Annals of Clinical Microbiology and Antimicrobials最新文献

{"title":"Successful treatment of Keratitis caused by Mycobacterium chelonae and an overview of previous cases in Europe.","authors":"Rudolf Kukla, Katerina Nouzovska, Lenka Ryskova, Petra Rozsivalova, Ivo Pavlik, Pavel Bostik","doi":"10.1186/s12941-024-00752-w","DOIUrl":"10.1186/s12941-024-00752-w","url":null,"abstract":"<p><strong>Introduction and purpose: </strong>Mycobacterium (M.) chelonae is responsible for a half of relatively rare nontuberculous mycobacteria (NTM) keratitis. We report a case of M. chelonae keratitis in a woman following sclerocorneal suture extraction after cataract surgery.</p><p><strong>Results: </strong>A 70-year-old woman presented with a red eye and corneal infiltration of her left eye six weeks following sclerocorneal suture extraction after an elective cataract surgery in another institute. She complained of a sharp, cutting pain and photophobia. Since initial corneal scrapes and conjunctival swabs proved no pathogen using culture and PCR methods, non-specific antibiotics and antifungal agents were administered. As keratitis was complicated by an inflammation in the anterior chamber and vitreous, samples of the vitreous fluid were sent for microbiologic examination. DNA of Epstein-Barr virus (EBV) was repeatedly detected. Since the intrastromal abscess had formed, corneal re-scrapings were performed and M. chelonae was detected using culture, MALDI-TOF MS and PCR methods. Therapy was changed to a combination of oral and topical clarithromycin, intravitreal, topical and intracameral amikacin, and oral and topical moxifloxacin. The successful therapy led to stabilization. The optical penetrating keratoplasty was performed and no signs of the infection recurrence were found.</p><p><strong>Conclusions: </strong>The diagnosis of nontuberculous mycobacterial keratitis is difficult and often delayed. An aggressive and prolonged antimicrobial therapy should include systemic and topical antibiotics. Surgical intervention in the form of corneal transplantation may be required in the active and nonresponsive infection. In the presented case this was necessary for visual rehabilitation due to scarring.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"92"},"PeriodicalIF":4.6,"publicationDate":"2024-10-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11465828/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142387446","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection.","authors":"Muyun Wei, Shaowei Mao, Shuangshuang Li, Kangyi Gu, Dejian Gu, Shengjie Bai, Xinhua Lu, Min Li","doi":"10.1186/s12941-024-00749-5","DOIUrl":"10.1186/s12941-024-00749-5","url":null,"abstract":"<p><strong>Background: </strong>Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited.</p><p><strong>Methods: </strong>To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis.</p><p><strong>Results: </strong>In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS.</p><p><strong>Conclusion: </strong>In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"88"},"PeriodicalIF":4.6,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11443791/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deciphering the possible role of MmpL7 efflux pump in SQ109 resistance in Mycobacterium tuberculosis.","authors":"Wei Jing, Fuzhen Zhang, Yuanyuan Shang, Wenhui Shi, Cong Yao, Xuxia Zhang, Naihui Chu, Jie Lu, Jinfeng Yuan","doi":"10.1186/s12941-024-00746-8","DOIUrl":"10.1186/s12941-024-00746-8","url":null,"abstract":"<p><strong>Background: </strong>SQ109 is a promising candidate drug for the treatment of patients with drug-resistant tuberculosis (DR-TB). The purpose of this study was to investigate the activity of SQ109 against clinical isolates of Mycobacterium tuberculosis (MTB) from patients with multidrug-resistant TB (MDR-TB) and pre-extensively drug-resistant TB (pre-XDR-TB), and to explore new drug-resistant mechanisms of SQ109.</p><p><strong>Methods: </strong>We evaluated the in vitro activity of SQ109 against clinical isolates from patients with MDR-TB and pre-XDR-TB using minimal inhibitory concentration (MIC) assay. The drug-resistant gene, mmpL3 of SQ109-resistant strains was sequenced, and a quantitative real-time PCR assay was used to analyze 28 efflux pump genes in SQ109-resistant strains without mmpL3 mutations. The role of candidate efflux pumps mmpL5 and mmpL7 on the MIC of SQ109 was evaluated using recombinantly cloned MmpL5 and MmpL7 expressed in Mycobacterium smegmatis.