 13 STs, with a predominance of representatives from the clonal complexes CC72 (ST72), CC8 (ST8), CC5 (ST5, ST6), and CC1 (ST188). Twenty-four isolates tested positive for mecA, with ST72 strains accounting for 20. In addition, we detected genes conferring acquired resistance to aminoglycosides, MLSB antibiotics, trimethoprim/sulfamethoxazole, and mutations for fluoroquinolone resistance in the isolate collection. Genes associated with biofilm formation, capsule synthesis, and exotoxin production were prevalent, in contrast to the infrequent detection of enterotoxins or exfoliative toxin genes.Conclusions. Our findings broaden our understanding of S. aureus infections in a largely understudied region and can enhance patient management and treatment strategies.

Application of metagenomic next-generation sequencing and targeted metagenomic next-generation sequencing in diagnosing pulmonary infections in immunocompetent and immunocompromised patients.

Background: Metagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale. Methods: From January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections. Results: Combined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280). Conclusions: Our findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.

Distribution of virulence genes in clinical isolates of hospital-associated and community-associated methicillin-susceptible Staphylococcus aureus from Terengganu, Malaysia.

Staphylococcus aureus is a common bacterial pathogen known to cause various kinds of infections due to its repertoire of virulence factors. This study aimed to investigate the distribution of 19 types of virulence genes among clinical isolates of methicillin-susceptible S. aureus (MSSA) using the polymerase chain reaction. A total of 109 MSSA isolates, i.e., 63 hospital-associated (HA) and 46 community-associated (CA) were collected from Hospital Sultanah Nur Zahirah, the main tertiary hospital in Terengganu, Malaysia, from July 2016 to June 2017. The most frequent virulence genes detected were hla (78.9%, n=86) and hld (78.0%, n=85) encoding hemolysins, lukED (56.9%, n=62) encoding leukotoxin ED, followed by seb (26.6%, n=29) and sea (24.8%, n=27) encoding enterotoxins. Among 34 (31.2%) isolates carrying six or more virulence genes, only five were multidrug resistant (MDR) while the remaining isolates were susceptible. Significant associations were discovered between the hld gene with CA-MSSA (p=0.016) and the seo gene with HA-MSSA (p=0.023). However, there is no significant association between virulence genes among the different types of infection. The clinical MSSA isolates in Terengganu showed high prevalence and high diversity of virulence gene carriage.

The Epidemiology of Pathogens in Community-Acquired Pneumonia Among Children in Southwest China Before, During and After COVID-19 Non-pharmaceutical Interventions: A Cross-Sectional Study.

OBJECTIVE: This study aimed to investigate the pathogen epidemiology of community-acquired pneumonia (CAP) among children in Southwest China before, during and after the COVID-19 non-pharmaceutical interventions (NPIs). METHODS: Pathogen data of hospitalised children with CAP, including multiple direct immunofluorescence test for seven viruses, bacterial culture and polymerase chain reaction (PCR) for Mycoplasma pneumoniae, were analysed across three phases: Phase I (pre-NPIs: 1 January 2019 to 31 December 2019), Phase II (NPI period: 1 January 2020 to 31 December 2020) and Phase III (post-NPIs: 1 January 2023 to 31 December 2023). RESULTS: A total of 7533 cases were enrolled, including 2444, 1642 and 3447 individuals in Phases I, II and III, respectively. M. pneumoniae predominated in Phases I and III (23.4% and 35.5%, respectively). In Phase II, respiratory syncytial virus (RSV) emerged as the primary pathogen (20.3%), whereas detection rates of influenza A virus (Flu A) and M. pneumoniae were at a low level (1.8% and 9.6%, respectively). In Phase III, both Flu A (15.8%) and M. pneumoniae epidemic rebounded, whereas RSV detection rate returned to Phase I level, and detection rates of Streptococcus pneumoniae and Haemophilus influenzae decreased significantly compared to those in Phase I. Detection rates of adenovirus and parainfluenza virus type 3 decreased phase by phase. Age-stratified analysis and monthly variations supported the above findings. Seasonal patterns of multiple pathogens were disrupted during Phases II and III. CONCLUSIONS: COVID-19 NPIs exhibited a distinct impact on CAP pathogen epidemic among children, with post-NPIs increases observed in M. pneumoniae and Flu A prevalence. Continuous pathogen monitoring is crucial for effective prevention and control of paediatric CAP.

