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Huang X, Toro M, Reyes-Jara A, Moreno-Switt AI, Adell AD, Oliveira CJB, Bonelli RR, Gutiérrez S, Álvarez FP, Rocha ADDL, Kraychete GB, Chen Z, Grim C, Brown E, Bell R, Meng J. Integrative genome-centric metagenomics for surface water surveillance: Elucidating microbiomes, antimicrobial resistance, and their associations. WATER RESEARCH 2024; 264:122208. [PMID: 39116611 DOI: 10.1016/j.watres.2024.122208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 07/30/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]
Abstract
Surface water ecosystems are intimately intertwined with anthropogenic activities and have significant public health implications as primary sources of irrigation water in agricultural production. Our extensive metagenomic analysis examined 404 surface water samples from four different geological regions in Chile and Brazil, spanning irrigation canals (n = 135), rivers (n = 121), creeks (n = 74), reservoirs (n = 66), and ponds (n = 8). Overall, 50.25 % of the surface water samples contained at least one of the pathogenic or contaminant bacterial genera (Salmonella: 29.21 %; Listeria: 6.19 %; Escherichia: 35.64 %). Furthermore, a total of 1,582 antimicrobial resistance (AMR) gene clusters encoding resistance to 25 antimicrobial classes were identified, with samples from Brazil exhibiting an elevated AMR burden. Samples from stagnant water sources were characterized by dominant Cyanobacteriota populations, resulting in significantly reduced biodiversity and more uniform community compositions. A significant association between taxonomic composition and the resistome was supported by a Procrustes analysis (p < 0.001). Notably, regional signatures were observed regarding the taxonomic and resistome profiles, as samples from the same region clustered together on both ordinates. Additionally, network analysis illuminated the intricate links between taxonomy and AMR at the contig level. Our deep sequencing efforts not only mapped the microbial landscape but also expanded the genomic catalog with newly characterized metagenome-assembled genomes (MAGs), boosting the classification of reads by 12.85 %. In conclusion, this study underscores the value of metagenomic approaches in surveillance of surface waters, enhancing our understanding of microbial and AMR dynamics with far-reaching public health and ecological ramifications.
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Affiliation(s)
- Xinyang Huang
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA
| | - Magaly Toro
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA; Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Angélica Reyes-Jara
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile (PUC), Santiago, Chile
| | - Aiko D Adell
- Escuela de Medicina Veterinaria, Facultad de Ciencias de La Vida, Universidad Andrés Bello, Santiago, Chile
| | - Celso J B Oliveira
- Laboratório de Avaliação de Produtos de Origem Animal, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Raquel R Bonelli
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Sebastián Gutiérrez
- Instituto de Nutrición y Tecnología de los Alimentos (INTA), Universidad de Chile, Santiago, Chile
| | - Francisca P Álvarez
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile (PUC), Santiago, Chile
| | - Alan Douglas de Lima Rocha
- Laboratório de Avaliação de Produtos de Origem Animal, Centro de Ciências Agrárias, Universidade Federal da Paraíba (UFPB), Areia, Brazil
| | - Gabriela B Kraychete
- Laboratório de Investigação em Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Zhao Chen
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA
| | - Christopher Grim
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Eric Brown
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Rebecca Bell
- Center for Food Safety and Applied Nutrition (CFSAN), Food and Drug Administration, College Park, MD, USA
| | - Jianghong Meng
- Joint Institute for Food Safety and Applied Nutrition (JIFSAN), Food Safety and Security Systems (CFS(3)), University of Maryland, College Park, MD, USA.
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Phuong-Nguyen K, McGee SL, Aston-Mourney K, Mcneill BA, Mahmood MQ, Rivera LR. Yoyo Dieting, Post-Obesity Weight Loss, and Their Relationship with Gut Health. Nutrients 2024; 16:3170. [PMID: 39339770 PMCID: PMC11435324 DOI: 10.3390/nu16183170] [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: 08/21/2024] [Revised: 09/13/2024] [Accepted: 09/18/2024] [Indexed: 09/30/2024] Open
Abstract
Excessive body weight is associated with many chronic metabolic diseases and weight loss, so far, remains the gold standard treatment. However, despite tremendous efforts exploring optimal treatments for obesity, many individuals find losing weight and maintaining a healthy body weight difficult. Weight loss is often not sustainable resulting in weight regain and subsequent efforts to lose weight. This cyclic pattern of weight loss and regain is termed "yoyo dieting" and predisposes individuals to obesity and metabolic comorbidities. How yoyo dieting might worsen obesity complications during the weight recurrence phase remains unclear. In particular, there is limited data on the role of the gut microbiome in yoyo dieting. Gut health distress, especially gut inflammation and microbiome perturbation, is strongly associated with metabolic dysfunction and disturbance of energy homeostasis in obesity. In this review, we summarise current evidence of the crosstalk between the gastrointestinal system and energy balance, and the effects of yoyo dieting on gut inflammation and gut microbiota reshaping. Finally, we focus on the potential effects of post-dieting weight loss in improving gut health and identify current knowledge gaps within the field, including gut-derived peptide hormones and their potential suitability as targets to combat weight regain, and how yoyo dieting and associated changes in the microbiome affect the gut barrier and the enteric nervous system, which largely remain to be determined.
