Journal of Microbiology Immunology and Infection最新文献

Background: Streptococcus pneumoniae Serotype 3 (SPN3) remains a significant cause of morbidity and mortality worldwide despite of pneumococcal conjugate vaccine (PCV) implementation. We explored genomic profile of SPN3 from children and adult groups to understand population structure and evolution dynamics of SPN3 in Indonesia.

Methods: We undertook whole genome sequencing (WGS) from 19 isolates of SPN3 in Indonesia between 2017 and 2021 prior to PCV introduction. This study assessed sequence types (STs), global pneumococcal sequence cluster (GPSC), genome prediction of antimicrobial resistance (AMR) profile, pangenome analysis, phylogenetic tree, and genome comparative of capsular polysaccharide (cps) locus.

Results: We identified ST451-GPSC234 (n = 5) and ST180-GPSC12 (n = 4), ST458-GPSC51 (n = 2), ST3805-GPSC12 (n = 2), ST4909-GPSC363 (n = 2), ST700-GPSC10 (n = 1), ST5292-GPSC309 (n = 1), ST505-GPSC12 (n = 1), and ST4233 (n = 1). Genome prediction of AMR discover isolates were resistant to tetracycline (n = 5); co-resistant of chloramphenicol and tetracycline (n = 2); co-trimoxazole and tetracycline (n = 1). We observed SPN3 possess closed pangenome characteristic, indicates more stable genetic repertoire. We found 5 absent genes in cps locus including cpsABCD and tnp in ST700-GPSC10 lineage.

Conclusions: SPN3 has potential genomic profile to enhance the ability of this strain to endure selective pressure such as PCV introduction.

Respiratory virus infection is an important cause of both community acquired pneumonia and hospital-acquired pneumonia. Various respiratory viruses, including influenza virus, avian influenza virus, respiratory syncytial virus (RSV), SARS-CoV, MERS-CoV, and SARS-CoV-2, result in severe fibrosis sequelae after the acute phase. Since the COVID-19 pandemic, respiratory virus infection, as an important cause of pulmonary fibrosis, has attracted increasing attention around the world. Respiratory virus infection usually triggers robust inflammation responses, leading to large amounts of proinflammatory mediator production, such as chemokine (C-C motif) ligand 2 (CCL2), a critical chemokine involved in the recruitment of various inflammatory cells. Moreover, CCL2 plays a pivotal role in the pathogenesis of fibrosis progression, through regulating recruitment of bone marrow-derived monocytes and increasing the expression of extracellular matrix proteins. This review provided a concise overview of the common fibrosis sequelae after virus infection. Then we discussed the elevated levels of CCL2 in various respiratory virus infection, underscoring its potent profibrotic role. Targeting the CCL2/CCR2 axis holds promise for alleviating fibrosis sequelae post-acute virus infection and warrants further investigation.

Background: Intestinal parasitic diseases affect millions of people worldwide. Numerous commercial molecular methods detecting digestive parasites have been developed recently, including multiplex PCR assays able to identify multiple parasites at once. Several studies have demonstrated that the efficacy of these molecular methods is dependent on the specific protocols employed at each stage of the process including pretreatment, extraction and amplification. However, previous studies have exclusively focused on one of these steps, without considering the others. The objective of the present study was to evaluate the performances of molecular tools for Cryptosporidium parvum detection in stool samples, considering all steps of the process simultaneously.

Methods: 30 distinct combinations of protocols were evaluated corresponding to three pre-treatment methods, four DNA extraction techniques and six DNA amplification assays. The performances of these combinations were evaluated in terms of detection limit.

Results: We showed that different combinations yielded varying results. The FTD® Stool Parasite technique proved to be the most effective, achieving 100 % detection. Manual extraction methods demonstrated excellent outcomes, although they are time-consuming. The optimal approach for detecting C. parvum DNA is a combination of mechanical pretreatment, the Nuclisens® Easymag® extraction method, and the FTD® Stool Parasite DNA amplification method.

Conclusion: This work shows that the molecular diagnosis should consider all stages. A PCR method may not be effective with an unsuitable extraction technique, but can yield optimal results with an appropriate one.

Background: COVID-19 is one of the most pressing public health issues worldwide. The sequelae of COVID-19 however remains unclear. We performed a systematic assessment of sequelae across all body systems, focusing on whether COVID-19 is associated with increased risk of hospitalization for various diseases.

Methods: In this cohort study, we examined 135 disorders in UK biobank (UKBB) (N = 412,096; age: 50-87). We also conducted analysis for new-onset and recurrent cases, and employed the prior event rate adjustment (PERR) approach to minimize effects of unmeasured confounders. Time-dependent effects were also tested.