Global Case Fatality of Bacterial Meningitis During an 80-Year Period: A Systematic Review and Meta-Analysis.

Importance: The impact of vaccination, antibiotics, and anti-inflammatory treatment on pathogen distribution and outcome of bacterial meningitis over the past century is uncertain. Objective: To describe worldwide pathogen distribution and case fatality ratios of community-acquired bacterial meningitis. Data Sources: Google Scholar and MEDLINE were searched in January 2022 using the search terms bacterial meningitis and mortality. Study Selection: Included studies reported at least 10 patients with bacterial meningitis and survival status. Studies that selected participants by a specific risk factor, had a mean observation period before 1940, or had more than 10% of patients with health care-associated meningitis, tuberculous meningitis, or missing outcome were excluded. Data Extraction and Synthesis: Data were extracted by 1 author and verified by a second author. The study followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses. Random-effects models stratified by age (ie, neonates, children, adults), Human Development Index (ie, low-income or high-income countries), and decade and meta-regression using the study period's year as an estimator variable were used. Main Outcome and Measure: Case fatality ratios of bacterial meningitis. Results: This review included 371 studies performed in 108 countries from January 1, 1935, to December 31, 2019, describing 157 656 episodes. Of the 33 295 episodes for which the patients' sex was reported, 13 452 (40%) occurred in females. Causative pathogens were reported in 104 598 episodes with Neisseria meningitidis in 26 344 (25%) episodes, Streptococcus pneumoniae in 26 035 (25%) episodes, Haemophilus influenzae in 22 722 (22%), other bacteria in 19 161 (18%) episodes, and unidentified pathogen in 10 336 (10%) episodes. The overall case fatality ratio was 18% (95% CI, 16%-19%), decreasing from 32% (95% CI, 24%-40%) before 1961 to 15% (95% CI, 12%-19%) after 2010. It was highest in meningitis caused by Listeria monocytogenes at 27% (95% CI, 24%-31%) and pneumococci at 24% (95% CI, 22%-26%), compared with meningitis caused by meningococci at 9% (95% CI, 8%-10%) or H influenzae at 11% (95% CI, 10%-13%). Meta-regression showed decreasing case fatality ratios overall and stratified by S pneumoniae, Escherichia coli, or Streptococcus agalactiae (P < .001). Conclusions and Relevance: In this meta-analysis with meta-regression, declining case fatality ratios of community-acquired bacterial meningitis throughout the last century were observed, but a high burden of disease remained.

Multiplex real-time PCR in non-invasive respiratory samples to reduce antibiotic use in community-acquired pneumonia: a randomised trial.

We assessed whether multiplex real-time PCR plus conventional microbiological testing is safe and more effective than conventional microbiological testing alone for reducing antibiotic use in community-acquired pneumonia (CAP). In this randomised trial, we recruited adults hospitalised with CAP at four Spanish hospitals. Patients were randomly assigned (1:1) to undergo either multiplex real-time PCR in non-invasive respiratory samples plus conventional microbiological testing or conventional microbiological testing alone. The primary endpoint was antibiotic use measured by days of antibiotic therapy (DOT). Between February 20, 2020, and April 24, 2023, 242 patients were enrolled; 119 were randomly assigned to multiplex real-time PCR plus conventional microbiological testing and 123 to conventional microbiological testing alone. All but one of the patients allocated to multiplex real-time PCR plus conventional microbiological testing underwent PCR, which was performed in sputum samples in 77 patients (65.2%) and in nasopharyngeal swabs in 41 (34.7%). The median DOT was 10.04 (IQR 7.98, 12.94) in the multiplex PCR plus conventional microbiological testing group and 11.33 (IQR 8.15, 16.16) in the conventional microbiological testing alone group (difference -1.04; 95% CI, -2.42 to 0.17; p = 0.093). No differences were observed in adverse events and 30-day mortality. Our findings do not support the routine implementation of multiplex real-time PCR in the initial microbiological testing in hospitalised patients with CAP. Clinicaltrials.gov registration: NCT04158492.