</p><p><strong>Results: </strong>The MIC₉₀, MIC₉₅ and MIC₉₉ values of SQ109 for 225 clinical isolates of MTB were 0.25 mg/L, 0.5 mg/L and 1.0 mg/L, respectively. Among the pre-XDR strains, six showed resistance to SQ109 despite the absence of gene mutations in mmpL3. In six resistant pre-XDR strains, the MIC of SQ109 decreased with the use of an efflux pump inhibitor, and there was significant upregulation of mmpL5 and mmpL7 in two strains after exposure to SQ109. The presence of MmpL7 in Mycobacterium smegmatis resulted in decreased susceptibility to SQ109, with the MIC increasing from 16 mg/L to 32 mg/L.</p><p><strong>Conclusions: </strong>Our data demonstrated that SQ109 exhibited excellent levels of in vitro activity against MTB. MmpL7 may be a potential gene for MTB resistance to SQ109, providing a useful target for detecting SQ109 resistance in MTB.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"87"},"PeriodicalIF":4.6,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11439249/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339822","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Prevalence, antimicrobial resistance, and genomic characterization of Salmonella strains isolated in Hangzhou, China: a two-year study.","authors":"Lifei Yu, Jianzhong Fan, Shanshan Lu, Junxin Zhou, Huangdu Hu, Caiping Mao, Xiaoting Hua, Yan Jiang, Ying Fu, Yunsong Yu, Xinhong Han","doi":"10.1186/s12941-024-00748-6","DOIUrl":"https://doi.org/10.1186/s12941-024-00748-6","url":null,"abstract":"<p><p>This study explored the molecular epidemiology and resistance mechanisms of 271 non-duplicate Salmonella enterica (S. enterica) strains, isolated mainly from adults (209/271) in a tertiary hospital in Hangzhou between 2020 and 2021. Through whole-genome sequencing and bioinformatics, the bacterial strains were classified into 46 serotypes and 54 sequence types (ST), with S. Enteritidis, S. 1,4,[5],12:i:-, and S. Typhimurium being the most prevalent serotypes and ST11, ST34, and ST19 the most common STs. The strains isolated from adults were primarily S. Enteritidis (59/209), while from children were mainly S. 1,4,[5],12:i:- (20/62). Worryingly, 12.55% strains were multi-drug resistant (MDR), with resistance rates to cefepime (FEP), ceftazidime (CAZ), ceftriaxone (CRO) and cefotaxime (CTX) of 7.38%, 9.23%, 15.87% and 16.24%, respectively, and resistance rates to levofloxacin (LEV) and ciprofloxacin (CIP) of 8.49% and 19.19%, respectively. It is worth noting that the resistance rates of CRO and CTX in children reached 30.65%. A total of 34 strains carried extended-spectrum β-lactamase (ESBL) genes, dominated by bla_CTX-M-65 (13/34) and bla_CTX-M-55 (12/34); it is notable that one strain of S. Saintpaul carried both bla_CTX-M-27 and bla_CTX-M-55. The resistance mechanism to cephalosporins was mainly due to ESBL genes (20/43), and other genes included AmpC and β-lactamase genes. The strains resistant to quinolones mainly carried qnrS1 (27/53), and others included qnrB6, aac(6')-Ib-cr, and mutations in gyrA and parC. One strain did not carry common quinolone resistance genes but had a parC (p.T57S) mutation to cause CIP resistance. This research provides vital insights into the molecular epidemiology and resistance mechanisms of clinical S. enterica, implicating possible infection control strategies.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"86"},"PeriodicalIF":4.6,"publicationDate":"2024-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11439225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339824","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Epidemiology, antimicrobial resistance profile and management of carbapenem-resistant Klebsiella pneumoniae among mothers with suspected sepsis in Ethiopia.","authors":"Eshetu Gadisa, Beverly Egyir, Bright Adu, Hawawu Ahmed, Guta Disasa, Tesfaye Sisay Tessema","doi":"10.1186/s12941-024-00745-9","DOIUrl":"https://doi.org/10.1186/s12941-024-00745-9","url":null,"abstract":"<p><strong>Background: </strong>Early detection and proper management of maternal sepsis caused by carbapenem-resistant Klebsiella pneumoniae (CRKP) can significantly reduce severe complications and maternal mortality. This study aimed to describe the epidemiology, antimicrobial resistance profile, and management of carbapenem-resistant K. pneumoniae among sepsis-suspected maternal cases in Ethiopia.</p><p><strong>Methods: </strong>A prospective cross-sectional study was conducted in five tertiary hospitals from June 2021 to December 2023. Isolation, identification, and antimicrobial susceptibility testing of the isolates were carried out following standard microbiological procedures as stated in the CLSI guidelines. Data on socio-demographics, risk factors, and management strategies were collected with structured questionnaires. Associations between variables were determined using logistic regression analysis in STATA-21. A p-value of less than 0.05 was statistically significant.