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Zou Z, Tang F, Qiao L, Wang S, Zhang H. Integrating sequencing methods with machine learning for antimicrobial susceptibility testing in pediatric infections: current advances and future insights. Front Microbiol 2025; 16:1528696. [PMID: 40109965 PMCID: PMC11919855 DOI: 10.3389/fmicb.2025.1528696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2024] [Accepted: 02/21/2025] [Indexed: 03/22/2025] Open
Abstract
Antimicrobial resistance (AMR) presents a critical challenge in clinical settings, particularly among pediatric patients with life-threatening conditions such as sepsis, meningitis, and neonatal infections. The increasing prevalence of multi- and pan-resistant pathogens is strongly associated with adverse clinical outcomes. Recent technological advances in sequencing methods, including metagenomic next-generation sequencing (mNGS), Oxford Nanopore Technologies (ONT), and targeted sequencing (TS), have significantly enhanced the detection of both pathogens and their associated resistance genes. However, discrepancies between resistance gene detection and antimicrobial susceptibility testing (AST) often hinder the direct clinical application of sequencing results. These inconsistencies may arise from factors such as genetic mutations or variants in resistance genes, differences in the phenotypic expression of resistance, and the influence of environmental conditions on resistance levels, which can lead to variations in the observed resistance patterns. Machine learning (ML) provides a promising solution by integrating large-scale resistance data with sequencing outcomes, enabling more accurate predictions of pathogen drug susceptibility. This review explores the application of sequencing technologies and ML in the context of pediatric infections, with a focus on their potential to track the evolution of resistance genes and predict antibiotic susceptibility. The goal of this review is to promote the incorporation of ML-based predictions into clinical practice, thereby improving the management of AMR in pediatric populations.
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Affiliation(s)
- Zhuan Zou
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Fajuan Tang
- Department of Emergency, West China Second University Hospital, Sichuan University, Chengdu, China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
| | - Lina Qiao
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Sisi Wang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
| | - Haiyang Zhang
- Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education, Chengdu, China
- Department of Pediatrics, West China Second University Hospital, Sichuan University, Chengdu, China
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Ghahramani A, Naghadian Moghaddam MM, Kianparsa J, Ahmadi MH. Overall status of carbapenem resistance among clinical isolates of Acinetobacter baumannii: a systematic review and meta-analysis. J Antimicrob Chemother 2024; 79:3264-3280. [PMID: 39392464 DOI: 10.1093/jac/dkae358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 09/19/2024] [Indexed: 10/12/2024] Open
Abstract
BACKGROUND Resistance to carbapenems, the first-line treatment for infections caused by Acinetobacter baumannii, is increasing throughout the world. The aim of the present study was to determine the global status of resistance to carbapenems in clinical isolates of this pathogen, worldwide. METHODS Electronic databases were searched using the appropriate keywords, including: 'Acinetobacter' 'baumannii', 'Acinetobacter baumannii' and 'A. baumannii', 'resistance', 'antibiotic resistance', 'antibiotic susceptibility', 'antimicrobial resistance', 'antimicrobial susceptibility', 'carbapenem', 'carbapenems', 'imipenem', 'meropenem' and 'doripenem'. Finally, following some exclusions, 177 studies from various countries were included in this study. The data were then subjected to a meta-analysis. RESULTS The average resistance rate of A. baumannii to imipenem, meropenem and doripenem was 44.7%, 59.4% and 72.7%, respectively. A high level of heterogeneity (I2 > 50%, P value < 0.05) was detected in the studies representing resistance to imipenem, meropenem and doripenem in A. baumannii isolates. Begg's and Egger's tests did not indicate publication bias (P value > 0.05). CONCLUSIONS The findings of the current study indicate that the overall resistance to carbapenems in clinical isolates of A. baumannii is relatively high and prevalent throughout the world. Moreover, time trend analysis showed that the resistance has increased from the year 2000 to 2023. This emphasizes the importance of conducting routine antimicrobial susceptibility testing before selecting a course of treatment, as well as monitoring and controlling antibiotic resistance patterns in A. baumannii strains, and seeking novel treatment options to lessen the emergence and spread of resistant strains and to reduce the treatment failure.
