Annals of Clinical Microbiology and Antimicrobials最新文献

Background: It has been revealed that carbapenem-resistant Klebsiella pneumoniae (CRKP) colonization is closely associated with subsequent clinical infections. This study aimed to investigate the resistance and epidemiology of CRKP isolated from anal swabs and subsequent clinical infection specimens in two pediatric intensive care unit (ICU) departments. Clinical characteristics were analyzed to identify the risk factors of CRKP infection.

Methods: A 3-year retrospective study was carried out in pediatric intensive care units (PICU) and neonatal intensive care units (NICU). CRKP isolates from colonization and infection samples were characterized by testing resistance genes and multilocus sequence typing (MLST). The results of MLST were analyzed to derive CCs by Bionumeric 8.0. Clinical variables such as gestational age, birth weight, mode of delivery, underlying diseases, exposure of antimicrobial agents, history of surgery, length of hospital stay, and prognosis were collected through the electronic medical record system and analyzed by SPSS 22.0.

Results: Of the 2225 patients who were screened for CRE colonization, 7.42% of patients were detected positive. The incidence of subsequent infection was 18.18%. Carbapenemase genes bla_KPC-2 and bla_NDM-1 were the most prevalent in the colonization and infection of CRKP. The majority of CRKP isolated from anal swabs and infection samples belonged to CC11/ST11. The distribution of CC11 in the PICU was significantly higher than in NICU. ST11/bla_KPC-2 was significantly higher in infection CRKP isolates. Age older than one year and usage of carbapenems within 3 months prior to detection of CRKP colonization were independent risk factors for CRKP clinical infection.

Conclusion: The main prevalence of CRKP varies in different departments. Colonization of ST11/bla_KPC-2 CRKP may increase the incidence of subsequent infections in pediatric ICU patients. Age and usage of carbapenems could increase the risk of CRKP infection in this study.

Objectives: Salmonella is recognized globally as a significant foodborne pathogen associated with foodborne outbreaks in both humans and animal. The rise of multidrug-resistant (MDR) Salmonella isolates poses a critical public health challenge. Given that the isolation of Salmonella within abattoirs is a prominent source of community infection especially through the consumption of contaminated meat. This study aims to determine the prevalence of Salmonella, the occurrence of virulence genes (invA, spvC), and specific resistance genes (tetA, sul1, aadA1, aac(3)- IV) in Salmonella isolates isolated from cattle in abattoirs. Additionally, the investigation assesses the potential exposure risks for abattoir workers in Mansoura City, Egypt.

Methods: In a study conducted from May to July 2024, a total of 150 samples were collected to investigate the presence of Salmonella in healthy Egyptian Baladi cattle and abattoir workers at the Mansoura abattoir, Mansoura City, Egypt. The sample collection comprised rectal swabs (n = 50) and meat swabs (n = 50) from cattle, in addition to 50 hand swabs obtained from abattoir workers. Salmonella isolation was done following standard microbiological techniques. Initially, pre-enrichment of the samples was conducted using buffered peptone water. Subsequently, selective enrichment was executed using Rappaport Vassiliadis broth, followed by cultivation on xylose-lysine-deoxycholate (XLD) agar to isolate suspected Salmonella colonies. These colonies were then subjected to a series of identification tests, including biochemical assays, slide agglutination tests, and polymerase chain reaction (PCR) targeting the invA gene, which is indicative of Salmonella presence. Furthermore, molecularly identified isolates were tested for the virulence gene spvC, which is related to the pathogenicity of Salmonella. The antimicrobial susceptibility of the isolates was assessed using the Kirby-Bauer disc diffusion method, providing insight into the resistance profiles of the observed isolates. In addition, a subset of 19 Salmonella isolates underwent multiplex PCR analysis to evaluate the presence of specific resistance genes: tetA, sul1, aadA1, and aac(3)-IV.