Advances in the pathogenesis and treatment of pneumococcal meningitis.

Streptococcus pneumoniae is a common pathogen associated with community-acquired bacterial meningitis, characterized by high morbidity and mortality rates. While vaccination reduces the incidence of meningitis, many survivors experience severe brain damage and corresponding sequelae. The pathogenesis of pneumococcal meningitis has not been fully elucidated. Currently, meningitis requires bacterial disruption of the blood - brain barrier, a process that involves the interaction of bacterial surface components with host cells and various inflammatory responses. This review delineates the global prevalence, pathogenesis, and treatment strategies of pneumococcal meningitis. The objective is to enhance the thorough comprehension of the clinical manifestations and biological mechanisms of the disease, thereby enabling more efficient prevention, diagnosis, and therapeutic interventions.

Diabetic Patient with CA-MRSA Pneumonia and Plasma Cell Neoplasm: A Case Report of Severe Complications and Prognosis.

BACKGROUND The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) has been increasing in recent years, becoming a cause of community-acquired infection. Interestingly, its role in malignancy recently started to be considered after a noticed increase in reported cases and studies discussing the potential association. CASE REPORT In the present case, the patient had known and uncontrolled diabetes mellitus and a history of multiple abscesses that were previously treated by incision and drainage. The patient received a diagnosis of severe pneumonia, and MRSA was found in blood cultures. Further tests for HIV, hemagglutinin type 1, and neuraminidase type 1 (H1N1) were negative. The D test was also performed for macrolide-inducible resistance and was negative, indicating the need for intravenous administration of clindamycin. An echocardiogram ruled out endocarditis. Subsequently, the patient experienced progressive back pain and weakness involving the lower limbs. A pathological fracture was discovered, along with nerve root compression. An urgent posterior spine fixation was then performed by a neurosurgeon. A biopsy was collected at the site of the pathological fracture, and histopathological tests indicated a plasma cell neoplasm. CONCLUSIONS MRSA is known to cause serious and dangerous infections, including necrotizing pneumonia. Furthermore, a link between MRSA and plasma cell dyscrasia has been considered in several reports. This necessitates the need for further studies to clarify this hidden association, which may help in the course and prognosis of these patients.

A review of the value of point-of-care testing for community-acquired pneumonia.

INTRODUCTION: Community-acquired pneumonia (CAP) is an infectious disease associated with high mortality worldwide. Although Streptococcus pneumoniae remains the most frequent pathogen in CAP, data from recent studies using molecular tests have shown that respiratory viruses play a key role in adults with pneumonia. The impact of difficult-to-treat pathogens on the outcomes of pneumonia is also important even though they represent only a small proportion of overall cases. Despite improvements in the microbiological diagnosis of CAP in recent decades, the identification of the causative pathogen is often delayed because of difficulties in obtaining good-quality sputum samples, issues in transporting samples, and slow laboratory processes. Therefore, the initial treatment of CAP is usually empirical. Point-of-care testing (POCT) was introduced to avoid treatment delays and reduce reliance on empirical antibiotics. AREAS COVERED: This review summarizes the main scientific evidence on the role of POCT in the diagnosis and management of patients with CAP. The authors searched for articles on POCT in pneumonia on PubMed from inception to 20 January 2024. The references in the identified articles were also searched. EXPERT OPINION: POCT involves rapid diagnostic assays that can be performed at the bedside especially in cases of severe CAP and immunocompromised patients. These tests can produce results that could help guide initial therapy and management.

Dynamical analysis of methicillin-resistant Staphylococcus aureus infection in North Cyprus with optimal control: prevalence and awareness.

