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Liang B, Chen Y, Liang Z, Li X, Cai H, Lai H, Zhong H, Xie Y, Huang L, Gao F, Long Y. Molecular characteristics and evaluation of the phenotypic detection of carbapenemases among Enterobacterales and Pseudomonas via whole genome sequencing. Front Cell Infect Microbiol 2024; 14:1357289. [PMID: 39027138 PMCID: PMC11254758 DOI: 10.3389/fcimb.2024.1357289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 06/20/2024] [Indexed: 07/20/2024] Open
Abstract
Background/purposes The continuously increasing carbapenem resistance within Enterobacterales and Pseudomonas poses a threat to public health, nevertheless, the molecular characteristics of which in southern China still remain limited. And carbapenemase identification is a key factor in effective early therapy of carbapenem-resistant bacteria infections. We aimed to determine the molecular characteristics of these pathogens and compare commercial combined disc tests (CDTs) with the modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) in detecting and distinguishing carbapenemases using whole genome sequencing (WGS). Methods A total of 78 Enterobacterales, 30 Pseudomonas were obtained from two tertiary hospitals in southern China. Susceptibility tests were conducted using an automated VITEK2 compact system with confirmation via the Kirby-Bauer method. The WGS was conducted on all clinical isolates and the molecular characteristics were analyzed by screening the whole genome sequences. CDTs with or without cloxacillin, mCIM, and eCIM, were performed and compared by taking WGS results as the benchmark. Results A total of 103 carbapenem non-susceptible and 5 carbapenem susceptible bacteria were determined, with Klebsiella pneumoniae (42.7%), Pseudomonas aeruginosa (23.3%) and Escherichia coli (18.4%) being most prevalent. Carbapenemase genes were detected in 58 (56.3%) of the 103 carbapenem-non-susceptible clinical isolates, including 46 NDM, 6 KPC, 3 IMP, 1 IPM+VIM,1NDM+KPC, and 1 OXA-181. Carbapenemase-producing isolates were detected more frequently in Enterobacterales (76.3%). Among K. pneumoniae, the major sequence types were st307 and st11, while among E. coli and P. aeruginosa, the most prevalent ones were st410 and st242 respectively. For carbapenemase detection in Enterobacterales, the mCIM method achieved 100.00% (95% CI, 92.13-100.00%) sensitivity and 94.44% (70.63-99.71%) specificity (kappa, 0.96); for Pseudomonas, detection sensitivity was 100% (5.46-100.00%), and 100% (84.50-100.00%) specificity (kappa, 0.65). Commercial CDT carbapenemase detection sensitivity for Enterobacterales was 96.49% (86.84-99.39%), and 95.24% (74.13-99.75%) specificity (kappa, 0.90); for Pseudomonas, carbapenemase detection sensitivity was 100.00% (5.46-100.00%) and 37.93% (21.30-57.64%) specificity (kappa, 0.04). When cloxacillin testing was added, CDT specificity reached 84.61% (64.27-94.95%). Conclusion The molecular epidemiology of carbapenem-non-susceptible isolates from pediatric patients in Southern China exhibited distinctive characteristics. Both the mCIM-eCIM combination and CDT methods effectively detected and differentiated carbapenemases among Enterobacterales isolates, and the former performed better than CDT among Pseudomonas.