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Affiliation(s)
- Ali Ghahramani
- Student Research Committee, School of Medicine, Shahed University, Tehran, Iran
| | | | - Joben Kianparsa
- Student Research Committee, School of Medicine, Shahed University, Tehran, Iran
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Nasr J, Abdessamad H, Mina J, Haykal T, Jamil Y, Abboud E, Mahdi A, Asmar R, Abi Assaad R, Alameddine D, Bourji A, Mahdi M, Abdulaal R, Tomassian S, El Ahmadieh H, Azzam W, Mokhbat JE, Moghnieh R, Rodriguez-Morales AJ, Husni R. The epidemiology of gram-negative bacteremia in Lebanon: a study in four hospitals. Ann Clin Microbiol Antimicrob 2024; 23:90. [PMID: 39385237 PMCID: PMC11465513 DOI: 10.1186/s12941-024-00740-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 08/16/2024] [Indexed: 10/12/2024] Open
Abstract
INTRODUCTION Gram-negative bacteremia is a life-threatening infection with high morbidity and mortality. Its incidence is rising worldwide, and treatment has become more challenging due to emerging bacterial resistance. Little data is available on the burden and outcome of such infections in Lebanon. METHODS We conducted this retrospective study in four Lebanese hospitals. Data on medical conditions and demographics of 2400 patients diagnosed with a bloodstream infection based on a positive blood culture were collected between January 2014 and December 2020. RESULTS Most bacteremias were caused by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii, with the more resistant organisms being hospital-acquired. Third-generation cephalosporin and quinolone resistance was steady throughout the study, but carbapenem resistance increased. Mortality with such infections is high, but carbapenem resistance or infection with Pseudomonas or Acinetobacter species were significant risk factors for poor outcomes. CONCLUSION This is the first multi-center study from Lebanon on gram-negative bacteremia, resistance patterns, and factors associated with a poor outcome. More surveillance is needed to provide data to guide empirical treatment for bacteremia in Lebanon.
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Affiliation(s)
- Janane Nasr
- Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Hilal Abdessamad
- Division of Infectious Diseases, Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Johnathan Mina
- Division of Infectious Diseases, Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Tony Haykal
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Yasser Jamil
- Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Emma Abboud
- Laboratory Director, Mount Lebanon Hospital University Medical Center, Beirut, 1102, Lebanon
| | - Ahmad Mahdi
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Rana Asmar
- Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Rawad Abi Assaad
- Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Dana Alameddine
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Alaa Bourji
- Department of Surgery, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Mahmoud Mahdi
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Razan Abdulaal
- Department of Internal Medicine, University of Balamand, Balamand, Lebanon
| | - Serge Tomassian
- Department of Internal Medicine, University of Balamand, Balamand, Lebanon
| | - Hanane El Ahmadieh
- Infection Control Coordination, Mount Lebanon Hospital University Medical Center, Beirut, 1102, Lebanon
| | - Wael Azzam
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Jacques E Mokhbat
- Division of Infectious Diseases, Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Rima Moghnieh
- Division of Infectious Diseases, Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
| | - Alfonso J Rodriguez-Morales
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon
- Master of Clinical Epidemiology and Biostatistics, Universidad Cientifica del Sur, Lima, 15067, Peru
| | - Rola Husni
- Division of Infectious Diseases, Department of Internal Medicine, Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, 1102, Lebanon.