The number of Methicillin-resistant Staphylococcus aureus (MRSA) cases in communities and hospitals is on the rise worldwide. In this work, a nonlinear deterministic model for the dynamics of MRSA infection in society was developed to visualize the significance of awareness in interventions that could be applied in the prevention of transmission with and without optimal control. Positivity and uniqueness were verified for the proposed corruption model to identify the level of resolution of infection factors in society. Furthermore, how various parameters affect the reproductive number R 0 and sensitivity analysis of the proposed model was explored through mathematical techniques and figures. The global stability of model equilibria analysis was established by using Lyapunov functions with the first derivative test. A total of seven years of data gathered from a private hospital consisting of inpatients and outpatients of MRSA were used in this model for numerical simulations and for observing the dynamics of infection by using a non-standard finite difference (NSFD) scheme. When optimal control was applied as a second model, it was determined that increasing awareness of hand hygiene and wearing a mask were the key controlling measures to prevent the spread of community-acquired MRSA (CA-MRSA) and hospital-acquired MRSA (HA-MRSA). Lastly, it was concluded that both CA-MRSA and HA-MRSA cases are on the rise in the community, and increasing awareness concerning transmission is extremely significant in preventing further spread.

Exploring the pathogenicity of Mycoplasma pneumoniae: Focus on community-acquired respiratory distress syndrome toxins.

Community-Acquired Respiratory Distress Syndrome Toxin (CARDS TX) is a unique exotoxin produced by Mycoplasma pneumoniae (MP) and has been confirmed to possess ADP-ribosyltransferase (ART) and vacuolating activities. CARDS TX binds to receptors on the surfaces of mammalian cells followed by entry into the cells through clathrin-mediated endocytosis, and exerts cytotoxic effects by undergoing retrograde transport and finally cleavage on endosomes and cellular organelles. In addition, CARDS TX can trigger severe inflammatory reactions resulting in airway dysfunction, producing allergic inflammation and asthma-like conditions. As a newly discovered virulence factor of MP, CARDS TX has been extensively studied in recent years. As resistance to macrolide drugs has increased significantly in recent years and there is no vaccine against MP, the development of a vaccine targeting CARDS TX is considered a potential preventive measure. This review focuses on recent studies and insights into this toxin, providing directions for a better understanding of MP pathogenesis and treatment. IMPORTANCE: A serious hazard to worldwide public health in recent years, Mycoplasma pneumoniae (MP) is a prominent bacterium that causes community-acquired pneumonia (CAP) in hospitalized children. Due to their high prevalence and fatality rates, MP infections often cause both respiratory illnesses and extensive extrapulmonary symptoms. It has recently been shown that MP produces a distinct exotoxin known as Community-Acquired Respiratory Distress Syndrome Toxin (CARDS TX). Mycoplasma pneumoniae pneumonia (MPP)-like tissue injury is caused by this toxin because it has both ADP-ribosyltransferase and vacuolating properties. A better knowledge of MP etiology and therapy is provided by this review, which focuses on latest research and insights into this toxin.

Incidence of drug-resistant pathogens in community-acquired pneumonia at a safety net hospital.

The 2019 Infectious Diseases Society of America guideline for the management of community-acquired pneumonia (CAP) emphasizes the need for clinician to understand local epidemiological data to guide selection of appropriate treatment. Currently, the local distribution of causative pathogens and their associated resistance patterns in CAP is unknown. A retrospective observational study was performed of patients admitted to an 870-bed safety net hospital between March 2016 and March 2021 who received a diagnosis of CAP or healthcare-associated pneumonia within the first 48 hours of admission. The primary outcome was the incidence of CAP caused by methicillin-resistant Staphylococcus aureus (MRSA) or Pseudomonas aeruginosa (PsA) as determined by comparing the number of satisfactory sputum cultures or blood cultures with these drug-resistant organisms to the total number of reviewed patients. Secondary outcomes studied included risk factors associated with CAP caused by drug-resistant organisms, utilization of broad-spectrum antibiotics, appropriate antibiotic de-escalation within 72 hours, and treatment duration. In this 220-patient cohort, MRSA or PsA was isolated from three sputum cultures and no blood cultures. The local incidence of drug-resistant pathogens among the analyzed sample of CAP patients was 1.4% (n = 3/220). The overall incidence of CAP caused by MRSA or PsA among admitted patients is low at our safety-net county hospital. Future research is needed to identify local risk factors associated with the development of CAP caused by drug-resistant pathogens.IMPORTANCEThis study investigates the incidence of drug-resistant pathogens including methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa among community-acquired pneumonia (CAP) patients at a safety net hospital. Understanding local bacteria resistance patterns when treating CAP is essential and supported by evidence-based guidelines. Our findings empower other clinicians to investigate resistance patterns at their own institutions and identify methods to improve antibiotic use. This has the potential to reduce the unnecessary use of broad-spectrum antibiotic agents and combat the development of antibiotic resistance.