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Affiliation(s)
- Bingshao Liang
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yuou Chen
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, China
| | - Zhuwei Liang
- Clinical Laboratory, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, China
| | - Xueying Li
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Hao Cai
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Hanyu Lai
- Clinical Laboratory, The First People’s Hospital of Zhaoqing, Zhaoqing, China
| | - Huamin Zhong
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yongqiang Xie
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Lianfen Huang
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Fei Gao
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
| | - Yan Long
- Clinical Laboratory, Guangzhou Women and Children’s Medical Center, Guangzhou Medical University, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou, China
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Silva A, Silva V, López M, Rojo-Bezares B, Carvalho JA, Castro AP, Sáenz Y, Igrejas G, Poeta P. Antimicrobial Resistance, Genetic Lineages, and Biofilm Formation in Pseudomonas aeruginosa Isolated from Human Infections: An Emerging One Health Concern. Antibiotics (Basel) 2023; 12:1248. [PMID: 37627668 PMCID: PMC10451160 DOI: 10.3390/antibiotics12081248] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (PA) is a leading nosocomial pathogen and has great versatility due to a complex interplay between antimicrobial resistance and virulence factors. PA has also turned into one the most relevant model organisms for the study of biofilm-associated infections. The objective of the study focused on analyzing the antimicrobial susceptibility, resistance genes, virulence factors, and biofilm formation ability of thirty-two isolates of PA. PA isolates were characterized by the following analyses: susceptibility to 12 antimicrobial agents, the presence of resistance genes and virulence factors in PCR assays, and the quantification of biofilm production as evaluated by two distinct assays. Selected PA isolates were analyzed through multilocus sequence typing (MLST). Thirty PA isolates have a multi-resistant phenotype, and most of the isolates showed high levels of resistance to the tested antibiotics. Carbapenems showed the highest prevalence of resistance. Various virulence factors were detected and, for the quantification of biofilm production, the effectiveness of different methods was assessed. The microtiter plate method showed the highest accuracy and reproducibility for detecting biofilm-producing bacteria. MLST revealed four distinct sequence types (STs) in clinical PA, with three of them considered high-risk clones of PA, namely ST175, ST235, and ST244. These clones are associated with multidrug resistance and are prevalent in hospitals worldwide. Overall, the study highlights the high prevalence of antibiotic resistance, the presence of carbapenemase genes, the diversity of virulence factors, and the importance of biofilm formation in PA clinical isolates. Understanding these factors is crucial for effective infection control measures and the development of targeted treatment strategies.
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Affiliation(s)
- Adriana Silva
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - Vanessa Silva
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | | | - Ana Paula Castro
- Medical Center of Trás-os-Montes e Alto Douro E.P.E., 5000-508 Vila Real, Portugal
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - Patrícia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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Gideskog M, Falkeborn T, Welander J, Melhus Å. Source Control of Gram-Negative Bacteria Using Self-Disinfecting Sinks in a Swedish Burn Centre. Microorganisms 2023; 11:microorganisms11040965. [PMID: 37110388 PMCID: PMC10143680 DOI: 10.3390/microorganisms11040965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 03/31/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Several retrospective studies have identified hospital sinks as reservoirs of Gram-negative bacteria. The aim of this study was to prospectively investigate the bacterial transmission from sinks to patients and if self-disinfecting sinks could reduce this risk. Samples were collected weekly from sinks (self-disinfecting, treated with boiling water, not treated) and patients in the Burn Centre at Linköping University Hospital, Sweden. The antibiotic susceptibility of Gram-negative isolates was tested, and eight randomly chosen patient isolates and their connected sink isolates were subjected to whole genome sequencing (WGS). Of 489 sink samples, 232 (47%) showed growth. The most frequent findings were Stenotrophomonas maltophilia (n = 130), Pseudomonas aeruginosa (n = 128), and Acinetobacter spp. (n = 55). Bacterial growth was observed in 20% of the samplings from the self-disinfecting sinks and in 57% from the sinks treated with boiling water (p = 0.0029). WGS recognized one transmission of Escherichia coli sampled from an untreated sink to a patient admitted to the same room. In conclusion, the results showed that sinks can serve as reservoirs of Gram-negative bacteria and that self-disinfecting sinks can reduce the transmission risk. Installing self-disinfecting sinks in intensive care units is an important measure in preventing nosocomial infection among critically ill patients.