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Chávez Rodríguez M, Mascareñas De Los Santos AH, Vaquera Aparicio DN, Aguayo Samaniego R, García Pérez R, Siller-Rodríguez D, Rosales-González SP, Castillo-Morales PL, Castillo Bejarano JI. Molecular epidemiology of carbapenemase encoding genes in A. baumannii-calcoaceticus complex infections in children: a systematic review. JAC Antimicrob Resist 2024; 6:dlae098. [PMID: 39005591 PMCID: PMC11242458 DOI: 10.1093/jacamr/dlae098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2024] [Accepted: 05/29/2024] [Indexed: 07/16/2024] Open
Abstract
Background Acinetobacter baumannii-calcoaeticus complex is the leader pathogen for the World Health Organization's list due to the escalating prevalence of multidrug-resistant strains. Insights into the molecular characterization of carbapenemase genes in A. baumannii-calcoaceticus complex infections among children are scarce. To address this gap, we conducted a systematic review to describe the molecular epidemiology of the carbapenemase genes in A. baumannii-calcoaceticus complex infections in the pediatric population. Methods Adhering to the PRISMA 2020 guidelines for reporting systematic reviews, we conducted a review of in chore bibliographic databases published in English and Spanish, between January 2020 and December 2022. All studies conducted in patients ≤6 years with molecular characterization of carbapenemase-encoding genes in A. baumannii-calcoaceticus infections were included. Results In total, 1129 cases were reviewed, with an overall carbapenem-resistance rate of 60.3%. A. baumannii-calcoaceticus was isolated from blood cultures in 66.6% of cases. Regionally, the Eastern Mediterranean exhibited the highest prevalence of carbapenem resistance (88.3%). Regarding the carbapenemase genes, blaKPC displayed an overall prevalence of 1.2%, while class B blaNDM had a prevalence of 10.9%. Class D blaOXA-23-like reported a prevalence of 64%, blaOXA-48 and blaOXA-40 had a prevalence of 33% and 18.1%, respectively. Notably, the Americas region showed a prevalence of blaOXA-23-like at 91.6%. Conclusion Our work highlights the high prevalence of carbapenem-resistant A. baumannii-calcoaceticus and class D carbapenemase genes in children. Of note the distribution of different carbapenemase genes reveals considerable variations across WHO regions. To enhance epidemiological understanding, further extensive studies in children are imperative.
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Affiliation(s)
- Mariana Chávez Rodríguez
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Abiel Homero Mascareñas De Los Santos
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Denisse Natalie Vaquera Aparicio
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Rebeca Aguayo Samaniego
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Rodrigo García Pérez
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Daniel Siller-Rodríguez
- Hospital Epidemiology and Surveillance Unit, Christus Muguerza Hospital Alta Especialidad, Hidalgo Avenue, Obispado, ZC 64060 Monterrey, México
| | - Sara Paulina Rosales-González
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - Patricia Lizeth Castillo-Morales
- Department of Endocrinology, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
| | - José Iván Castillo Bejarano
- Department of Pediatrics/Infectious Diseases Service, Hospital Universitario “Dr. José Eleuterio González”, Universidad Autónoma de Nuevo León, Francisco I. Madero Avenue, Mitras Centro, ZC 64460 Monterrey, México
- Hospital Epidemiology and Surveillance Unit, Christus Muguerza Hospital Alta Especialidad, Hidalgo Avenue, Obispado, ZC 64060 Monterrey, México
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Kang HM, Kim KR, Kim G, Lee DG, Kim YJ, Choi EH, Lee J, Yun KW. Antimicrobial resistance genes harbored in invasive Acinetobacter calcoaceticus-baumannii complex isolated from Korean children during the pre-COVID-19 pandemic periods, 2015-2020. Front Cell Infect Microbiol 2024; 14:1410997. [PMID: 39027135 PMCID: PMC11254764 DOI: 10.3389/fcimb.2024.1410997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/15/2024] [Indexed: 07/20/2024] Open
Abstract
Background Acinetobacter baumannii (AB) has emerged as one of the most challenging pathogens worldwide, causing invasive infections in the critically ill patients due to their ability to rapidly acquire resistance to antibiotics. This study aimed to analyze antibiotic resistance genes harbored in AB and non-baumannii Acinetobacter calcoaceticus-baumannii (NB-ACB) complex causing invasive diseases in Korean children. Methods ACB complexes isolated from sterile body fluid of children in three referral hospitals were prospectively collected. Colistin susceptibility was additionally tested via broth microdilution. Whole genome sequencing was performed and antibiotic resistance genes were analyzed. Results During January 2015 to December 2020, a total of 67 ACB complexes were isolated from sterile body fluid of children in three referral hospitals. The median age of the patients was 0.6 (interquartile range, 0.1-7.2) years old. Among all the isolates, 73.1% (n=49) were confirmed as AB and others as NB-ACB complex by whole genome sequencing. Among the AB isolates, only 22.4% susceptible to carbapenem. In particular, all clonal complex (CC) 92 AB (n=33) showed multi-drug resistance, whereas 31.3% in non-CC92 AB (n=16) (P<0.001). NB-ACB showed 100% susceptibility to all classes of antibiotics except 3rd generation cephalosporin (72.2%). The main mechanism of carbapenem resistance in AB was the bla oxa23 gene with ISAba1 insertion sequence upstream. Presence of pmr gene and/or mutation of lpxA/C gene were not correlated with the phenotype of colistin resistance of ACB. All AB and NB-ACB isolates carried the abe and ade multidrug efflux pumps. Conclusions In conclusion, monitoring and research for resistome in ACB complex is needed to identify and manage drug-resistant AB, particularly CC92 AB carrying the bla oxa23 gene.
