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226700.9923MOLECULAR CHARACTERIZATION AND DETECTION OF MULTIDRUGRESISTANT GENE IN BACTERIAL ISOLATES CAUSING LOWER RESPIRATORY TRACT INFECTIONS (LRTI) AMONG HIV/AIDS PATIENTS ON HIGHLY ACTIVE ANTIRETROVIRAL THERAPY (HAART) IN UYO, SOUTH-SOUTH NIGERIA. BACKGROUND: Antibiotic-resistant genes (ARGs) pose a significant challenge in modern medicine, rendering infections increasingly difficult to treat as bacteria acquire mechanisms to resist antibiotics. Addressing ARGs necessitates a multifaceted approach, encompassing surveillance efforts to monitor their presence and the development of strategies aimed at managing and curbing the spread of antibiotic resistance. Hence, this study characterized the genetic determinants of antibiotic resistance among isolates responsible for Lower Respiratory Tract Infections (LRTIs) in People Living with HIV/AIDS (PLWHA) in Uyo. METHODS: Sputum samples were collected from 61 LRTI suspects, with bacterial isolates identified using VITEK-2 technology. Polymerase chain reaction assays were employed to detect resistance genes within the isolates. RESULTS: Results revealed a bacterial etiology in 39.3% of the samples, with a majority (79.2%) originating from St. Luke Hospital, Anua (SLHA), and the remainder (20.8%) from the University of Uyo Teaching Hospital (UUTH). Staphylococcus aureus emerged as the predominant isolate (46.6%), while resistance was notably high against Gentamicin and Sulphamethazole/Trimethoprim. Conversely, Azithromycin, imipenem, clindamycin, erythromycin, and ceftriaxone displayed relatively lower resistance levels across all isolates. Notably, four resistance genes CTX-M, Aac, KPC, and MecA were identified, with CTX-M detected in all multidrug-resistant isolates. This underscores the predominantly community-acquired nature of resistance as conferred by CTX-M. CONCLUSION: In conclusion, this study underscores the critical importance of continued vigilance and proactive measures in combating antibiotic resistance, particularly within vulnerable populations such as PLWHA. By elucidating the genetic mechanisms underlying antibiotic resistance, informed targeted interventions can be mitigated to curb threats posed by multidrug-resistant bacteria in clinical settings.202440385712
226810.9920Profile of Bacteria with ARGs Among Real-World Samples from ICU Admission Patients with Pulmonary Infection Revealed by Metagenomic NGS. BACKGROUND: Treatment of pulmonary infections in the intensive care unit (ICU) represents a great challenge, especially infections caused by antibiotic resistance pathogens. A thorough and up-to-date knowledge of the local spectrum of antibiotic resistant bacteria can improve the antibiotic treatment efficiency. In this study, we aimed to reveal the profile of bacteria with antibiotic resistance genes (ARGs) in real-world samples from ICU admission patients with pulmonary infection in Mainland, China, by metagenomic next-generation sequencing (mNGS). METHODS: A total of 504 different types of clinical samples from 452 ICU admission patients with pulmonary infection were detected by mNGS analysis. RESULTS: A total of 485 samples from 434 patients got successful mNGS results. Among 434 patients, one or more bacteria with ARGs were detected in 192 patients (44.24%, 192/434), and ≥2 bacteria with ARGs were detected in 85 (19.59%, 85/434) patients. The predominant detected bacteria were Corynebacterium striatum (C. striatum) (11.76%, 51/434), Acinetobacter baumannii (A. baumannii) (11.52%, 50/434) and Enterococcus faecium (E. faecium) (8.99%, 39/434). ermX conferred resistance to MSL(B) and cmx to phenicol were the only two ARGs detected in C. striatum; in A. baumannii, most of ARGs were resistance-nodulation-division (RND)-type efflux pumps genes, which conferred resistance to multi-drug; ermB conferred resistance to MSL(B) and efmA to multi-drug were the predominant ARGs in E. faecium. Bacteria with ARGs were detected in 50% (140/280) bronchoalveolar lavage fluid (BALF) and 50.5% (48/95) sputum samples, which were significantly higher than in blood and cerebrospinal fluid (CSF) samples. CONCLUSION: High level of bacteria with ARGs was observed in clinical samples, especially BALF and sputum samples from ICU admission patients with pulmonary infection in Mainland, China. And C. striatum resistant to MSL(B) and/or phenicol, multi-drug resistance A. baumannii and E. faecium were the lead bacteria.202134866919
581920.9919Application of mNGS in the Etiological Analysis of Lower Respiratory Tract Infections and the Prediction of Drug Resistance. Lower respiratory tract infections (LRTIs) have high morbidity and mortality rates. However, traditional etiological detection methods have not been able to meet the needs for the clinical diagnosis and prognosis of LRTIs. The rapid development of metagenomic next-generation sequencing (mNGS) provides new insights for the diagnosis and treatment of LRTIs; however, little is known about how to interpret the application of mNGS results in LRTIs. In this study, lower respiratory tract specimens from 46 patients with suspected LRTIs were tested simultaneously using conventional microbiological detection methods and mNGS. