Annals of Clinical Microbiology and Antimicrobials最新文献

Background: Hypervirulent K. pneumoniae (hvKp) strains are characterized by their enhanced ability to evade immune responses and disseminate systemically. Rapid identification of hvKp strains is critical for guiding clinical management and implementing effective infection control measures. Loop-Mediated Isothermal Amplification (LAMP) assays provide a rapid and cost-effective method for detecting bacterial pathogens. This study evaluates the performance of the Eazyplex^® hvKp assay for the direct detection of hvKp strains from spiked blood cultures.

Methods: We collected 20 K. pneumoniae (Kp) isolates between December 2021 and August 2024 from two hospitals in Northern Spain. Capsular serotyping and virulence gene detection were performed using PCR and whole-genome sequencing (WGS). The Eazyplex^® hvKp LAMP assay was tested on spiked blood cultures inoculated with hvKp isolates. Virulence profiles were assessed using the Kleborate scoring system.

Results: Seventeen Kp isolates had a Kleborate score of ≥ 2, suggesting high virulence. The LAMP assay detected 87 out of 95 virulence targets, demonstrating an overall accuracy of 91.5%. Although eight target genes were not directly detected, fluorescence signals indicated amplification in all cases. The assay identified 16 strains with high virulence profiles (score ≥ 3), with 14 strains scoring 4 or 5. The LAMP-based test effectively detected hvKp directly from blood cultures, with time-to-results ranging from 6:43 to 17:11 min.

Conclussion: The Eazyplex^R hvKp LAMP assay is a rapid and effective method for identifying hvKp strains directly from blood cultures. This study supports its potential utility in clinical microbiology for early detection and epidemiological surveillance of hvKp infections. However, limitations in the Kleborate scoring system indicate that additional virulence biomarkers may be needed to improve the accuracy of hvKp classification.

The mcr-9 allele is typically located on IncHI2 type plasmids, but there are only few reports describing the co-occurrence of the bla_NDM gene on the same plasmid. Our aims were to describe the spread of an IncHI2A plasmid harboring both the mcr-9 and the bla_NDM-1 genes in a multicenter study in Israel. All New-Delhi Metallo-β-lactamase-producing Enterobacterales (NDME) isolated from three medical centres in Israel between January 2018 and July 2019 were included. The mcr-9.1 gene was identified in 37/212 (17.4%) of the isolates, mostly in Enterobacter cloacae (34/37, 92%). The mcr-9.1 gene was also identified in Klebsiella pneumoniae sequence types (ST)-76 (n = 2) and Escherichia coli ST-69 (n = 1). In one hospital, out of 32 E. cloacae isolates, 19 (51.35%) were clustered into five transmission clusters of the ST-511, ST-1261 and ST-1750. Four subtypes of a ~ 290 kb IncHI2A type plasmid were identified in all isolates that co-harbored the mcr-9.1 and the bla_NDM-1 genes. This plasmid was identified in all isolates, with four sub-communities (sc), with sc-4 identified in all three species. The resistance genes were surrounded by the IS26 (mcr-9.1) or by the ISAba125 and the IS300 (bla_NDM-1) mobile elements. The dissemination of the mcr-9.1 and the bla_NDM-1 genes was accelerated via clonal spread and the dual carriage on a single plasmid.

Background: The emergence of MDR K. pneumoniae poses a critical challenge in treating respiratory-associated pneumonia. Bacteriophages are promising antibiotic alternatives with unique features. This study aimed to isolate new bacteriophages from the hospital environment and investigate their therapeutic potential and mechanisms.

Methods: We employed plaque assays, transmission electron microscopy, and whole-genome sequencing to systematically characterize the biological properties, morphology, and genomic profiles of the phages in parallel. The bacteriostatic curve, biofilm staining quantification, and biofilm inhibition rate assay were employed to evaluate the in vitro lytic efficacy of the phage. More importantly, we established the murine pneumonia infection models through nasal instillation, assessed the therapeutic potential of the phage in vivo by observing pathological morphology via HE staining, detecting pro-inflammatory cytokine levels via qPCR and ELISA, and monitoring bacterial load changes in lung tissue through PCR analysis.

Results: Phages vB_KpnP_XY3 and vB_KpnP_XY4, taxonomically classified as Siphoviridae, demonstrated broad temperature (4-60 °C), pH (4-11) tolerance, chloroform resistance, latent periods of 40/35 min, and burst sizes of 340/126 PFU/cell. Both genomes contained circular dsDNA genomes (47,466 bp/50,036 bp) without virulence or antibiotic resistance genes. The bacterial concentration markedly decreased at 2 h post-treatment, reaching its biological nadir by 6 h. Concurrent biofilm assays demonstrated 80% biofilm inhibition and rapid bacterial clearance. In murine pneumonia models, both phage monotherapy and phage-antibiotic combinations significantly reduced bacterial loads compared with antibiotics alone (P < 0.05), concurrently attenuating inflammation (IL-1β/IL-6/TNF-a. P < 0.0001) and restoring alveolar architecture with reduced necrosis.