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Affiliation(s)
- Hyun Mi Kang
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Kyung Ran Kim
- Department of Pediatrics, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Gahee Kim
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Dong-gun Lee
- Vaccine Bio Research Institute, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
- Department of Internal Medicine, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yae Jean Kim
- Department of Pediatrics, Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, Republic of Korea
| | - Eun Hwa Choi
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Jina Lee
- Department of Pediatrics, Asan Medical Center, University of Ulsan College of Medicine, Seoul, Republic of Korea
| | - Ki Wook Yun
- Department of Pediatrics, College of Medicine, Seoul National University, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University Children’s Hospital, Seoul, Republic of Korea
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Kim KR, Park HJ, Baek SY, Choi SH, Lee BK, Kim S, Kim JM, Kang JM, Kim SJ, Choi SR, Kim D, Choi JS, Yoon Y, Park H, Kim DR, Shin A, Kim S, Kim YJ. The Impact of an Antimicrobial Stewardship Program on Days of Therapy in the Pediatric Center: An Interrupted Time-Series Analysis of a 19-Year Study. J Korean Med Sci 2024; 39:e172. [PMID: 38832477 PMCID: PMC11147790 DOI: 10.3346/jkms.2024.39.e172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND We aimed to analyze the effects of an antimicrobial stewardship program (ASP) on the proportion of antimicrobial-resistant pathogens in bacteremia, antimicrobial use, and mortality in pediatric patients. METHODS A retrospective single-center study was performed on pediatric inpatients under 19 years old who received systemic antimicrobial treatment from 2001 to 2019. A pediatric infectious disease attending physician started ASP in January 2008. The study period was divided into the pre-intervention (2001-2008) and the post-intervention (2009-2019) periods. The amount of antimicrobial use was defined as days of therapy per 1,000 patient-days, and the differences were compared using delta slope (= changes in slopes) between the two study periods by an interrupted time-series analysis. The proportion of resistant pathogens and the 30-day overall mortality rate were analyzed by the χ². RESULTS The proportion of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae bacteremia increased from 17% (39 of 235) in the pre-intervention period to 35% (189 of 533) in the post-intervention period (P < 0.001). The total amount of antimicrobial use significantly decreased after the introduction of ASP (delta slope value = -16.5; 95% confidence interval [CI], -30.6 to -2.3; P = 0.049). The 30-day overall mortality rate in patients with bacteremia did not increase, being 10% (55 of 564) in the pre-intervention and 10% (94 of 941) in the post-intervention period (P = 0.881). CONCLUSION The introduction of ASP for pediatric patients reduced the delta slope of the total antimicrobial use without increasing the mortality rate despite an increased incidence of ESBL-producing gram-negative bacteremia.
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Affiliation(s)
- Kyung-Ran Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hyo Jung Park
- Department of Pharmacy, Samsung Medical Center, Seoul, Korea
- Sungkyunkwan University School of Pharmacy, Suwon, Korea
| | - Sun-Young Baek
- Research Institute for Future Medicine, Samsung Medical Center, Seoul, Korea
| | - Soo-Han Choi
- Department of Pediatrics, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
| | - Byung-Kee Lee
- Department of Pediatrics, Seoulsan Boram Hospital, Ulsan, Korea
| | - SooJin Kim
- Samsung Dream Pediatric Clinic, Suwon, Korea
| | - Jong Min Kim
- Department of Pediatrics, Myongji Hospital, Goyang, Korea
| | - Ji-Man Kang
- Department of Pediatrics, Severance Children's Hospital, Yonsei University College of Medicine, Seoul, Korea
| | - Sun-Ja Kim
- Samsung Dream Pediatric Clinic, Jeju, Korea
| | | | - Dongsub Kim
- Department of Pediatrics, Kyungpook National University Hospital, Kyungpook National University School of Medicine, Daegu, Korea
| | - Joon-Sik Choi
- Department of Pediatrics, Gangnam Severance Hospital, Seoul, Korea
| | - Yoonsun Yoon
- Department of Pediatrics, Korea University Guro Hospital, Korea University College of Medicine, Seoul, Korea
| | - Hwanhee Park
- Department of Pediatrics, Soonchunhyang University Bucheon Hospital, Soonchunhyang University College of Medicine, Bucheon, Korea
| | - Doo Ri Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Areum Shin
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seonwoo Kim
- Academic Research Service Headquarter, LSK Global PS, Seoul, Korea
| | - Yae-Jean Kim
- Department of Pediatrics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Seoul, Korea.