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], genomic coverage, and relative abundance of the organism in predicting the true-positive pathogenic bacteria. True-positive viruses were identified according to the lg(RPKM) threshold of bacteria. We also evaluated the ability to predict drug resistance genes using mNGS. Compared to that using conventional detection methods, the false-positive detection rate of pathogenic bacteria was significantly higher using mNGS. It was concluded from the ROC curves that the lg(RPKM) and genomic coverage contributed to the identification of pathogenic bacteria, with the performance of lg(RPKM) being the best (area under the curve [AUC] = 0.99). The corresponding lg(RPKM) threshold for identifying the pathogenic bacteria was -1.35. Thirty-five strains of true-positive virus were identified based on the lg(RPKM) threshold of bacteria, with the detection of human gammaherpesvirus 4 being the highest and prone to coinfection with Pseudomonas aeruginosa, Acinetobacter baumannii, and Stenotrophomonas maltophilia. Antimicrobial susceptibility tests (AST) revealed the resistance of bacteria containing drug resistance genes (detected by mNGS). However, the drug resistance genes of some multidrug-resistant bacteria were not detected. As an emerging technology, mNGS has shown many advantages for the unbiased etiological detection and the prediction of antibiotic resistance. However, a correct understanding of mNGS results is a prerequisite for its clinical application, especially for LRTIs. IMPORTANCE LRTIs are caused by hundreds of pathogens, and they have become a great threat to human health due to the limitations of traditional etiological detection methods. As an unbiased approach to detect pathogens, mNGS overcomes such etiological diagnostic challenges. However, there is no unified standard on how to use mNGS indicators (the sequencing reads, genomic coverage, and relative abundance of each organism) to distinguish between pathogens and colonizing microorganisms or contaminant microorganisms. Here, we selected the mNGS indicator with the best identification performance and established a cutoff value for the identification of pathogens in LRTIs using ROC curves. In addition, we also evaluated the accuracy of antibiotic resistance prediction using mNGS.202235171007
224330.9919Clinical and metagenomic predicted antimicrobial resistance in pediatric critically ill patients with infectious diseases in a single center of Zhejiang. BACKGROUND: Antimicrobial resistance (AMR) poses a significant threat to pediatric health; therefore, precise identification of pathogens as well as AMR is imperative. This study aimed at comprehending antibiotic resistance patterns among critically ill children with infectious diseases admitted to pediatric intensive care unit (PICU) and to clarify the impact of drug-resistant bacteria on the prognosis of children. METHODS: This study retrospectively collected clinical data, identified pathogens and AMR from 113 children's who performed metagenomic next-generation sequencing for pathogen and antibiotic resistance genes identification, and compared the clinical characteristic difference and prognostic effects between children with and without AMR detected. RESULTS: Based on the presence or absence of AMR test results, the 113 patients were divided into Antimicrobial resistance test positive group (AMRT+, n = 44) and Antimicrobial resistance test negative group (AMRT-, n = 69). Immunocompromised patients (50% vs. 28.99%, P = 0.0242) and patients with underlying diseases (70.45% vs. 40.58%, P = 0.0019) were more likely to develop resistance to antibiotics. Children in the AMRT + group showed significantly increased C-reaction protein, score of pediatric sequential organ failure assessment and pediatric risk of mortality of children and longer hospital stay and ICU stay in the AMRT + group compared to the AMRT+- group (P < 0.05). Detection rate of Gram-negative bacteria was significantly higher in the AMRT + group rather than Gram-positive bacteria (n = 45 vs. 31), in contrast to the AMRT- group (n = 10 vs. 36). Cephalosporins, β-lactams/β-Lactamase inhibitors, carbapenems and sulfonamides emerged as the most common types of drug resistance in children. Resistance rates to these antibiotics exhibited considerable variation across common pathogens, including Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii. CONCLUSIONS: The development of drug resistance in bacteria will significantly affect the prognosis of patients. The significant differences in drug resistance of common pathogenic bacteria indicate that identification of drug resistance is important for the rational use of antibiotics and patient prognosis.202439707302