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Affiliation(s)
- Maria Gideskog
- Department of Communicable Disease and Infection Control, Linköping University Hospital, SE-581 85 Linköping, Sweden
- Department of Biomedical and Clinical Sciences, Linköping University, SE-581 85 Linköping, Sweden
| | - Tina Falkeborn
- Department of Biomedical and Clinical Sciences, Linköping University, SE-581 85 Linköping, Sweden
- Department of Clinical Microbiology, Linköping University Hospital, SE-581 85 Linköping, Sweden
| | - Jenny Welander
- Department of Biomedical and Clinical Sciences, Linköping University, SE-581 85 Linköping, Sweden
- Department of Clinical Microbiology, Linköping University Hospital, SE-581 85 Linköping, Sweden
| | - Åsa Melhus
- Section of Clinical Microbiology, Department of Medical Sciences, Uppsala University, SE-751 85 Uppsala, Sweden
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Estimation, Evaluation and Characterization of Carbapenem Resistance Burden from a Tertiary Care Hospital, Pakistan. Antibiotics (Basel) 2023; 12:antibiotics12030525. [PMID: 36978392 PMCID: PMC10044297 DOI: 10.3390/antibiotics12030525] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/09/2023] Open
Abstract
Carbapenem resistance has become major concern in healthcare settings globally; therefore, its monitoring is crucial for intervention efforts to halt resistance spread. During May 2019–April 2022, 2170 clinical strains were characterized for antimicrobial susceptibility, resistance genes, replicon and sequence types. Overall, 42.1% isolates were carbapenem-resistant, and significantly associated with Klebsiella pneumoniae (K. pneumoniae) (p = 0.008) and Proteus species (p = 0.043). Carbapenemases were detected in 82.2% of isolates, with blaNDM-1 (41.1%) associated with the ICU (p < 0.001), cardiology (p = 0.042), pediatric medicine (p = 0.013) and wound samples (p = 0.041); blaOXA-48 (32.6%) was associated with the ICU (p < 0.001), cardiology (p = 0.008), pediatric medicine (p < 0.001), general surgery (p = 0.001), general medicine (p = 0.005) and nephrology (p = 0.020); blaKPC-2 (5.5%) was associated with general surgery (p = 0.029); blaNDM-1/blaOXA-48 (11.4%) was associated with general surgery (p < 0.001), and wound (p = 0.002), urine (p = 0.003) and blood (p = 0.012) samples; blaOXA-48/blaVIM (3.1%) was associated with nephrology (p < 0.001) and urine samples (p < 0.001). Other detected carbapenemases were blaVIM (3.0%), blaIMP (2.7%), blaOXA-48/blaIMP (0.1%) and blaVIM/blaIMP (0.3%). Sequence type (ST)147 (39.7%) represented the most common sequence type identified among K. pneumoniae, along with ST11 (23.0%), ST14 (15.4%), ST258 (10.9%) and ST340 (9.6%) while ST405 comprised 34.5% of Escherichia coli (E. coli) isolates followed by ST131 (21.2%), ST101 (19.7%), ST10 (16.0%) and ST69 (7.4%). Plasmid replicon types IncFII, IncA/C, IncN, IncL/M, IncFIIA and IncFIIK were observed. This is first report describing the carbapenem-resistance burden and emergence of blaKPC-2-ST147, blaNDM-1-ST340 and blaNDM-1-ST14 in K. pneumoniae isolates and blaNDM-1-ST69 and blaNDM-1/blaOXA-48-ST69 in E. coli isolates coharboring extended-spectrum beta-lactamases (ESBLs) from Pakistan.
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Siew SW, Musa SM, Sabri N'A, Farida Asras MF, Ahmad HF. Evaluation of pre-treated healthcare wastes during COVID-19 pandemic reveals pathogenic microbiota, antibiotics residues, and antibiotic resistance genes against beta-lactams. ENVIRONMENTAL RESEARCH 2023; 219:115139. [PMID: 36565841 PMCID: PMC9771581 DOI: 10.1016/j.envres.2022.115139] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/25/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
The disposal of healthcare waste without prior elimination of pathogens and hazardous contaminants has negative effects on the environment and public health. This study aimed to profile the complete microbial community and correlate it with the antibiotic compounds identified in microwave pre-treated healthcare wastes collected from three different waste operators in Peninsular Malaysia. The bacterial and fungal compositions were determined via amplicon sequencing by targeting the full-length 16S rRNA gene and partial 18S with full-length ITS1-ITS2 regions, respectively. The antibiotic compounds were characterized using high-throughput spectrometry. There was significant variation in bacterial and fungal composition in three groups of samples, with alpha- (p-value = 0.04) and beta-diversity (p-values <0.006 and < 0.002), respectively. FC samples were found to acquire more pathogenic microorganisms than FA and FV samples. Paenibacillus and unclassified Bacilli genera were shared among three groups of samples, meanwhile, antibiotic-resistant bacteria Proteus mirabilis, Enterococcus faecium, and Enterococcus faecalis were found in modest quantities. A total of 19 antibiotic compounds were discovered and linked with the microbial abundance detected in the healthcare waste samples. The principal component analysis demonstrated a positive antibiotic-bacteria correlation for genera Pseudomonas, Aerococcus, Comamonas, and Vagococcus, while the other bacteria were negatively linked with antibiotics. Nevertheless, deep bioinformatic analysis confirmed the presence of blaTEM-1 and penP which are associated with the production of class A beta-lactamase and beta-lactam resistance pathways. Microorganisms and contaminants, which serve as putative indicators in healthcare waste treatment evaluation revealed the ineffectiveness of microbial inactivation using the microwave sterilization method. Our findings suggested that the occurrence of clinically relevant microorganisms, antibiotic contaminants, and associated antibiotic resistance genes (ARGs) represent environmental and human health hazards when released into landfills via ARGs transmission.