Results: Compared to individuals with no known COVID-19 history, those with severe COVID-19 (hospitalized) exhibited increased hazards of hospitalization due to multiple disorders (median follow-up = 261 days), including disorders of respiratory, cardiovascular, neurological, gastrointestinal, genitourinary, musculoskeletal systems, as well as injuries, infections and non-specific symptoms. Notably, severe COVID-19 was associated with increased hospitalization risks in 77 out of the 107 disease categories with ≥ 5 events in both groups. These results remained largely consistent in sensitivity analyses. Mild (non-hospitalized) COVID-19 was associated with increased risk of hospitalization for several disorders: aspiration pneumonitis, musculoskeletal pain and other general signs/symptoms. The risk of hospitalizations following infection was generally higher during the pre-vaccination era.

Conclusion: This study revealed increased risk of hospitalization from a wide variety of pulmonary and extra-pulmonary diseases after COVID-19, especially for severe infections. The findings may have important clinical implications, such as the need for closer monitoring and risk assessment of relevant sequelae, and allocating more resources toward prevention and treatment of such sequelae.

Background: To determine susceptibility of imipenem-non-susceptible Escherichia coli (INS-EC) and Klebsiella pneumoniae (INS-KP) isolates collected during 2020-2022 through a national surveillance program in Taiwan to novel antibiotics, and to compare the results with those obtained during 2012-2018.

Methods: Minimum inhibitory concentrations were determined by broth microdilution methods. Genes encoding carbapenemases including bla_KPC, metallo-β-lactamase (MBL) genes, and bla_OXA-48 were detected via multiplex PCR. Data retrieved from our 2012-2018 study were used for comparison.

Results: Of 3260 E. coli and 1457 K. pneumoniae isolates collected during 2020-2022, 0.9 % and 9.5 %, were INS-EC and INS-KP, respectively. Cefepime-zidebactam, ceftazidime-avibactam, imipenem-relebactam, and meropenem-vaborbactam were active against 100 %, 75.9 %, 65.5 %, and 79.3 % of 29 INS-EC isolates respectively; and against 100 %, 90.6 %, 64.5 %, and 67.4 % of 138 INS- KP isolates, respectively. Susceptibility was contingent upon carbapenemase types. Susceptibility rates of cefepime-zidebactam and ceftazidime-avibactam remained constant from 2012 to 2018 through 2020-2022 but those of imipenem-relebactam and meropenem-vaborbactam decreased significantly, which may be partially attributable to the increasing prevalence of bla_OXA-48. Eighteen MBL-gene-positive isolates and two bla_KPC-positive isolates were resistant to ceftazidime-avibactam, whereas all were susceptible to cefepime-zidebactam. Tigecycline had a higher susceptibility rate than eravacycline and omadacycline for K. pneumoniae isolates. Lascufloxacin and delafloxacin were effective against fewer than 10 % of INS isolates. Susceptibilities to novel tetracyclines and fluoroquinolones remained similar from 2012 to 2018 through 2020-2022.

Conclusions: This study highlights significant resistance patterns of INS-EC and INS-KP isolates in Taiwan. The declining susceptibility rates and the rising prevalence of genetic resistance determinants highlight the importance of ongoing surveillance and antimicrobial stewardship.

Background: Chlamydia trachomatis infection is one of the most common sexually transmitted infections (STIs). This study investigated the prevalence and genotype distribution of C. trachomatis, and treatment response, focusing on the recent emergence of genovariant L2b in Taiwan.

Methods: This prospective study was conducted from August 2021 to September 2023, enrolling 1023 participants, including 492 people who received pre-exposure prophylaxis (PrEP) for HIV and 531 people with HIV (PWH). Multiple-site sampling and genotyping of C. trachomatis identified were performed. Participants testing positive for C. trachomatis received a 7-day course of doxycycline and test-of-cure (TOC) assessments were conducted post-treatment.

Results: Among the participants, mostly MSM (92.7%), 26.4% tested positive for C. trachomatis, with 77.8% identified in the rectum. The prevalent genotypes were J (26.4%), G (24.0%), and B (17.7%). Treatment with a 7-day course of doxycycline resulted in clearance for most cases (91.1%). Genotyping investigations for those repeatedly testing positive (8.9%) showed reinfections with different genotypes. Eighteen cases of asymptomatic rectal carriage of genovariant L2b were detected, predominantly in PWH (88.9%). The L2b genovariant was cleared with 7 days of doxycycline on TOC assessments. The prevalence of L2b increased over time, with multi-locus sequence typing showing ST53 as the predominant strain.

Conclusions: C. trachomatis was prevalent among PWH and PrEP users and the prevalence of L2b genovariant was increasing in Taiwan. A 7-day course of doxycycline was effective in clearing L2b genovariant in asymptomatic participants. Continued surveillance to monitor the evolving epidemiology of chlamydia in Taiwan is warranted.

Neutralizing anti-interferon (IFN)-α autoantibodies can lead to immune dysregulation, potentially resulting in critical coronavirus disease 2019 (COVID-19). We report a case presenting with severe COVID-19 who was subsequently diagnosed to have thymoma and neutralizing anti-IFN-α autoantibodies.