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Kim KJ, Yun SG, Cho Y, Lee CK, Nam MH. Rapid Direct Identification of Microbial Pathogens and Antimicrobial Resistance Genes in Positive Blood Cultures Using a Fully Automated Multiplex PCR Assay. J Korean Med Sci 2024; 39:e157. [PMID: 38711319 DOI: 10.3346/jkms.2024.39.e157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 04/22/2024] [Indexed: 05/08/2024] Open
Abstract
This study assessed the performance of the BioFire Blood Culture Identification 2 (BCID2) panel in identifying microorganisms and antimicrobial resistance (AMR) profiles in positive blood cultures (BCs) and its influence on turnaround time (TAT) compared with conventional culture methods. We obtained 117 positive BCs, of these, 102 (87.2%) were correctly identified using BCID2. The discordance was due to off-panel pathogens detected by culture (n = 13), and additional pathogens identified by BCID2 (n = 2). On-panel pathogen concordance between the conventional culture and BCID2 methods was 98.1% (102/104). The conventional method detected 19 carbapenemase-producing organisms, 14 extended-spectrum beta-lactamase-producing Enterobacterales, 18 methicillin-resistant Staphylococcus spp., and four vancomycin-resistant Enterococcus faecium. BCID2 correctly predicted 53 (96.4%) of 55 phenotypic resistance patterns by detecting AMR genes. The TAT for BCID2 was significantly lower than that for the conventional method. BCID2 rapidly identifies pathogens and AMR genes in positive BCs.
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Affiliation(s)
- Keun Ju Kim
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Seung Gyu Yun
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Yunjung Cho
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Chang Kyu Lee
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea
| | - Myung-Hyun Nam
- Department of Laboratory Medicine, Korea University College of Medicine, Seoul, Korea.
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Anwer R. Molecular epidemiology and molecular typing methods of Acinetobacter baumannii: An updated review. Saudi Med J 2024; 45:458-467. [PMID: 38734425 PMCID: PMC11147555 DOI: 10.15537/smj.2024.45.5.20230886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/13/2024] Open
Abstract
The aim of this study was to go through the molecular methods used for typing of carbapenem-resistant Acientobacter baumannii (CRAB) isolates for investigating the molecular epidemiology all over the world. Multiple typing techniques are required to understand the source and nature of outbreaks caused by Acientobacter baumannii (A. baumannii) and acquired resistance to antimicrobials. Nowadays, there is gradual shift from traditional typing methods to modern molecular methods to study molecular epidemiology and infection control. Molecular typing of A. baumannii strains has been revolutionized significantly in the last 2 decades. A few sequencing-based techniques have been proven as a breakthrough and opened new prospects, which have not been achieved by the traditional methods. In this review, discussed different pre-existing and recently used typing methods to explore the molecular epidemiology of A. baumannii pertaining in context with human infections.
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Affiliation(s)
- Razique Anwer
- From the Department of Pathology, College of Medicine, Imam Mohammad Ibn Saud Islamic University, Riyadh, Kingdom of Saudi Arabia.