512240.9918Clinical long-read metagenomic sequencing of culture-negative infective endocarditis reveals genomic features and antimicrobial resistance. BACKGROUND: Infective endocarditis (IE) poses significant diagnostic challenges, particularly in blood culture-negative cases where fastidious bacteria evade detection. Metagenomic-based nanopore sequencing enables rapid pathogen detection and provides a new approach for the diagnosis of IE. METHOD: Two cases of blood culture-negative infective endocarditis (IE) were analyzed using nanopore sequencing with an in silico host-depletion approach. Complete genome reconstruction and antimicrobial resistance gene annotation were successfully performed. RESULTS: Within an hour of sequencing, EPI2ME classified nanopore reads, identifying Corynebacterium striatum in IE patient 1 and Granulicatella adiacens in IE patient 2. After 18 h, long-read sequencing successfully reconstructed a single circular genome of C. striatum in IE patient 1, whereas short-read sequencing was used to compare but produced fragmented assemblies. Based on these results, long-read sequencing was exclusively used for IE patient 2, allowing for the complete and accurate assembly of G. adiacens, confirming the presence of these bacteria in the clinical samples. In addition to pathogen identification, antimicrobial resistance (AMR) genes were detected in both genomes. Notably, in C. striatum, regions containing a class 1 integron and multiple novel mobile genetic elements (ISCost1, ISCost2, Tn7838 and Tn7839) were identified, collectively harbouring six AMR genes. This is the first report of such elements in C. striatum, highlighting the potential of nanopore long-read sequencing for comprehensive pathogen characterization in IE cases. CONCLUSIONS: This study highlights the effectiveness of host-depleted, long-read nanopore metagenomics for direct pathogen identification and accurate genome reconstruction, including antimicrobial resistance gene detection. The approach enables same-day diagnostic reporting within a matter of hours. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12879-025-11741-5.202541087996
224950.9918Tracking Multidrug Resistance in Gram-Negative Bacteria in Alexandria, Egypt (2020-2023): An Integrated Analysis of Patient Data and Diagnostic Tools. BACKGROUND: The rise in carbapenem-resistant Enterobacteriaceae (CRE) in Egypt, particularly in hospital settings, poses a significant public health challenge. This study aims to develop a combined epidemiological surveillance tool utilizing the Microreact online platform (version 269) and molecular microarray technology to track and analyze carbapenem-resistant Escherichia coli strains in Egypt. The objective is to integrate molecular diagnostics and real-time data visualization to better understand the spread and evolution of multidrug-resistant (MDR) bacteria. METHODS: The study analyzed 43 E. coli isolates collected from Egyptian hospitals between 2020 and 2023. Nanopore sequencing and microarray analysis were used to identify carbapenemase genes and other resistance markers, whereas the VITEK2 system was employed for phenotypic antibiotic susceptibility testing. Microreact was used to visualize epidemiological data, mapping the geographic and temporal distribution of resistant strains. RESULTS: We found that 72.09% of the isolates, predominantly from pediatric patients, carried the blaNDM-5 gene, while other carbapenemase genes, including blaOXA-48 and blaVIM, were also detected. The microarray method demonstrated 92.9% diagnostic sensitivity and 87.7% diagnostic specificity compared to whole-genome sequencing. Phenotypic resistance correlated strongly with next-generation sequencing (NGS) genotypic data, achieving 95.6% sensitivity and 95.2% specificity. CONCLUSIONS: This method establishes the utility of combining microarray technology, NGS and real-time data visualization for the surveillance of carbapenem-resistant Enterobacteriaceae, especially E. coli. The high concordance between genotypic and phenotypic data underscores the potential of DNA microarrays as a cost-effective alternative to whole-genome sequencing, especially in resource-limited settings. This integrated approach can enhance public health responses to MDR bacteria in Egypt.202439766575
210160.9917Antibiotic resistance genes circulating in Nigeria: a systematic review and meta-analysis from the One Health perspective. BACKGROUND: The misuse of antibiotics in developing countries has created serious threats to public healthcare systems and reduced treatment options. Multidrug-resistant bacteria harbour antibiotic resistance genes that help them subdue the effectiveness of several available antibiotics. This review aimed to assess antimicrobial resistance genes circulating in Nigeria via a systematic review and meta-analysis. METHODS: A comprehensive literature search was performed using five electronic databases: PubMed, Web of Science, Scopus, Google Search, and African Journals Online (AJOL). Articles related to antibiotic resistance genes in Nigeria, published between January 1, 2015 and October 31, 2024, were included. The Newcastle-Ottawa scale (NOS) was used to assess the risk of bias. The meta-analysis for random effects was performed to determine the proportions and pooled prevalence of the resistance genes from the various One Health domains, as well as heterogeneity in the data, using R software (Version 4.3.3) and the metaprop package. RESULTS: Of the 762 articles retrieved, 56 (humans [n = 33], animals [n = 8], environment [n = 12], human/animal [n = 1], and human/animal/environment [n = 2]) from the six geopolitical zones in Nigeria met the inclusion criteria. The extended-spectrum beta-lactamase (ESBL) gene with the highest pooled prevalence was blaSHV (24.0% [95% CI: 12.0–44.0]), followed by blaCTX-M (23.0% [95% CI: 14.0–37.0]), and the least was blaTEM (18.0% [95% CI: 8.0–37.0]). Among the carbapenemase genes, blaKPC (33.0% [95% CI: 7.0–76.0]) was the most prevalent, followed by blaNDM (21.0% [95% CI: 9.0–41.0]), blaOXA (11.0% [95% CI: 2.0–46.0]) and the least was blaVIM (9.0% [95% CI: 3.0–26.0]). The mecA gene also had a high pooled prevalence (51.0% [95% CI: 14.0–86.0]). The pooled prevalence of the erm, sul, tet, and qnr genes ranged from 19.0% (95% CI: 8.0–38.0) to 27.0% (95% CI: 13.0–47.0). Some antibiotic resistance genes were shared among the three domains. CONCLUSION: This systematic review and meta-analysis has demonstrated the co-existence of antibiotic resistance genes among bacteria causing infection in Nigeria, via the One Health approach. There is a need for future research on the circulation of antibiotic resistance genes in developing countries using internationally approved approaches to track down this menace. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12920-025-02163-y.202540619397
224870.9916Predictive Application Value of Metagenomic Next-Generation Sequencing in the Resistance of Carbapenem-Resistant Enterobacteriaceae. Objective: Although metagenomic next-generation sequencing (mNGS) technology has achieved notable outcomes in pathogen detection, there remains a gap in the research regarding its application in predicting the antibiotic resistance of pathogenic bacteria. This study aims to analyze the clinical application value of mNGS in predicting the resistance of carbapenem-resistant Enterobacteriaceae (CRE), as well as the relevant influencing factors, thereby providing valuable insights for clinical antimicrobial therapy. Methods: Nonduplicate isolates of Enterobacterales bacteria collected from Liaocheng People's Hospital from April 2023 to June 2024 were selected, and CRE bacteria were screened. mNGS was used to detect resistance genes, and the results were compared with those of polymerase chain reaction (PCR) to evaluate the specificity and sensitivity of gene detection. Furthermore, the performance of mNGS in identifying pathogenic microorganisms and predicting antibiotic resistance was assessed by comparing the sequencing results with those of antimicrobial susceptibility testing (AST). Results: A total of 46 isolates were confirmed as CRE through traditional AST and were further identified using the Vitek MS and Vitek 2 systems. The results indicated 27 isolates of Klebsiella pneumoniae, 14 isolates of Escherichia coli, 2 isolates of Enterobacter hormaechei, 2 isolates of Enterobacter cloacae, and 1 isolate of Citrobacter freundii. These isolates were subjected to both mNGS and PCR for detection. The calculation of the area under the receiver operating characteristic (ROC) curve demonstrated the reliability of mNGS in detecting resistance genes. Conclusion: mNGS demonstrated high sensitivity in predicting the presence of carbapenemase resistance genes in CRE, showing potential in early indication of isolate resistance information, thereby facilitating timely guidance for clinical treatment strategies.202539816186
519280.9915Genome Sequencing Analysis of a Rare Case of Blood Infection Caused by Flavonifractor plautii. BACKGROUND Flavonifractor plautii belongs to the clostridium family, which can lead to local infections as well as the bloodstream infections. Flavonifractor plautii caused infection is rarely few in the clinic. To understand better Flavonifractor plautii, we investigated the drug sensitivity and perform genome sequencing of Flavonifractor plautii isolated from blood samples in China and explored the drug resistance and pathogenic mechanism of the bacteria. CASE REPORT The Epsilometer test method was used to detect the sensitivity of flavonoid bacteria to antimicrobial agents. PacBio sequencing technology was employed to sequence the whole genome of Flavonifractor plautii, and gene prediction and functional annotation were also analyzed. Flavonifractor plautii displayed sensitivity to most drugs but resistance to fluoroquinolones and tetracycline, potentially mediated by tet (W/N/W). The total genome size of Flavonifractor plautii was 4,573,303 bp, and the GC content was 59.78%. Genome prediction identified 4,506 open reading frames, including 9 ribosomal RNAs and 66 transfer RNAs. It was detected that the main virulence factor-coding genes of the bacteria were the capsule, polar flagella and FbpABC, which may be associated with bacterial movement, adhesion, and biofilm formation. CONCLUSIONS The results of whole-genome sequencing could provide relevant information about the drug resistance mechanism and pathogenic mechanism of bacteria and offer a basis for clinical diagnosis and treatment.202438881048