Conclusion: The phages vB_KpnP_XY3 and vB_KpnP_XY4 demonstrated robust environmental adaptability. Its antibacterial effect is related to its specific biofilm dissolution performance in vivo and in vitro. These findings provide strong evidence for the precise phage treatment of MDR K. pneumoniae infections.

Background: Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.

Methods: We performed whole-genome sequencing and phenotypic antimicrobial susceptibility testing on 109 Mab isolates collected at zhongshan hospital from 2018 to 2023.

Results: The results indicate that recombination, especially distributed conjugation transfer, promotes the formation and sustained diversity of Mab subspecies. Through pangenome analysis, the synergistic gain/loss of accessory genes was found to contribute to different metabolic profiles and the ability to adapt to oxidative stress, facilitating strain adaptation to host environments. We conducted phenotypic antimicrobial susceptibility testing, revealing resistance to macrolide antibiotics differed among subspecies. We identified 24 genes whose gain or loss may increase the likelihood of macrolide resistance, including those involved in biofilm formation, the stress response, virulence, biotin synthesis, and fatty acid metabolism. Genomic variations within Mab species may have significant implications for disease epidemiology, infection pathogenesis, and host interactions.

Conclusions: Our findings provide a valuable genetic basis for the success of Mab as a highly adaptive and drug-resistant pathogen, informing current efforts to control and treat Mab infections, including strategies targeting specific sequence types or lineages.

Background: Sepsis remains a major public health challenge, leading to high mortality and morbidity rates, particularly among low-income populations such as those in sub-Saharan Africa. Its management is complicated by the emergence of multidrug-resistant bacterial strains, necessitating microbiological surveillance and adaptation of antibiotic therapy. This study examines the microbiological profile of sepsis and the antibiotic susceptibility of pathogens among critically ill patients in Lubumbashi, Democratic Republic of Congo.

Methods: A prospective study was conducted from January 2021 to December 2023 across three ICU units in Lubumbashi. Patients suspected of having sepsis were included, and microbiological samples were collected from various sources (blood, urine, pus, biological fluids). Bacterial identification and antibiotic susceptibility testing were performed according to Clinical and Laboratory Standards Institute (CLSI) guidelines. Data were analyzed using SPSS version 23^® and Excel 365^®.

Results: Among the 76 patients included, 40% had confirmed bacterial sepsis. The predominant isolates were Gram-negative bacilli (62.7%), with Escherichia coli (28.35%) and Klebsiella pneumoniae (22.73%) being the most common species. Gram-positive bacteria accounted for 33.89%, primarily coagulase-negative streptococci (15.11%) and Enterococcus faecium (5.61%). Antimicrobial resistance profiles revealed a high level of resistance to commonly used antibiotics, particularly cephalosporins, fluoroquinolones, and cotrimoxazole. However, greater sensitivity was observed with amikacin (41.3%), fosfomycin (37%), and meropenem (33.8%).

Conclusion: This study highlights the high prevalence of Gram-negative bacteria and concerning resistance to first-line antibiotics, jeopardizing the effectiveness of empirical treatments. These findings underscore the urgency of strengthening microbiological surveillance, rationalizing antibiotic use, and implementing antimicrobial resistance control policies in the DRC. Developing treatment protocols tailored to local data and enforcing stricter antibiotic regulations are essential to improving sepsis management and reducing associated mortality.

Background: Neisseria meningitidis (Nm), traditionally recognized as a nasopharyngeal commensal causing invasive meningococcal disease (IMD), has recently emerged as an etiological agent of urethritis worldwide, with sporadic urogenital cases in China raising epidemiological concerns.

Methods: Three urogenital Nm isolates were characterized to investigate their evolutionary features and transmission patterns. Through comprehensive laboratory characterization encompassing culture identification (Gram staining, oxidase testing, MALDI-TOF MS), antimicrobial susceptibility profiling, whole-genome sequencing, and functional colonization assays on urethral epithelial cells under nitrite-supplemented microaerobic conditions, three multidrug-resistant Nm isolates were identified.

Results: All isolates demonstrated resistance to penicillin and sulfamethoxazole/trimethoprim, with isolate 24-SHSP-NM2 exhibiting additional ciprofloxacin resistance. The resistance was attributed to penA variants, mtrR promoter mutations, and gyrA substitutions. Phylogenetically, one isolate clustered with Japanese ST-11,026 strains and 2 clustered with Australian ST-1466 strains. Genomic characterization identified complete denitrification operons (aniA-norB) in all three isolates, which enable nitrite-enhanced epithelial colonization. ST-1466 isolates showed meningococcal B (MenB) vaccine component FHbp antigenic homology through FHbp variant 1.1.

Conclusions: These findings collectively demonstrate the convergent evolution of urogenital tropism, antimicrobial resistance (AMR) emergence, and metabolic adaptation to genitourinary microenvironments, underscoring the threat of genitourinary Nm infections. The study highlights the critical need to enhance molecular surveillance, implement rapid AMR screening, and prioritize MenB vaccination strategies in high-risk populations.

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.