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Lan M, Dongmei K, Guodong S, Haifeng Y, Guofeng C, Mengting C, Xiaoyun F. Risk factors for bacteremic pneumonia and mortality (28-day mortality) in patients with Acinetobacter baumannii bacteremia. BMC Infect Dis 2024; 24:448. [PMID: 38671347 PMCID: PMC11046916 DOI: 10.1186/s12879-024-09335-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Patients infected with Acinetobacter baumannii (AB) bacteremia in hospital have high morbidity and mortality. We analyzed the clinical characteristics of pneumonia and nonpneumonia-related AB bloodstream infections (AB BSIs) and explored the possible independent risk factors for the incidence and prognosis of pneumonia-related AB BSIs. METHODS A retrospective monocentric observational study was performed. All 117 episodes of hospital-acquired AB bacteremia sorted into groups of pneumonia-related AB BSIs (n = 45) and nonpneumonia-related AB BSIs (n = 72) were eligible. Univariate/multivariate logistic regression analysis was used to explore the independent risk factors. The primary outcome was the antibiotic susceptibility in vitro of pneumonia-related AB BSIs group. The secondary outcome was the independent risk factor for the pneumonia-related AB BSIs group. RESULTS Among 117 patients with AB BSIs, the pneumonia-related group had a greater risk of multidrug resistant A. baumannii (MDRAB) infection (84.44%) and carbapenem-resistant A. baumannii (CRAB) infection (80%). Polymyxin, minocycline and amikacin had relatively high susceptibility rates (> 80%) in the nonpneumonia-related group. However, in the pneumonia-related group, only polymyxin had a drug susceptibility rate of over 80%. Univariate analysis showed that survival time (day), CRAB, MDRAB, length of hospital stay prior to culture, length of ICU stay prior to culture, immunocompromised status, antibiotics used prior to culture (n > = 3 types), endotracheal tube, fiberoptic bronchoscopy, PITT, SOFA and invasive interventions (n > = 3 types) were associated with pneumonia-related AB bacteremia. The multivariate logistic regression analysis revealed that recent surgery (within 1 mo) [P = 0.043; 0.306 (0.098-0.962)] and invasive interventions (n > = 3 types) [P = 0.021; 0.072 (0.008-0.671)] were independent risk factors related to pneumonia-related AB bacteremia. Multivariate logistic regression analysis revealed that length of ICU stay prior to culture [P = 0.009; 0.959 (0.930-0.990)] and recent surgery (within 1 mo) [P = 0.004; 0.260 (0.105-0.646)] were independent risk factors for mortality in patients with pneumonia-related AB bacteremia. The Kaplan‒Meier curve and the timing test showed that patients with pneumonia-related AB bacteremia had shorter survival time compared to those with nonpneumonia-related AB bacteremia. CONCLUSIONS Our study found that A. baumannii had a high rate of antibiotic resistance in vitro in the pneumonia-related bacteremia group, and was only sensitive to polymyxin. Recent surgery was a significantly independent predictor in patients with pneumonia-related AB bacteremia.
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Affiliation(s)
- Meng Lan
- Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230032, China
| | - Kang Dongmei
- International Medicine Depaterment, Division of Life Science and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Shen Guodong
- Anhui Province Key Laboratory of Geriatric Immunology and Nutrition Therapy, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Yao Haifeng
- Information Center, Division of Life Sciences and Medicine, The First Affiliated Hospital of USTC, University of Science and Technology of China, Hefei, 230001, Anhui, China
| | - Cui Guofeng
- Anhui Geriatric Institute, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, PR China
| | - Chen Mengting
- Anhui Geriatric Institute, the First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230022, PR China
| | - Fan Xiaoyun
- Department of Geriatric Respiratory and Critical Care Medicine, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui, 230032, China.