247790.9915Evaluation of targeted next-generation sequencing for microbiological diagnosis of acute lower respiratory infection. PURPOSE: To evaluate the performance of targeted next-generation sequencing (tNGS) in pathogen detection in acute lower respiratory infection. METHODS: The retrospective study was conducted between July 2023 and May 2024 at the Yantai Yuhuangding Hospital. Patients with acute lower respiratory infections were included. Qualified sputum or bronchoalveolar lavage fluid samples were collected for tNGS and conventional microbiological tests(CMTs), including culture, staining, polymerase chain reaction (PCR), and reverse transcription-PCR (RT-PCR). The time required and cost were counted. RESULTS: A total of 968 patients were enrolled. Study analysis discovered 1,019 strains of bacteria, 259 strains of fungi, 302 strains of viruses, 76 strains of Mycoplasma pneumoniae, and two strains of Chlamydia psittaci using tNGS. In addition, tNGS also identified 39 mecA, four KPC, 19 NDM, and two OXA-48 genes. The positive rates for bacteria, fungi, viruses, mycoplasma, and chlamydia obtained using tNGS were significantly higher than those determined using traditional methods. Among them, tNGS showed high consistence with mycobacterium DNA test, influenza A (H1N1) virus nucleic acid test and COVID-19 nucleic acid test. Poor consistency between drug resistance genes and bacterial resistance phenotypes was found. In addition, tNGS also had advantages over traditional methods in terms of detection time and cost. CONCLUSION: Compared to traditional methods, tNGS had higher sensitivity in detecting bacteria, fungi, viruses, and other pathogens in acute lower respiratory infection, and also had the advantages of timeliness and cost-effectiveness, making it a promising method for guiding clinical diagnosis.202540901079
2115100.9915Assessment of carbapenemase genes and antibiotic resistance profiles in ceftazidime-avibactam resistant Klebsiella pneumoniae isolates: A single-center cross-sectional study. BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKp) is an urgent global health threat due to its rapid spread and limited treatment options. Ceftazidime-avibactam exhibits broad efficacy against gram-negative bacteria, including CRKp; however, emerging resistance to this agent is increasingly reported. Understanding the prevalence of ceftazidime-avibactam resistance and the underlying carbapenemase genes is critical for optimizing antimicrobial stewardship and guiding clinical management. This study aimed to determine the prevalence of ceftazidime avibactam resistance among CRKp isolates collected from various clinical specimens, and to analyze their associated carbapenemase genes and antibiotic resistance profiles. METHODS: This cross-sectional study analyzed 312 K pneumoniae isolates obtained from various clinical specimens of hospitalized patients at a tertiary care hospital in Turkey. Antibiotic susceptibility testing was performed using the disk diffusion method for ceftazidime-avibactam and broth microdilution for both colistin and ceftazidime-avibactam. Molecular detection of carbapenemase genes was carried out using polymerase chain reaction. RESULTS: Ceftazidime-avibactam resistance was identified in 21.5% (67/312) of CRKp isolates. Among these isolates, 37.3% harbored both OXA-48 and NDM genes, 13.4% carried NDM alone, 10.4% carried OXA-48 alone, and 38.8% lacked these genes. The majority of resistant isolates originated from urine (31.3%), followed by tracheal aspirate (29.9%), and blood (22.4%) specimens. The prevalence of colistin susceptibility among ceftazidime-avibactam-resistant CRKp isolates was 56.7%. CONCLUSIONS: The coexistence of NDM and OXA-48 genes is a major contributor to ceftazidime-avibactam resistance in CRKp isolates, particularly in urinary and respiratory tract infections. These findings underscore the need for ongoing surveillance and tailored antibiotic stewardship programs to control the spread of resistance in hospital settings.202541088587
2269110.9915Genomic detection of Panton-Valentine Leucocidins encoding genes, virulence factors and distribution of antiseptic resistance determinants among Methicillin-resistant S. aureus isolates from patients attending regional referral hospitals in Tanzania. BACKGROUND: Methicillin-resistant Staphylococcus aureus (MRSA) is a formidable public scourge causing worldwide mild to severe life-threatening infections. The ability of this strain to swiftly spread, evolve, and acquire resistance genes and virulence factors such as pvl genes has further rendered this strain difficult to treat. Of concern, is a recently recognized ability to resist antiseptic/disinfectant agents used as an essential part of treatment and infection control practices. This study aimed at detecting the presence of pvl genes and determining the distribution of antiseptic resistance genes in Methicillin-resistant Staphylococcus aureus isolates through whole genome sequencing technology. MATERIALS AND METHODS: A descriptive cross-sectional study was conducted across six regional referral hospitals-Dodoma, Songea, Kitete-Kigoma, Morogoro, and Tabora on the mainland, and Mnazi Mmoja from Zanzibar islands counterparts using the archived isolates of Staphylococcus aureus bacteria. The isolates were collected from Inpatients and Outpatients who attended these hospitals from January 2020 to Dec 2021. Bacterial analysis was carried out using classical microbiological techniques and whole genome sequencing (WGS) using the Illumina Nextseq 550 sequencer platform. Several bioinformatic tools were used, KmerFinder 3.2 was used for species identification, MLST 2.0 tool was used for Multilocus Sequence Typing and SCCmecFinder 1.2 was used for SCCmec typing. Virulence genes were detected using virulenceFinder 2.0, while resistance genes were detected by ResFinder 4.1, and phylogenetic relatedness was