Mobile genetic element-driven genomic changes in a community-associated methicillin-resistant Staphylococcus aureus clone during its transmission in a regional community outbreak in Japan.

Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections are now a public health concern in both community and healthcare settings worldwide. We previously identified a suspected case of a maternity clinic-centred outbreak of CA-MRSA skin infection in a regional community in Japan by PFGE-based analysis. In this study, we performed genome sequence-based analyses of 151 CA-MRSA isolates, which included not only outbreak-related isolates that we previously defined based on identical or similar PFGE patterns but also other isolates obtained during the same period in the same region. Our analysis accurately defined 133 isolates as outbreak-related isolates, collectively called the TDC clone. They belonged to a CA-MRSA lineage in clonal complex (CC) 30, known as the South West Pacific (SWP) clone. A high-resolution phylogenetic analysis of these isolates combined with their epidemiological data revealed that the TDC clone was already present and circulating in the region before the outbreak was recognized, and only the isolates belonging to two sublineages (named SL4 and SL5) were directly involved in the outbreak. Long persistence in patients/carriers and frequent intrahousehold transmission of the TDC clone were also revealed by this analysis. Moreover, by systematic analyses of the genome changes that occurred in this CA-MRSA clone during transmission in the community, we revealed that most variations were associated with mobile genetic elements (MGEs). Variant PFGE types were generated by alterations of prophages and genomic islands or insertion sequence (IS)-mediated insertion of a plasmid or a sequence of unknown origin. Dynamic changes in plasmid content, which were linked to changes in antimicrobial resistance profiles in specific isolates, were generated by frequent gain and loss of plasmids, most of which were self-transmissible or mobilizable. The introduction of IS256 by a plasmid (named pTDC02) into sublineage SL5 led to SL5-specific amplification of IS256, and amplified IS256 copies were involved in some of the structural changes of chromosomes and plasmids and generated variations in the repertoire of virulence-related genes in limited isolates. These data revealed how CA-MRSA genomes change during transmission in the community and how MGEs are involved in this process.

Genomic Profile of a Multidrug-Resistant Klebsiella pneumoniae Strain Isolated from a Urine Specimen.

Klebsiella pneumoniae is an opportunistic pathogen mostly found in health care-associated infections but can also be associated with community-acquired infections and is in critical need of new antimicrobial agents for strains resistant to carbapenems. The prevalence of carbapenemase-encoding genes varies among studies. Multidrug-resistant K. pneumoniae strains can harbor several antimicrobial-resistant determinants and mobile genetic elements (MGEs), along with virulence genetic determinants in community settings. We aim to determine the genetic profile of a multidrug-resistant K. pneumoniae strain isolated from a patient with community-acquired UTI. We isolated a K. pneumoniae strain UABC-Str0120, from a urine sample of community-acquired urinary tract infection. Antimicrobial susceptibility tests and Whole-genome sequencing (WGS) were performed. The phylogenetic relationship was inferred by SNPs calling and filtering. UABC-Str0120 showed resistance toward ß-lactams, combinations with ß-lactamase inhibitors, and carbapenems. WGS revealed the presence of genes conferring resistance to aminoglycosides, ß-lactams, carbapenems, quinolones, sulfonamides, phosphonates, phenicols, and quaternary ammonium compounds, 77 subsystems of virulence genes were identified, and an uncommon sequence type ST5889 was also determined. The sequenced strain harbors several MGEs. The UABC-Str0120 recovered from a urine sample harbors several virulence and antimicrobial resistance determinants, which assembles an endangering combination for an immunocompromised or a seemly healthy host, given its presence in a community setting.