</p><p><strong>Results: </strong>Of the 5613 total women suspected of having maternal sepsis, 609 (10.8%) of them were infected with K. pneumoniae. The prevalence rates of MDR, XDR, and PDR K. pneumoniae strains were 93.9%, 24.3%, and 10.9%, respectively. The resistance rates for the last-resort antibiotics; amikacin, tigecycline, carbapenem, and third-generation cephalosporin were 16.4%, 29.1%, 31.9%, and 93.0%, respectively. The combination of carbapenem with tigecycline or amikacin therapy was used to manage maternal sepsis caused by cephalosporin-and carbapenem-resistant strains. Sepsis associated risk factors, including septic abortion [AOR = 5.3; 95%CI:2.2-14.4]; extended hospitalization [AOR = 3.7; 95%CI: 1.6-19.4]; dilatation and curettage [AOR = 2.2; 95%CI:1.3-13.4]; cesarean wound infection [AOR = 4.1; 95%CI:2.0-9.2]; indwelling catheterization [AOR = 2.1;95%CI: 1.4-6.2]; ICU admission [AOR = 4.3; 95%CI:2.4-11.2]; post abortion [AOR = 9.8; 95%CI:5.7-16.3], and recurrent UTI [AOR = 3.3; 95%CI: 1.6-13.2] were significantly associated with maternal sepsis caused by K. pneumoniae.</p><p><strong>Conclusions: </strong>The prevalence of maternal sepsis caused by carbapenem- resistant K. pneumoniae is high and serious attention needs to be given to combat transmission. Therefore, improving awareness, early diagnosis, IPC, integrated maternal surveillance, improved sanitation and efficient antimicrobial stewardship are crucial to combating bacterial maternal sepsis.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"85"},"PeriodicalIF":4.6,"publicationDate":"2024-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11423506/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142339823","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Retrospective clinical and microbiologic analysis of metagenomic next-generation sequencing in the microbiological diagnosis of cutaneous infectious granulomas","authors":"Hsingmei Liu, Qiao Ran, Jianchi Ma, Jing Zhang, Ni Tan, Liyan Xi, Xiqing Li, Junmin Zhang, Sha Lu","doi":"10.1186/s12941-024-00744-w","DOIUrl":"https://doi.org/10.1186/s12941-024-00744-w","url":null,"abstract":"Cutaneous infectious granulomas (CIG) are localized and chronic skin infection caused by a variety of pathogens such as protozoans, bacteria, worms, viruses and fungi. The diagnosis of CIG is difficult because microbiological examination shows low sensitivity and the histomorphological findings of CIG caused by different pathogens are commonly difficult to be distinguished. The objective of this study is to explore the application of mNGS in tissue sample testing for CIG cases, and to compare mNGS with traditional microbiological methods by evaluating sensitivity and specificity. We conducted a retrospective study at the Department of Dermatology of Sun Yat-sen Memorial Hospital, Sun Yat-sen University from January 1st, 2020, to May 31st, 2024. Specimens from CIG patients with a clinical presentation of cutaneous infection that was supported by histological examination were retrospectively enrolled. Specimens were delivered to be tested for microbiological examinations and mNGS. Our data show that mNGS detected Non-tuberculosis mycobacteria, Mycobacterium tuberculosis, fungi and bacteria in CIG. Compared to culture, mNGS showed a higher positive rate (80.77% vs. 57.7%) with high sensitivity rate (100%) and negative predictive value (100%). In addition, mNGS can detect more pathogens in one sample and can be used to detect variable samples including the samples of paraffin-embedded tissue with shorter detective time. Of the 21 patients who showed clinical improvement within a 30-day follow-up, eighteen had their treatments adjusted, including fifteen who continued treatment based on the results of mNGS. mNGS could provide a potentially rapid and effective alternative detection method for diagnosis of cutaneous infectious granulomas and mNGS results may affect the clinical prognosis resulting from enabling the patients to initiate timely treatment.","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"4 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142200108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic changes of respiratory microbiota associated with treatment outcome in drug-sensitive and drug-resistant pulmonary tuberculosis","authors":"Yuan Lin, Zhuozhi Liang, Xingshan Cai, Yang Luo, Bitong Wu, Yongzhong Feng, Zhiqun Cai, Xiaopeng Liang, Shouyong Tan","doi":"10.1186/s12941-024-00742-y","DOIUrl":"https://doi.org/10.1186/s12941-024-00742-y","url":null,"abstract":"Respiratory microbiota is closely related to tuberculosis (TB) initiation and progression. However, the dynamic changes of respiratory microbiota during treatment and its association with TB progression remains unclear. A total of 16 healthy individuals and 16 TB patients (10 