Results: The overall occurrence of Salmonella isolates across all examined samples was 12.7%. This included 4% from cattle carcass swabs, 12% from rectal swabs, and a notable 22% from workers' hands. The most prevalent serotypes identified were Salmonella Enteritidis and Salmonella Typhimurium, exhibiting incidences of 26.3% (n = 5) and 21% (n = 4), respectively. Other serotypes included Salmonella Infantis at 15.8% (n = 3), Salmonella Kentucky and Salmonella Tsevie each at 10.5% (n = 2), and Salmonella Paratyphi A, Salmonella Haifa, and Salmonella Virchow at 5.3% ((n = 1) each). From the tested Salmonella isolates, 100% (19/19) were positive for the invA and 89.5% (17/19) carried Spvc genes. Resistance profiling ca

Background: COVID-19 associated pulmonary aspergillosis (CAPA) has been globally reported to be a life-threatening complication of severe COVID-19. Previous studies primarily focused on an association between secondary Aspergillus infection and elevated mortality risk in COVID-19 patients, while potential confounding factors and alternative pathogenic mechanisms remain insufficiently investigated. The risk factors and outcomes of patients with secondary SARS-CoV-2 infection following invasive pulmonary aspergillosis (IPA) were not been well explored either.

Methods: This retrospective monocentric study enrolled 152 hospitalized IPA patients with and without SARS-CoV-2 infection from 1 November 2022 to 31 October 2023. The characteristics of IPA patients and related risk factors were investigated, and the relationship between different SARS-CoV-2 infection status and the prognosis in IPA patients was further evaluated.

Results: Our analysis demonstrated that IPA patients subsequently diagnosed with SARS-CoV-2 infection exhibited significantly elevated mortality risk compared to those without viral coinfection (53.6% vs. 22.9%, P < 0.001). SARS-CoV-2 infection status (OR 3.708; P = 0.001; 95%CI 1.674-8.212), albumin concentration (OR 0.885; P = 0.005; 95%CI 0.813-0.964), and C-reactive protein level (OR 1.007; P = 0.012; 95%CI 1.002-1.013) were statistically significant independent risk factors for prognosis of IPA patients. Subsequent analysis established a multivariate risk prediction model incorporating independent prognostic factors, which exhibited robust discriminative capacity for mortality risk stratification via ROC curve validation (AUC = 0.792, 95%CI 0.721-0.862, P < 0.0001). A statistically significant difference in mortality rate existed between IPA patients with secondary SARS-CoV-2 infection and CAPA patients (63.2% and 33.3%, P = 0.037). Notably, comparative analysis revealed no statistically significant differences in 28-day (22/96, 22.9% vs. 6/18, 33.3%) or 90-day mortality rates (22/96, 22.9% vs. 6/18, 33.3%) between patients with IPA without SARS-CoV-2 infection and IPA patients with secondary SARS-CoV-2 infection.

Conclusions: IPA patients with secondary SARS-CoV-2 coinfection had a lower mortality compared to those with CAPA. Considering the high mortality rate, more medical cares are needed for these patients.

Tuberculosis (TB) remains a significant global health issue, with drug-resistant TB posing a major challenge. The genetic lineage of Mycobacterium tuberculosis (Mtb) is known to influence various aspects, including drug resistance. Still, the relationship between different lineages and drug resistance levels, especially in the context of the Beijing genotype, requires further exploration. This study aimed to investigate the disparities in drug resistance among diverse lineages of Mtb. We analyzed 193 clinical isolates from drug-resistant TB patients, among them 91.2% were MDR/pre-XDR-TB. Samples were collected from patients at specific hospitals between 2014 and 2020. The isolates were subjected to smear microscopy, sputum culture, minimum inhibitory concentration (MIC) testing, and whole-genome sequencing (WGS). The MIC distributions and resistance levels of drugs like INH, AMK, RIF, EMB, and FQ were analyzed, and the association between lineages and drug resistance was determined using statistical tests. Our results showed significant differences in the MIC distributions and resistance levels of INH and AMK between lineages 2.2 and 2.3. Lineage 2.3.2 was a protective factor for high-level INH resistance, and lineage 2.3 was a protective factor for high-level AMK resistance. The L2.3.6 strain had a high proportion of high-level resistance to INH and AMK. This study provides evidence for the evolution and spread of the modern Beijing genotype of Mtb. It suggests that L2.3.6 will have the potential to become the main sublineage of tuberculosis for the spread of drug-resistant tuberculosis and the necessity of pedigree testing of drug-resistant strains in clinical treatment.