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Yang Q, Kamat S, Mohamed N, Valdez RR, Lin S, Su M, Quintana A, Kiratisin P, Rodríguez-Zulueta AP, Brink A. Antimicrobial Susceptibility Among Gram-Negative Isolates in Pediatric Patients in Latin America, Africa-Middle East, and Asia From 2016-2020 Compared to 2011-2015: Results From the ATLAS Surveillance Study. J Pediatric Infect Dis Soc 2023; 12:459-470. [PMID: 37643742 PMCID: PMC10797666 DOI: 10.1093/jpids/piad055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 08/09/2023] [Indexed: 08/31/2023]
Abstract
BACKGROUND Antimicrobial resistance (AMR) data in the pediatric population are limited, particularly in developing countries. This study assessed the AMR profile and key resistance phenotypes and genotypes for Gram-negative bacteria (GNB) isolates collected as part of the Antimicrobial Testing Leadership and Surveillance program from pediatric patients in Latin America, Africa-Middle East, and Asia in 2016-2020 versus 2011-2015. METHODS Minimum inhibitory concentrations by broth microdilution methodology were interpreted per the Clinical and Laboratory Standards Institute. European Committee on Antimicrobial Susceptibility Testing breakpoints were used for interpreting colistin activity. β-lactamase genes were screened by polymerase chain reaction and sequencing. RESULTS For Acinetobacter baumannii, low susceptibility (<60.0%) was observed for all antimicrobials, except colistin (≥92.9%), across regions and year periods. Ceftazidime-avibactam, amikacin, colistin, and meropenem were mostly active (78.6%-100.0%) against Enterobacter cloacae, Escherichia coli, and Klebsiella pneumoniae. For Pseudomonas aeruginosa, susceptibility to ceftazidime-avibactam, amikacin, and colistin was ≥85.9%. Among resistance phenotypes, carbapenem-resistant (CR, ≥44.8%) and difficult-to-treat resistant (DTR, ≥37.1%) rates were the highest in A. baumannii. A consistent increase in CR and DTR K. pneumoniae was noted across regions over time. Extended-spectrum β-lactamases (ESBL)-producing K. pneumoniae (32.6%-55.6%) were more frequent than ESBL-producing E. coli (25.3%-37.1%). CTX-M was the dominant ESBL among Enterobacterales. NDM-positive Enterobacterales species and VIM-positive P. aeruginosa were identified across regions. CONCLUSIONS This study identified high susceptibility to few agents for key GNB in pediatric patients. Continued surveillance of resistance phenotypes and genotypes at regional levels may help to guide appropriate treatment decisions.
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Affiliation(s)
- Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | | | | | | | | | - Ming Su
- Pfizer Ltd., Shanghai, China
| | | | - Pattarachai Kiratisin
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Adrian Brink
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- National Health Laboratory Service, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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11
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Kim SH, Wi YM, Peck KR. Clinical Effectiveness of Tetracycline-Class Agents Based Regimens in Patients With Carbapenem-Resistant Acinetobacter baumannii Bacteremia: A Single-Center Retrospective Cohort Study. J Korean Med Sci 2023; 38:e263. [PMID: 37644679 PMCID: PMC10462474 DOI: 10.3346/jkms.2023.38.e263] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/21/2023] [Indexed: 08/31/2023] Open
Abstract
This study evaluated the clinical outcome of carbapenem-resistant Acinetobacter baumannii (CRAB) bacteremia and the clinical effectiveness of tetracyclines-based therapy. In a retrospective cohort study over 5 years period, 108 patients were included in the study. The overall 30-day mortality rate was 71.4%. Pitt's bacteremia score (PBS) (adjusted hazard ratio [aHR], 1.32; 95% confidence interval [CI], 1.22-1.42 per 1-point), colistin-single regimens (aHR, 0.34; 95% CI, 0.17-0.69), and tetracyclines single/tetracyclines-colistin combination regimens (aHR, 0.18; 95% CI, 0.07-0.48) were independently associated with 30-day mortality. Among patients with a PBS < 6, only tetracycline-containing regimens were associated with decreased mortality. Among patients receiving appropriate definite antimicrobials, the tetracyclines-colistin combination (7 of 7, 100%) tended to a higher 30-day survival rate compared to a tetracycline (7 of 12, 57.1%) or colistin single regimen (10 of 22, 41.6%, P = 0.073). Our findings suggest tetracyclines might be effective for treating CRAB infections when combined with colistin.
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Affiliation(s)
- Si-Ho Kim
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea
| | - Yu Mi Wi
- Division of Infectious Diseases, Samsung Changwon Hospital, Sungkyunkwan University School of Medicine, Changwon, Korea.
| | - Kyong Ran Peck
- Division of Infectious Diseases, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea.