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Affiliation(s)
- Shing Wei Siew
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia.
| | - Siti Munirah Musa
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia.
| | - Nurul 'Azyyati Sabri
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia; Group of Environment, Microbiology and Bioprocessing (GERMS), Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia.
| | - Mohd Fazli Farida Asras
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia; Group of Environment, Microbiology and Bioprocessing (GERMS), Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia.
| | - Hajar Fauzan Ahmad
- Faculty of Industrial Sciences and Technology, Universiti Malaysia Pahang, Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia; Group of Environment, Microbiology and Bioprocessing (GERMS), Lebuhraya Tun Razak, 26300, Gambang, Pahang, Malaysia.
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Antimicrobial Susceptibility and Genetic Prevalence of Extended-Spectrum β-Lactamases in Gram-Negative Rods Isolated from Clinical Specimens in Pakistan. Antibiotics (Basel) 2022; 12:antibiotics12010029. [PMID: 36671229 PMCID: PMC9854846 DOI: 10.3390/antibiotics12010029] [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: 09/30/2022] [Revised: 12/20/2022] [Accepted: 12/21/2022] [Indexed: 12/28/2022] Open
Abstract
The prevalence of extended-spectrum β-lactamase (ESBL) genes has increased remarkably, resulting in multidrug-resistant gram-negative rods (GNRs) in clinical specimens. This cross-sectional study aimed to determine the antimicrobial susceptibility of ESBL-producing GNRs and its correlation with corresponding genes. Two hundred and seventy-two (n = 272) samples were evaluated for the molecular identification of ESBL genes by polymerase chain reaction after confirmation with the modified double-disc synergy test. E. coli 64.0% (n = 174) was the most prevalent ESBL producer, followed by Klebsiella species 27.2% (n = seventy-four), Acinetobacter species 6.6% (n = eighteen) and others 2.2% (n = six). These ESBL-producing isolates showed resistance to β-lactam antibiotics, i.e., sulbactam/cefoperazone (41.5%), piperacillin/tazobactam (39.3%), meropenem (36.0%), imipenem (34.2%) and non- β-lactam antibiotics, i.e., nalidixic acid (89.0%), co-trimoxazole (84.9%), ciprofloxacin (82.4%), gentamicin (46.3%), nitrofurantoin (24.6%), amikacin (19.9%) and fosfomycin (19.9%). The incidences of the ESBLs-producing genes blaCTX-M, blaTEM, blaOXA and blaSHV were 91.2%, 61.8%, 39.3% and 17.6%, respectively. Among nine multiple-gene combinations, blaCTX-M + blaTEM (30.5%) was the most prevalent combination, followed by blaCTX-M + blaOXA + blaTEM (14.0%), blaCTX-M + blaOXA (13.6%), blaCTX-M + blaTEM + blaSHV (7.0%), blaCTX-M + blaSHV (2.2%), blaCTX-M + blaOXA + blaSHV (2.2%) and blaOXA + blaTEM (1.8%). ESBLs producing GNRs carrying blaCTX-M, blaTEM, blaOXA and blaSHV showed resistances to β-lactam antibiotics, i.e., ampicillin, amoxillin-clavulanic acid, cefotaxime and ceftazidime but were susceptible to carbapenems (meropenem and imipenem), β-lactam-β-lactamase inhibitor combination (piperacillin/tazobactam) and non-β-lactam antibiotics i.e., aminoglycoside (amikacin and gentamicin), nitrofurantoin and fosfomycin. These antibiotics that demonstrated activity may be used to treat infections in clinical settings.