Background: Since the incidence of vancomycin-resistant enterococci (VRE) is increasing and treatment options remain limited, we aimed to investigate the epidemiology of vancomycin- and tigecycline-resistant enterococci in a university hospital using whole genome sequencing (WGS).

Methods: Between April and December 2021, 102 VRE isolates were collected from a single tertiary care hospital in the Czech Republic. Forty selected isolates underwent antimicrobial susceptibility testing and WGS (Illumina short reads and long reads with MinION in selected isolates).

Results: All Enterococcus faecium isolates were resistant to ampicillin, carrying the PBP5_Met485Ala, PBP5_Glu629Val, and fluoroquinolones carrying the GyrA_Ser83Ile and ParC_Ser80Ile substitutions. The vanA operon was found on pELF2-like plasmids and plasmids carrying rep17 and/or rep18b genes. The novel Tn1546 structural variants were identified in vanA-carrying isolates. The vanB operon was located on the chromosome within a Tn1549 structural variant. Linezolid resistance was detected in one isolate carrying the 23S rDNA_G2576T substitution. Twenty-two isolates were resistant to tigecycline (tet(L), tet(M) and rpsJ_del 155-166 or RpsJ_Lys57Arg). Discrepancies between phenotypic and genotypic resistance profiles were observed for daptomycin (RpoB_Ser491Phe), trimethoprim/sulfamethoxazole (dfrG gene), nitrofurantoin (NmrA_Gln48Lys substitution without the EF0404 and EF0648 genes) and tetracycline (truncated TetM). The two multilocus sequence typing (MLST) schemes identified different numbers of STs: 5 STs, with ST117 as the predominant one (n = 32, 80%), versus 10 STs, with ST138 (27.5%), ST136 (25%), and ST1067 (20%) being the most frequent, respectively. The whole genome MLST revealed clonal clustering (0-7 allele differences) among isolates of the same ST. When comparing ST117 isolates from our study with 2,204 ST117 isolates from 15 countries, only one Czech isolate clustered closely with strains from Germany and the Netherlands, differing by just 16 alleles.

Conclusions: The spread of E. faecium isolates ST117 resistant to vancomycin and tigecycline was identified. The discrepancies between resistance genotypes and phenotypes highlight the importance of combining molecular and phenotypic surveillance in antimicrobial resistance monitoring.

Objectives: To investigate the mechanisms of ceftazidime/avibactam (CZA) resistance and the nosocomial dissemination of carbapenem-resistant Pseudomonas aeruginosa (CRPA) and carbapenem-resistant Klebsiella pneumoniae (CRKP) in an intensive care unit (ICU) in China.

Methods: Clinical CRPA and CRKP isolates were obtained from an ICU of a tertiary hospital in China from August 2020 to February 2021. Antimicrobial susceptibility was determined according to CLSI. WGS, cloning experiments and kinetic parameters were conducted to reveal resistance mechanisms, molecular characteristics and dissemination of CRPA and CRKP.

Results: We isolated 32 CZA-resistant strains, including 12 CRPA and 20 CRKP strains from an ICU between August 2020 and February 2021. CZA resistance was associated with the presence of NDM and efflux pumps in CRKP strains, whereas bla_AFM-2, bla_KPC-87, and bla_PER-1 contributed to CZA resistance in CRPA strains. Compared to KPC-2, KPC-87 exhibited a 1.5-fold elevation in k_cat/K_m for ceftazidime, a 7.5-fold increase in K_i for avibactam, and a loss of carbapenem hydrolysis. bla_KPC-87 was located in the NTE_KPC-IIa like element based on the Tn3. Insertion of 656 bp Δbla_TEM-1 upstream of bla_KPC-87 introduced an additional promoter that increased KPC-87 expression. Cluster 2 and 3 of CRKP represented two different clones of ST11 transmitted between patients. KPC-87-producing ST270 CRPA strains exhibited a small-scale dissemination and cross-regional transfer with the referral of a patient. The evolutionary pathways of AFM-2-producing ST275 CRPA strains were more complex to elucidate the transmission events.