determined by CSI Phylogeny 1.4 tools. RESULTS: Out of the 80 MRSA isolates analyzed, 11 (14%) were found to harbor LukS-PV and LukF-PV, pvl-encoding genes in their genome; therefore pvl-positive MRSA. The majority (82%) of the MRSA isolates bearing pvl genes were also found to exhibit the antiseptic/disinfectant genes in their genome. Moreover, all (80) sequenced MRSA isolates were found to harbor SCCmec type IV subtype 2B&5. The isolates exhibited 4 different sequence types, ST8, ST88, ST789 and ST121. Notably, the predominant sequence type among the isolates was ST8 72 (90%). CONCLUSION: The notably high rate of antiseptic resistance particularly in the Methicillin-resistant S. aureus strains poses a significant challenge to infection control measures. The fact that some of these virulent strains harbor the LukS-PV and LukF-PV, the pvl encoding genes, highlight the importance of developing effective interventions to combat the spreading of these pathogenic bacterial strains. Certainly, strengthening antimicrobial resistance surveillance and stewardship will ultimately reduce the selection pressure, improve the patient's treatment outcome and public health in Tanzania.202539833938
2538120.9915Passenger pathogens on physicians. BACKGROUND: Hospital acquired infections pose a significant risk for patients undergoing hematopoietic stem cell transplantation. Horizontal transfer of antimicrobial resistance genes contributes to prevalence of multidrug-resistant infections in this patient population. METHODS: At an academic bone marrow transplantation center, we performed whole genome DNA sequencing (WGS) on commonly used physician items, including badges, stethoscopes, soles of shoes, and smart phones from 6 physicians. Data were analyzed to determine antimicrobial resistance and virulence factor genes. RESULTS: A total of 1,126 unique bacterial species, 495 distinct bacteriophages, 91 unique DNA viruses, and 175 fungal species were observed. Every item contained bacteria with antibiotic and/or antiseptic resistance genes. Stethoscopes contained greatest frequency of antibiotic resistance and more plasmid-carriage of antibiotic resistance. DISCUSSION AND CONCLUSIONS: These data indicate that physician examination tools and personal items possess potentially pathogenic microbes. Infection prevention policies must consider availability of resources to clean physical examination tools as well as provider awareness when enacting hospital policies. Additionally, the prevalence of antimicrobial resistance genes (eg, encoding resistance to aminoglycosides, β-lactams, and quinolones) reinforces need for antimicrobial stewardship, including for immunocompromised patients. Further research is needed to assess whether minute quantities of microbes on physician objects detectable by WGS represents clinically significant inoculums for immunocompromised patients.202336306861
2196130.9914Antibiotic resistance profiles in Gram-negative bacteria causing bloodstream and urinary tract infections in paediatric and adult patients in Ndola District, Zambia, 2020-2021. BACKGROUND: Bloodstream infections (BSIs) and urinary tract infections (UTIs) caused by antibiotic resistant bacteria (ARB) have unfavourable treatment outcomes and negative economic impacts. OBJECTIVES: The main objective of this study was to determine antibiotic resistance profiles in Gram-negative bacteria (GNB) causing BSIs and UTIs. METHOD: A prospective study from October 2020 to January 2021 at Ndola Teaching Hospital and Arthur Davison Children's Hospital in the Ndola district, Zambia. Blood and urine samples collected from inpatients and outpatients presenting with fever and/or urinary tract infection symptoms were submitted for microbiological analysis. Pathogen identification and antibiotic susceptibility was determined by the automated VITEK 2 Compact machine. Resistance genes to commonly used antibiotics were determined using polymerase chain reaction. Data were analysed using SPSS version 28.0. RESULTS: One hundred and ten GNB were isolated, E. coli (45.5%) was predominant, with varying resistance profiles to different antibiotic classes. Resistance to third-generation cephalosporin was highest in Enterobacter cloacae (75%) and Klebsiella pneumoniae (71%), respectively. Emergence of carbapenem resistance was noted with the highest being 17% in Acinetobacter baumannii. Notably, the prevalence of multi-drug resistance was 63% and extensively drug-resistance was 32%. Resistance gene determinants identified included bla (CTX-M,) qnrA and bla (NDM). CONCLUSION: High level antibiotic resistance was observed in GNB known to be prevalent causative agents of BSIs and UTIs locally in Zambia. Improving microbiology diagnostic capacity, strengthening antimicrobial stewardship programs and enforcing infection prevention and control measures are of utmost importance in promoting rational use of antibiotics and preventing the spread and emergence of resistant pathogens.202540585877