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Zhang H, Wang M, Han X, Wang T, Lei Y, Rao Y, Xu P, Wang Y, Gu H. The application of targeted nanopore sequencing for the identification of pathogens and resistance genes in lower respiratory tract infections. Front Microbiol 2022; 13:1065159. [PMID: 36620015 PMCID: PMC9822541 DOI: 10.3389/fmicb.2022.1065159] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/28/2022] [Indexed: 12/24/2022] Open
Abstract
Objectives Lower respiratory tract infections (LRTIs) are one of the causes of mortality among infectious diseases. Microbial cultures commonly used in clinical practice are time-consuming, have poor sensitivity to unculturable and polymicrobial patterns, and are inadequate to guide timely and accurate antibiotic therapy. We investigated the feasibility of targeted nanopore sequencing (TNPseq) for the identification of pathogen and antimicrobial resistance (AMR) genes across suspected patients with LRTIs. TNPseq is a novel approach, which was improved based on nanopore sequencing for the identification of bacterial and fungal infections of clinical relevance. Methods This prospective study recruited 146 patients suspected of having LRTIs and with a median age of 61 years. The potential pathogens in these patients were detected by both TNPseq and the traditional culture workups. We compared the performance between the two methods among 146 LRTIs-related specimens. AMR genes were also detected by TNPseq to prompt the proper utilization of antibiotics. Results At least one pathogen was detected in 133 (91.1%) samples by TNPseq, but only 37 (25.3%) samples contained positive isolates among 146 cultured specimens. TNPseq possessed higher sensitivity than the conventional culture method (91.1 vs. 25.3%, P < 0.001) in identifying pathogens. It detected more samples with bacterial infections (P < 0.001) and mixed infections (P < 0.001) compared with the clinical culture tests. The most frequent AMR gene identified by TNPseq was bla TEM (n = 29), followed by bla SHV (n = 4), bla KPC (n = 2), bla CTX-M (n = 2), and mecA (n = 2). Furthermore, TNPseq discovered five possible multi-drug resistance specimens. Conclusion TNPseq is efficient to identify pathogens early, thus assisting physicians to conduct timely and precise treatment for patients with suspected LRTIs.
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Affiliation(s)
- Hongying Zhang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China,*Correspondence: Hongying Zhang ✉
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, China
| | - Ximei Han
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Ting Wang
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Yanjuan Lei
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yu Rao
- Department of Pulmonary Medicine, Fuzhou Pulmonary Hospital of Fujian, Fuzhou, China
| | - Peisong Xu
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Yunfei Wang
- Department of Medicine, Zhejiang ShengTing Biotech Co., Ltd., Hangzhou, China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, China,Graduate School, University of Science and Technology of China, Hefei, China,Hongcang Gu ✉
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Viaggi B, Cangialosi A, Langer M, Olivieri C, Gori A, Corona A, Finazzi S, Di Paolo A. Tissue Penetration of Antimicrobials in Intensive Care Unit Patients: A Systematic Review-Part II. Antibiotics (Basel) 2022; 11:antibiotics11091193. [PMID: 36139972 PMCID: PMC9495066 DOI: 10.3390/antibiotics11091193] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/28/2022] [Accepted: 09/01/2022] [Indexed: 11/18/2022] Open
Abstract
In patients that are admitted to intensive care units (ICUs), the clinical outcome of severe infections depends on several factors, as well as the early administration of chemotherapies and comorbidities. Antimicrobials may be used in off-label regimens to maximize the probability of therapeutic concentrations within infected tissues and to prevent the selection of resistant clones. Interestingly, the literature clearly shows that the rate of tissue penetration is variable among antibacterial drugs, and the correlation between plasma and tissue concentrations may be inconstant. The present review harvests data about tissue penetration of antibacterial drugs in ICU patients, limiting the search to those drugs that mainly act as protein synthesis inhibitors and disrupting DNA structure and function. As expected, fluoroquinolones, macrolides, linezolid, and tigecycline have an excellent diffusion into epithelial lining fluid. That high penetration is fundamental for the therapy of ventilator and healthcare-associated pneumonia. Some drugs also display a high penetration rate within cerebrospinal fluid, while other agents diffuse into the skin and soft tissues. Further studies are needed to improve our knowledge about drug tissue penetration, especially in the presence of factors that may affect drug pharmacokinetics.