drug-sensitive TB (DS-TB) and 6 drug-resistant TB (DR-TB)) were recruited. Sputum samples were collected at baseline for all anticipants and after anti-TB treatment at Month-6 for TB patients. High throughput 16 S RNA sequencing was used to characterize the respiratory microbiota composition. Compared to the healthy individuals, TB patients exhibited lower respiratory microbiota diversity (p < 0.05). This disruption was alleviated after anti-TB treatment, especially for DS-TB patients. Parvimonas spp. numbers significantly increased after six months of anti-TB treatment in both DS-TB and DR-TB patients (p < 0.05). Rothia spp. increase during treatment was associated with longer sputum-culture conversion time and worse pulmonary lesion absorption (p < 0.05). Besides, Moraxella spp. prevalence was associated with longer sputum-culture conversion time, while Gemella spp. increase was associated with worsening resolving of pulmonary lesions (p < 0.05). Dynamic changes of respiratory microbiota during anti-TB treatment is closely related to TB progression. The involvement of critical microorganisms, such as Parvimonas spp., Rothia spp., Moraxella, and Gemella spp., appears to be associated with pulmonary inflammatory conditions, particularly among DR-TB. These microorganisms could potentially serve as biomarkers or even as targets for therapeutic intervention to enhance the prognosis of tuberculosis patients.","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"16 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142200107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Clinical characteristics and mortality of mucormycosis in hematological malignancies: a retrospective study in Eastern China.","authors":"Tao Suo, Mengmeng Xu, Qixia Xu","doi":"10.1186/s12941-024-00738-8","DOIUrl":"https://doi.org/10.1186/s12941-024-00738-8","url":null,"abstract":"<p><strong>Background: </strong>Mucormycosis is a significant cause of morbidity and mortality in patients with hematological malignancies, but its characteristics are not fully understood. This study aimed to gain a better understanding of the clinical features of mucormycosis in patients with hematological malignancies in eastern China.</p><p><strong>Methods: </strong>A single-center retrospective analysis was conducted on the demographic profile, microbiology, management, and 90-day mortality of mucormycosis patients with hematological malignancies between 2018 and 2023.</p><p><strong>Results: </strong>A total of 50 cases were included in the study, consisting of 11 proven and 39 probable cases of mucormycosis. The median age of the patients was 39.98 ± 18.52 years, with 52% being male. Among the cases, 46% had acute myeloid leukemia (AML), 16% had acute lymphoblastic leukemia (ALL), and 16% had myelodysplastic syndrome. The most common manifestations of mucormycosis were pulmonary (80%), disseminated (16%), and rhinocerebral (4%). The diagnosis was confirmed through histology, culture, microscopy, and molecular diagnostic techniques. The most commonly identified fungal species were Cunninghamella (40%), Rhizopus (26%), and Rhizomucor (22%). Treatment involved antifungals in 84% of cases and surgery in 10% of cases. The 90-day mortality rate was 76%. Logistic regression analysis revealed that treatment with amphotericin B and surgery was associated with improved survival, while neutropenia and administration of voriconazole prior to diagnosis was associated with higher mortality.</p><p><strong>Conclusions: </strong>Mucormycosis continues to have a high mortality rate in patients with hematological malignancies. Early diagnosis using various techniques, including molecular biology, along with the appropriate use of amphotericin B and surgery when possible, is vital for the successful treatment of mucormycosis.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"82"},"PeriodicalIF":4.6,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11363688/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103749","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Detection of multidrug-resistance in Mycobacterium tuberculosis by phenotype- and molecular-based assays.","authors":"Laima Vasiliauskaitė, Zofia Bakuła, Edita Vasiliauskienė, Daiva Bakonytė, Przemysław Decewicz, Mikołaj Dziurzyński, Małgorzata Proboszcz, Edita Valerija Davidavičienė, Birutė Nakčerienė, Rafał Krenke, Tomas Kačergius, Petras Stakėnas, Tomasz Jagielski","doi":"10.1186/s12941-024-00741-z","DOIUrl":"10.1186/s12941-024-00741-z","url":null,"abstract":"<p><strong>Background: </strong>The whole-genome sequencing (WGS) is becoming an increasingly effective tool for rapid and accurate detection of drug resistance in Mycobacterium tuberculosis complex (MTBC). This approach, however, has still been poorly evaluated on strains from Central and Eastern European countries. The purpose of this study was to assess the performance of WGS against conventional drug susceptibility testing (DST) for the detection of multi-drug resistant (MDR) phenotypes among MTBC clinical strains from Poland and Lithuania.