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12
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Karampatakis T, Tsergouli K, Roilides E. Infection control measures against multidrug-resistant Gram-negative bacteria in children and neonates. Future Microbiol 2023; 18:751-765. [PMID: 37584552 DOI: 10.2217/fmb-2023-0072] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023] Open
Abstract
The increase in infections caused by multidrug-resistant (MDR) Gram-negative bacteria in neonatal and pediatric intensive care units over recent years is alarming. MDR Klebsiella pneumoniae, Pseudomonas aeruginosa and Acinetobacter baumannii have constituted the main causes of the MDR Gram-negative bacteria problem. The implementation of infection control measures such as hand hygiene, cohorting of patients, contact precautions, active surveillance and environmental cleaning could diminish their spread. Recently, water safety has been identified as a major component of infection control policies. The aim of the current review is to highlight the effectiveness of these infection control measures in managing outbreaks caused by MDR Gram-negative bacteria in neonatal and pediatric intensive care units and highlight future perspectives on the topic.
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Affiliation(s)
| | - Katerina Tsergouli
- Microbiology Department, Agios Pavlos General Hospital, Thessaloniki, 551 34, Greece
| | - Emmanuel Roilides
- Infectious Disease Unit, 3rd Department of Pediatrics, School of Health Sciences, Hippokration General Hospital, Thessaloniki, 546 42, Greece
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13
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Yang X, Liu X, Li W, Shi L, Zeng Y, Xia H, Huang Q, Li J, Li X, Hu B, Yang L. Epidemiological Characteristics and Antimicrobial Resistance Changes of Carbapenem-Resistant Klebsiella pneumoniae and Acinetobacter baumannii under the COVID-19 Outbreak: An Interrupted Time Series Analysis in a Large Teaching Hospital. Antibiotics (Basel) 2023; 12:antibiotics12030431. [PMID: 36978298 PMCID: PMC10044178 DOI: 10.3390/antibiotics12030431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 01/14/2023] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
Background: To investigate the epidemiological characteristics and resistance changes of carbapenem-resistant organisms (CROs) under the COVID-19 outbreak to provide evidence for precise prevention and control measures against hospital-acquired infections during the pandemic. Methods: The distribution characteristics of CROs (i.e., carbapenem-resistant Klebsiella pneumoniae and Acinetobacter baumannii) were analyzed by collecting the results of the antibiotic susceptibility tests of diagnostic isolates from all patients. Using interrupted time series analysis, we applied Poisson and linear segmented regression models to evaluate the effects of COVID-19 on the numbers and drug resistance of CROs. We also conducted a stratified analysis using the Cochran–Mantel–Haenszel test. Results: The resistance rate of carbapenem-resistant Acinetobacter baumannii (CRAB) was 38.73% higher after the COVID-19 outbreak compared with before (p < 0.05). In addition, the long-term effect indicated that the prevalence of CRAB had a decreasing trend (p < 0.05). However, the overall resistance rate of Klebsiella pneumoniae did not significantly change after the COVID-19 outbreak. Stratified analysis revealed that the carbapenem-resistant Klebsiella pneumoniae (CRKP) rate increased in females (OR = 1.98, p < 0.05), those over 65 years old (OR = 1.49, p < 0.05), those with sputum samples (OR = 1.40, p < 0.05), and those in the neurology group (OR = 2.14, p < 0.05). Conclusion: The COVID-19 pandemic has affected the change in nosocomial infections and resistance rates in CROs, highlighting the need for hospitals to closely monitor CROs, especially in high-risk populations and clinical departments. It is possible that lower adherence to infection control in crowded wards and staffing shortages may have contributed to this trend during the COVID-19 pandemic, which warrants further research.
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Affiliation(s)
- Xinyi Yang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Xu Liu
- Department of Infectious Disease, The Fifth Affiliated Hospital, Sun Yat-sen University, Zhuhai 519000, China
| | - Weibin Li
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Lin Shi
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Yingchao Zeng
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Haohai Xia
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Qixian Huang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
| | - Jia Li
- Department of Pharmacy, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510080, China
| | - Xiaojie Li
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
| | - Bo Hu
- Department of Laboratory Medicine, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou 510630, China
- Correspondence: (B.H.); (L.Y.)
| | - Lianping Yang
- School of Public Health, Sun Yat-sen University, Guangzhou 510080, China
- Correspondence: (B.H.); (L.Y.)
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Correlative factor of death in patients with infected pancreatic necrosis after surgical intervention. JOURNAL OF PANCREATOLOGY 2022. [DOI: 10.1097/jp9.0000000000000115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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