Conclusions: In CRKP and CRPA, diverse resistance mechanisms contributed to CZA resistance. These CZA-resistant strains were transmitted among patients in the ICU and even across regions to the other healthcare unit when the patient was transferred.

Background: To address the overuse of antibiotics, this study examined the clinical characteristics and outcomes associated with antibiotic duration and carbapenem-sparing regimens in hematological patients with Escherichia coli (E. coli) and Klebsiella pneumoniae (K. pneumoniae) bloodstream infections (BSI).

Methods: We conducted a retrospective analysis of hematological patients with E. coli or K. pneumoniae BSI from 2017 to 2023. Propensity score matching (PSM) controlled for confounding variables, and data were analyzed using multivariate regression models.

Results: A total of 1,862 patients were included (E. coli: n = 932; K. pneumoniae: n = 930). Among 1,105 patients in the antibiotic duration cohort, 48.96% (n = 541) received short-course therapy (median: 8 days, IQR: 7-9), while others received prolonged-course therapy (median: 14 days, IQR: 12-17). No significant differences in 30-day mortality or 90-day recurrence rates were observed between the two groups, either before or after PSM. In the antibiotic regimen cohort (n = 1,606), we assessed the effectiveness of carbapenem-containing versus carbapenem-sparing regimens, as well as monotherapy versus combination therapy. Among 1,488 patients with non-carbapenem-resistant Enterobacteriaceae (non-CRE) infections, 567 had infections caused by extended-spectrum beta-lactamase (ESBL)-producing bacteria. In this subgroup, 30-day mortality rates also showed no significant differences between carbapenem-containing and carbapenem-sparing regimens, both before and after PSM.

Conclusion: In conclusion, short-course antibiotic therapy is as effective as prolonged therapy for treating E. coli and K. pneumoniae BSI in hematological patients. Similarly, carbapenem-sparing regimens are non-inferior to carbapenem-based regimens. These findings highlight the potential for optimizing antibiotic use, but further validation through randomized controlled trials is warranted.

Background: Oral bacteria have been associated with several systemic diseases, and studies have highlighted their potential role in carcinogenesis. A biofilm is considered an antimicrobial resistance gene reservoir, and the oral cavity provides an excellent environment for biofilm formation. The aim of this study was to evaluate the pathogen spectrum and antimicrobial resistance rates of clinical isolates from head and neck infections in the Hungarian population.

Methods: A total of 5185 bacterial isolates were analyzed from 1978 patients between 2018 and 2023. Antimicrobial resistance rates were reported according to the EUCAST guidelines. The primary diagnoses of the patients were categorized into three major groups: abscesses, necrotizing lesions and surgical site infections of patients treated for malignant tumors. Pearson's chi-square test was used to compare the percentages of bacteria in the different patient groups.

Results: The most frequently isolated bacteria were Streptococcus (18.8%) and Prevotella spp. (13.5%), followed by Staphylococcus (13.2%) and Fusobacterium spp. (9.1%). Differences in the pathogen spectrum of three patient groups ('abscess', 'necrosis' and 'tumor') were also evaluated. Compared with the other two patient groups, cancer patients had significantly greater percentages of Enterobacter spp., Enterococcus spp., Pseudomonas spp. and beta-hemolytic streptococci. Substantial resistance rates to clindamycin were observed for Prevotella, Streptococcus and Staphylococcus spp. at 40.9% (95% CI [37.3-44.7%]), 34.8% (95% CI [31.8-37.9%]) and 32.3% (95% CI [28.8-35.9%]), respectively. The percentage of methicillin-resistant Staphylococcus aureus isolates was 13.8% (95% CI [9.2-19.5%]). The percentage of vancomycin-resistant Enterococcus spp. isolates was 2.8% (95% CI [0.6-8.0%]), and the percentages of extended-spectrum beta-lactamase-producing E. coli and Klebsiella spp. isolates were 1% (95% CI [0.02-5.6%]) and 2.6% (95% CI [0.8-5.9%]), respectively.

Conclusion: Our evaluation revealed high percentages of Enterobacterales in patients with diseases such as osteonecrosis or oral cancer. Further investigation of the role of the oral microbiota and its potential impact on the morbidity of patients with advanced disease is needed. Substantial antimicrobial resistance rates, particularly to clindamycin, pose a major concern for treating bacterial infections in the head and neck region.