2207140.9914Precision medicine in practice: unravelling the prevalence and antibiograms of urine cultures for informed decision making in federal tertiary care- a guide to empirical antibiotics therapy. BACKGROUND AND OBJECTIVES: Urinary tract infections (UTIs), one of the most prevalent bacterial infections, are facing limited treatment options due to escalating concern of antibiotic resistance. Urine cultures significantly help in identification of etiological agents responsible for these infections. Assessment of antibiotic susceptibility patterns of these bacteria aids in tackling the emerging concern of antibiotic resistance and establishment of empirical therapy guidelines. Our aim was to determine various agents responsible for urinary tract infections and to assess their antibiotic susceptibility patterns. MATERIALS AND METHODS: This cross-sectional study was performed over a period of six months from January 2023 to July 2023 in Department of Microbiology of Pakistan Institute of Medical Sciences (PIMS). RESULTS: Out of 2957 positive samples, Gram negative bacteria were the most prevalent in 1939 (65.6%) samples followed by Gram positive bacteria in 418 (14.1%) and Candida spp. in 269 (9.1%) samples. In gram negative bacteria, Escherichia coli (E. coli) was the most prevalent bacteria isolated from 1070 samples (55.2%) followed by Klebsiella pneumoniae in 397 samples (20.5%). In Gram positive bacteria, Enterococcus spp. was the most common bacteria in 213 samples (51%) followed by Staphylococcus aureus in 120 samples (28.7%). Amikacin was the most sensitive drug (91%) for Gram negative bacteria. Gram positive bacteria were most susceptible to linezolid (97%-100%). CONCLUSION: The generation of a hospital tailored antibiogram is essential for the effective management of infections and countering antibiotic resistance. By adopting antimicrobial stewardship strategies by deeper understanding of sensitivity patterns, we can effectively combat antibiotic resistance.202439267930
2103150.9914Antibiotic resistance in hospital wastewater in West Africa: a systematic review and meta-analysis. BACKGROUND: The occurrence of antibiotic-resistant bacteria (ARB) has become a global menace and therefore increases morbidity, mortality and healthcare costs. Globally, hospital wastewater (HWW) has been identified as a significant source of antibiotic-resistant elements. OBJECTIVES: This review aims to systematically review and to perform meta-analyses from evidence on antibiotic resistance studies in HWW in West Africa. METHODS: The review was conducted in compliance with PRISMA and included studies published between 1990 and 2024 in West Africa from the Scopus, PubMed, and Web of Science databases. Eligible studies that characterized resistant bacteria, genes, or antibiotic residues in HWW were included. Meta-analyses for resistant bacteria and genes as well risk of bias using the Newcastle-Ottawa scale were conducted. RESULTS: Out of 23 studies reviewed, resistant bacteria were reported in 39% (E. coli), 26% (K. pneumoniae), and 17% (P. aeruginosa), while 17 studies reported ARGs, with blaTEM (29%), blaOXA- 48 (18%), blaSHV (18%), and mecA (18%) being the most common. Only 4% and 9% of studies focused on toxin genes and antibiotic residues, respectively. Meta-analysis showed pooled prevalence rates for resistant bacteria: E. coli 42.6% (95% CI: 26.7%-60.3%) and K. pneumoniae 32.1% (95% Cl: 28.8%- 36.5%), and ARGs: blaTEM 76.0% (95% CI = 64.6%-84.6%) and blaSHV 59.3% (95% CI = 19.5%-89.8%). CONCLUSION: This systematic review highlights significant findings of high levels of ARGs and ARBs of public health concern in HWW in West Africa. This highlights the need to improve upon the monitoring of antibiotic resistance and treatment of HWW in West Africa.202540217451
2265160.9914Genotypic Patterns of Multidrug-Resistant Acinetobacter baumannii: A Systematic Review. Acinetobacter baumannii (A. baumannii) is one of the most common bacteria in nosocomial infections. Inappropriate usage of antibiotics has led to expanding emergence resistance to A. baumannii as a multidrug-resistant (MDR) strain. Empirical antibiotic therapy is necessary to evaluate the resistant gene pattern of MDR A. baumannii. For this purpose, the present study evaluated the resistance genes pattern of MDR A. baumannii collected from hospitalized patients using a genotypic diagnostic technique. To find evidence related to the study objectives, databases were searched such as Google Scholar, Web of Science, Science Direct, PubMed, and Scopus from 2000 to 2022, with specified keywords in the title and text of the articles. Articles were included based on inclusion and exclusion criteria. The mentioned database displayed 284 articles. After screening, 65 eligible articles were included. The results showed that various b-lactamases genes, aminoglycoside-modifying enzymes (AMEs) genes, and pump-expressing genes are resistance gene patterns in MDR A. baumannii isolates. MDR A. baumannii has significantly become resistant to b-lactams, carbapenems, and aminoglycosides.202337200758