</p><p><strong>Methods: </strong>The study included 208 MTBC strains (130 MDR; 78 drug susceptible), recovered from as many tuberculosis patients in Lithuania and Poland between 2018 and 2021. Resistance to rifampicin (RIF) and isoniazid (INH) was assessed by Critical Concentration (CC) and Minimum Inhibitory Concentration (MIC) DST as well as molecular-based techniques, including line-probe assay (LPA) and WGS. The analysis of WGS results was performed using bioinformatic pipeline- and software-based tools.</p><p><strong>Results: </strong>The results obtained with the CC DST were more congruent with those by LPA compared to pipeline-based WGS. Software-based tools showed excellent concordance with pipeline-based analysis in prediction of RIF/INH resistance. The RIF-resistant strains demonstrated a relatively homogenous MIC distribution with the mode at the highest tested MIC value. The most frequent RIF-resistance conferring mutation was rpoB S450L. The mode MIC for INH was two-fold higher among double katG and inhA mutants than among single katG mutants. The overall rate of discordant results between all methods was calculated at 5.3%. Three strains had discordant results by both genotypic methods (LPA and pipeline-based WGS), one strain by LPA only, three strains by MIC DST, two strains by both MIC DST and pipeline-based WGS, and the remaining two strains showed discordant results with all three methods, compared to CC DST.</p><p><strong>Conclusions: </strong>Considering MIC DST results, current CCs of the first-line anti-TB drugs might be inappropriately high and may need to be revised. Both molecular methods demonstrated 100% specificity, while pipeline-based WGS had slightly lower sensitivity for RIF and INH than LPA, compared to CC DST.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"81"},"PeriodicalIF":4.6,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11360294/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142091628","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Global status of antimicrobial resistance in clinical Enterococcus faecalis isolates: systematic review and meta-analysis.","authors":"Lingbo Guan, Masoumeh Beig, Lina Wang, Tahereh Navidifar, Samaneh Moradi, Faezeh Motallebi Tabaei, Zahra Teymouri, Mahya Abedi Moghadam, Mansour Sedighi","doi":"10.1186/s12941-024-00728-w","DOIUrl":"10.1186/s12941-024-00728-w","url":null,"abstract":"<p><strong>Background: </strong>Due to the increasing emergence of antibiotic resistance in Enterococcus faecalis (E. faecalis), it indicated as potentially opportunistic pathogen causing various healthcare-associated and life-threatening diseases around the world.</p><p><strong>Objective: </strong>The aim of this meta-analysis was to evaluate the weighted pooled resistance rates in clinical E. faecalis isolates based on over time, areas, antimicrobial susceptibility testing (AST), and infection source.</p><p><strong>Methods: </strong>We searched the studies in PubMed, Scopus, and Web of Science (November 30, 2022). All statistical analyses were carried out using the statistical package R.</p><p><strong>Results: </strong>The analysis encompassed a total of 74 studies conducted in 28 countries. According to the meta-regression, the chloramphenicol, fosfomycin, imipenem, linezolid, minocycline, norfloxacin, quinupristin-dalfopristin, and tetracycline resistance rate increased over time. Analysis revealed statistically significant differences in antibiotic resistance rates for ampicillin, chloramphenicol, erythromycin, gentamicin, penicillin, rifampicin, teicoplanin, tetracycline, and vancomycin across various countries.</p><p><strong>Conclusions: </strong>Globally, the prevalence of drug resistant E. faecalis strains are on the increase over time. Daptomycin and tigecycline can be an effective agent for the treatment of clinical E. faecalis infections. Considering the low prevalence of antibiotic resistance in continents of Europe and Australia, it is suggested to take advantage of their preventive strategies in order to obtain efficient results in other places with high prevalence of resistance.</p>","PeriodicalId":8052,"journal":{"name":"Annals of Clinical Microbiology and Antimicrobials","volume":"23 1","pages":"80"},"PeriodicalIF":4.6,"publicationDate":"2024-08-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11344933/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142054751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}