Background: This study examines colistin resistance in Gram-negative bacteria in Egypt, analyzing prevalence, trends, geographic variations, colistin-carbapenem resistance correlation, and mcr-mediated plasmid resistance.

Methods: We conducted a systematic search of articles published between 2014 and 2024 that reported on colistin or mcr-mediated resistance in Gram-negative bacteria isolated from human infections in Egypt, with clearly defined susceptibility testing methods. A random-effects meta-analysis was conducted to estimate colistin resistance prevalence based on broth microdilution (BMD) findings, the gold standard method. To explore the influence of study-level factors-including alternative susceptibility testing methods-a multivariate meta-regression analysis was performed. The results of the meta-regression are reported as regression coefficients (β), representing the difference in colistin resistance, expressed in percentage points. All statistical analyses were conducted using R software.

Results: This analysis included 55 studies. Based on BMD susceptibility testing, colistin resistance was observed in 9% of all recovered Gram-negative isolates (95% CI: 6-14%) and was significantly higher among carbapenem-resistant isolates (31%, 95% CI: 25-38%), with p < 0.001. Multivariate meta-regression analysis further confirmed that colistin resistance was significantly higher in carbapenem-resistant isolates compared to the total recovered isolates (β = 9.8% points, p = 0.001). Additionally, colistin resistance has significantly increased over time, with a β = 1.8% points per year (p = 0.001). The use of the VITEK 2 system was associated with lower detected colistin resistance compared to BMD (β = -7.0, p = 0.02). Geographically, resistance rates were higher in Upper Egypt (β = 9.3, p = 0.04). Regarding mcr plasmid-mediated resistance, mcr-1 was the most prevalent resistance gene, particularly in E. coli. In contrast, mcr-2 was rare, detected sporadically in K. pneumoniae and P. aeruginosa.

Conclusion: In Egypt, BMD testing identified colistin resistance in 9% of Gram-negative bacteria, increasing to 31% in carbapenem-resistant isolates. This higher resistance in carbapenem-resistant strains suggests stronger selective pressure from frequent colistin use. Additionally, colistin resistance has shown a rising trend over time, likely driven by increased usage and the spread of plasmid-mediated resistance. These findings underscore the urgent need for strict antimicrobial stewardship and alternative therapies to curb resistance evolution.

Background: WHO strategy to end Tuberculosis (TB) calls for drug susceptibility testing of Mycobacterium tuberculosis (MTB) for all patients, in high TB burden settings. Thus, this study aimed to investigate the MTB drug resistance profiles and related risk factors among patients presenting to the Antituberculosis Center of Brazzaville, Republic of Congo.

Methods: A cross-sectional study was carried out from July 2022 to August 2023 involving 1,121 presumptive pulmonary tuberculosis patients enrolled to the Antituberculosis Center of Brazzaville. Sputum samples were collected from all the study participants for the diagnosis of tuberculosis and rifampicin resistance, using the Xpert MTB/RIF (Cepheid, USA) assay. Samples positive for MTB with drug resistance to RIF were further tested for the second line anti-MTB drug susceptibility using the 10-color Xpert MTB/XDR assay.

Result: Out of 1,121 presumptive TB patients tested, 302/1,121 (26.9%) were MTB positive. Among these, 18/302 (6.0%) had received previous TB treatment and 15/302 (5.0%) were HIV co-infected. The mean age of the study population was 34 years, with a higher prevalence in males (69.2%). Of the MTB isolates, 25/302 (8.3%) were Rifampicin-resistant, with 24/25 (96%) further confirmed as multi-resistant strains, including 6/24 (25%) pre-XDR. Risk factors for MDR-TB included a history of TB treatment (AOR = 8.96, p = 0.002) and chronic cough (AOR = 7.14, p = 0.003).

Conclusions: This study reveals a high level of drug-resistant tuberculosis in Brazzaville, with previous TB treatment being a significant risk factor. The findings underscore the need to strengthen molecular surveillance and TB management and control measures in the Republic of Congo.