1462170.9914Phenotypic synergy testing of ceftazidime-avibactam with aztreonam in a university hospital having high number of metallobetalactamase producing bacteria. BACKGROUND: Ceftazidime-avibactam combination with aztreonam and role of rapid synergy reporting has not been widely evaluated. Also the synergy correlation with various betalactamases has not been widely studied. METHODS: We studied phenotypic synergy testings and molecular detection of betalactamases in our university hospital where we have large number of mellatobetalactmase producing bacteria. We tested two phenotypic synergy methods for ceftazidime-avibactam with aztreonam (Disc-E strip method, E strip-Agar method) for rapid reporting to clinicians (153 isolates). The treatment (colistin, ceftazidime-avibactam, ceftazidime-avibactam with aztreonam) was guided as indicated in the synergy testings. The resistance genes in bacteria were identified by polymerase chain reaction (PCR) and correlated with synergy results. RESULTS: The highest synergy was seen in Klebsiella pneumoniae by Disc-E strip and E strip-Agar method (86% and 84% respectively). About 70% of Pseudomonas aeruginosa and 29% of Escherichia coli showed synergy. Molecular methods revealed multiple resistance gene combinations and bla(NDM) (96%) was predominant gene in isolates showing synergy. Among isolates that were sensitive to ceftazidime-avibactam, the predominant genes were bla(OXA-48) and bla(IMP.) Rapid laboratory reporting led to proper utilization of antibiotic combinations. CONCLUSIONS: Ceftazidime-avibactam and aztreonam rapid synergy testing will be highly beneficial in treatment of infections by metallobetalactamase producing resistant bacteria, especially K. pneumoniae and P. aeruginosa.202032628575
2210180.9913Beyond Culture: Real-Time PCR Performance in Detecting Causative Pathogens and Key Antibiotic Resistance Genes in Hospital-Acquired Pneumonia. Introduction: The rise in hospital-acquired pneumonia (HAP) due to antibiotic-resistant bacteria is increasing morbidity, mortality, and inappropriate empirical antibiotic use. This prospective research aimed to evaluate the performance of a real-time polymerase chain reaction (PCR) assay for detecting causative microorganisms and antibiotic-resistance genes from respiratory specimens compared to traditional methods. Additionally, we aimed to determine the molecular epidemiology of antibiotic resistance genes among HAP patients at The University of Jordan hospital. Methods: Lower respiratory tract samples were collected from HAP patients, including those with ventilator-associated pneumonia (VAP), between May 2024 and October 2024. Clinical data from the medical files were used to collect and analyze demographic and clinical information, including clinical outcomes. Real-time PCR was run to detect causative microbes and antibiotic resistance genes. Results: Among 83 HAP patients (median age 63, 61.45% male), 48.15% died. Culture identified Klebsiella (25.53%), Acinetobacter (22.34%), and Candida (24.47%) as the most common pathogens, while qPCR showed higher detection rates, including for A. baumannii (62.20%, p = 0.02) and K. pneumoniae (45.12%, p < 0.001). Carbapenem resistance was high; A. baumannii showed 100% resistance to most antibiotics except colistin (92.31%). The resistance genes ndm (60%) and oxa-48 (58.46%) were frequently detected and significantly associated with phenotypic resistance (p < 0.001). The qPCR identified resistance genes in all carbapenem-resistant cases. No gene significantly predicted mortality. Conclusions: Real-time PCR diagnostic technique combined with epidemiology of antibiotic resistance genes data may be a rapid and effective tool to improve HAP management. Large, multicenter studies are needed in the future to validate the performance of real-time PCR in HAP diagnosis, and appropriate management is also required.202541009915
2193190.9913Distributions and Types of Multidrug-Resistant Acinetobacter baumannii in Different Departments of a General Hospital. BACKGROUND: Acinetobacter baumannii is the most prevalent strain in hospitals and different clinical departments. OBJECTIVES: The current study aimed to investigate the genetic characteristics and resistance mechanisms of A. baumannii isolated from clinical samples in Shaoxing people's hospital affiliated to Zhejiang University, Shaoxing, China. PATIENTS AND METHODS: Acinetobacter baumannii strains were isolated from blood, phlegm and skin of the patients hospitalized in different departments as respiratory medicine, plastic surgery and intensive care unit (ICU). Multilocus sequence typing (MLST) was used to characterize the isolates. Kirby-Bauer test was used to evaluate antibiotic resistance of the bacteria. The expression of resistance inducing genes was detected by reverse transcription polymerase chain reaction (RT-PCR). The results were analyzed and compared. RESULTS: Two bacterial types, ST208, and ST218, were identified in all 140 samples. The ST208 mainly came from ICU and department of respiratory medicine, while ST218 from department of plastic surgery; 70.21% of ST208 and 84.78% of ST218 were carbapenem-resistant Acinetobacter baumannii (CRAB) and carbapenem-susceptible Acinetobacter baumannii (CSAB), respectively. Multidrug-resistance genes in CRAB isolated from the hospital mainly included, oxa-23, oxa-5, intl 1 and qaceΔ1-sul 1. Besides, the highest and lowest antibiotic resistance was observed in the strains isolated from blood samples and wounds, respectively. CONCLUSIONS: The distribution of AB varies in different clinical departments and samples. In the hospital under study, the main types of AB were ST208 and ST218. The genes which affect the ability of antibiotic-resistance were oxa-23, oxa-51, intl 1 and qaceΔ1-sul 1.201526487921