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Affiliation(s)
- Bruno Viaggi
- Department of Anesthesiology, Neuro-Intensive Care Unit, Careggi University Hospital, 50139 Florence, Italy
- Associazione GiViTI, c/o Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Alice Cangialosi
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
| | - Martin Langer
- Associazione GiViTI, c/o Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Carlo Olivieri
- Anesthesia and Intensive Care, Sant’Andrea Hospital, ASL VC, 13100 Vercelli, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Foundation Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Ca’ Granda Ospedale Maggiore Policlinico, 20122 Milan, Italy
| | - Alberto Corona
- ICU and Accident & Emergency Department, ASST Valcamonica, 25043 Breno, Italy
| | - Stefano Finazzi
- Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 24020 Ranica, Italy
| | - Antonello Di Paolo
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy
- Correspondence:
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Haider MH, McHugh TD, Roulston K, Arruda LB, Sadouki Z, Riaz S. Correction: Detection of carbapenemases bla OXA48-bla KPC-bla NDM-bla VIM and extended-spectrum-β-lactamase bla OXA1-bla SHV-bla TEM genes in Gram-negative bacterial isolates from ICU burns patients. Ann Clin Microbiol Antimicrob 2022; 21:34. [PMID: 35799176 PMCID: PMC9264670 DOI: 10.1186/s12941-022-00519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Muhammad Hayat Haider
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan.,Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, UK
| | - Timothy D McHugh
- Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, UK
| | - Kerry Roulston
- Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, UK
| | - Liã Bárbara Arruda
- Wellcome Connecting Science, Wellcome Genome Campus, Hinxton, CB10 1RQ, UK
| | - Zahra Sadouki
- Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, University College London, London, UK
| | - Saba Riaz
- Institute of Microbiology and Molecular Genetics, University of the Punjab, Lahore, Pakistan. .,525-A Citilab and Research Centre CRC, Faisal Town, Lahore, Pakistan.
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10
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Kuzina ES, Novikova TS, Astashkin EI, Fedyukina GN, Kislichkina AA, Kurdyumova NV, Savin IA, Ershova ON, Fursova NK. Rectal and Tracheal Carriage of Carbapenemase Genes and Class 1 and 2 Integrons in Patients in Neurosurgery Intensive Care Unit. Antibiotics (Basel) 2022; 11:886. [PMID: 35884140 PMCID: PMC9312170 DOI: 10.3390/antibiotics11070886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 06/28/2022] [Accepted: 07/01/2022] [Indexed: 11/17/2022] Open
Abstract
The spread of multidrug-resistant Gram-negative bacteria, which is associated with the distribution of beta-lactamase genes and class 1 and 2 integrons, is a global problem. In this study, in the Moscow neurosurgery intensive care unit (neuro-ICU), the high prevalence of the above-stated genes was found to be associated with intestinal and tracheal carriage. Seven-point prevalence surveys, which included 60 patients in the neuro-ICU, were conducted weekly in the period from Oct. to Nov. 2019. A total of 293 clinical samples were analyzed, including 146 rectal and 147 tracheal swabs; 344 Gram-negative bacteria isolates were collected. Beta-lactamase genes (n = 837) were detected in the isolates, including beta-lactamase blaTEM (n = 162), blaSHV (n = 145), cephalosporinase blaCTX-M (n = 228), carbapenemase blaNDM (n = 44), blaKPC (n = 25), blaOXA-48 (n = 126), blaOXA-51-like (n = 54), blaOXA-40-like (n = 43), blaOXA-23-like (n = 8), and blaVIM (n = 2), as well as class 1 (n = 189) and class 2 (n = 12) integrons. One extensively drug-resistant Klebsiella pneumoniae strain (sequence type ST39 and capsular type K23), simultaneously carried beta-lactamase genes, blaSHV-40 and blaTEM-1B, three carbapenemase genes, blaNDM, blaKPC, and blaOXA-48, the cephalosporinase gene blaCTX-M, and two class 1 integrons. Before this study, such heavily armed strains have not been reported, suggesting the ongoing evolution of antibiotic resistance.
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Affiliation(s)
- Ekaterina S. Kuzina
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia;
| | - Tatiana S. Novikova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (T.S.N.); (E.I.A.)
| | - Evgeny I. Astashkin
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (T.S.N.); (E.I.A.)
| | - Galina N. Fedyukina
- Department of Immunobiochemistry of Pathogenic Microorganisms, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia;
| | - Angelina A. Kislichkina
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia;
| | - Natalia V. Kurdyumova
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (N.V.K.); (I.A.S.); (O.N.E.)
| | - Ivan A. Savin
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (N.V.K.); (I.A.S.); (O.N.E.)
| | - Olga N. Ershova
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia; (N.V.K.); (I.A.S.); (O.N.E.)
| | - Nadezhda K. Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia; (T.S.N.); (E.I.A.)
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