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Affiliation(s)
- Kate Phuong-Nguyen
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Sean L McGee
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Kathryn Aston-Mourney
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Bryony A Mcneill
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Malik Q Mahmood
- School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
| | - Leni R Rivera
- Institute for Mental and Physical Health and Clinical Translation (IMPACT), School of Medicine, Deakin University, Waurn Ponds, VIC 3216, Australia
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Aljarba TM, Abdel Bar FM, Sherif AE, Elekhnawy E, Magdy G, Samra RM. HPLC-PDA Analysis of Polyacetylene Glucosides from Launaea capitata and Their Antibacterial and Antibiofilm Properties against Klebsiella pneumoniae. Pharmaceuticals (Basel) 2024; 17:1214. [PMID: 39338376 PMCID: PMC11434657 DOI: 10.3390/ph17091214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2024] [Revised: 09/07/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Background/Objectives: Bacterial resistance and virulence are challenges in treating bacterial infections, especially in Klebsiella pneumoniae. Plants of the Launaea Cass. genus are used traditionally to address a variety of diseases, including infections, but the potential bioactive compounds are unknown. Our goals were to verify the potential contribution of two major polyacetylene glycosides isolated from our previous study, (3S,6E,12E)-6,12-tetradecadiene-8,10-diyne-1-ol 3-O-β-D-glucopyranoside (1) and bidensyneoside A (syn. gymnasterkoreaside A) [(3R,8E)-3-hydroxy-8-decene-4,6-diyn-1-yl β-D-glucopyranoside] (2), to the anti-infective properties of Launaea capitata and to develop a dependable HPLC method for their quantification; Methods: On a panel of K. pneumoniae clinical isolates, the antibacterial action of 1, 2, and the methanol extract of the whole L. capitata plant were evaluated by broth microdilution assay, while their antibiofilm action was evaluated by the crystal violet assay. qRT-PCR investigated luxS, mrkA, wzm, and wbbm genes that encode biofilm formation and quorum sensing (QS). The antibacterial activity of 1 was revealed by employing mice infection. Chromatographic separation was conducted using isocratic elution on a Hypersil BDS C18 column using a photodiode array (PDA) detector; Results: Compound 1 showed antibacterial activity with MIC values of 16-128 µg/mL. It remarkably reduced strong and moderate biofilm-forming bacterial isolates from 84.21% to 42.1% compared with the extract (68.42%) and 2 (78.95%). Compound 1 also downregulated the QS genes, luxS, mrkA, wzm, and wbbm, and exhibited in vivo antibacterial action through the enhancement of the histological construction of the liver and spleen, decreased TNF-α immunoreaction, bacterial burden, and the inflammatory mediators IL-1β and IL-6. A successful HPLC-PDA approach was developed to separate the binary mixture of 1 and 2 in less than 10 min with high sensitivity, with detection limits down to 0.518 and 0.095 µg/mL for 1 and 2, respectively; Conclusions: Compound 1 exhibited remarkable antibacterial and antibiofilm properties and may contribute to the anti-infectious traditional uses of L. capitata, meriting further clinical studies and serving as a reliable quality control biomarker for the plant.
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Affiliation(s)
- Tariq M Aljarba
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
| | - Fatma M Abdel Bar
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Asmaa E Sherif
- Department of Pharmacognosy, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj 11942, Saudi Arabia
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
| | - Engy Elekhnawy
- Pharmaceutical Microbiology Department, Faculty of Pharmacy, Tanta University, Tanta 31527, Egypt
| | - Galal Magdy
- Pharmaceutical Analytical Chemistry Department, Faculty of Pharmacy, Kafrelsheikh University, Kafrelsheikh 33511, Egypt
- Department of Pharmaceutical Analytical Chemistry, Faculty of Pharmacy, Mansoura National University, Gamasa 7731168, Egypt
| | - Reham M Samra
- Department of Pharmacognosy, Faculty of Pharmacy, Mansoura University, Mansoura 35516, Egypt
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Worku M, Belay S, Molla T, Aynalem M, Assefa M. Prevalence and antimicrobial susceptibility pattern of Klebsiella pneumoniae isolated from various clinical specimens at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. BMC Infect Dis 2024; 24:917. [PMID: 39232652 PMCID: PMC11373452 DOI: 10.1186/s12879-024-09811-1] [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: 07/19/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND K. pneumoniae become multidrug-resistant (MDR) and commonly poses a serious health threat to patients due to limited therapeutic options. As a result, determining the prevalence and antimicrobial susceptibility patterns of K. pneumoniae isolates from clinical specimens is substantial to patient diagnosis and treatment. METHODS AND MATERIALS A retrospective cross-sectional study was conducted from July 2021 to July 2022 at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. Sociodemographic and laboratory data were collected from registered books using a data collection sheet. All types of samples were collected and processed using standard procedures. Identification of K. pneumoniae was done using Gram stain, colony characterization on culture media, anda series of biochemical tests. Antimicrobial susceptibility testing was done by the Kirby Bauer disc diffusion technique. The data were entered using Epi-info version 7 and exported to SPSS version 20 for analysis. RESULTS Among 2600 clinical specimens, 735 (28.3%) were positive for bacteria, and K. pneumoniae isolates accounted for 147 (20%). Most of them were isolated from neonates and mainly obtained from blood specimens (81.6%). These isolates were 100% resistant to Nalidixic acid, Cefotaxime, and Cefazolin. About 84% and 83.3% of the isolates were also resistant to Ceftriaxone and Tetracycline, respectively. However, they are sensitive to Nitrofurantoin (86.6%), Imipenem (85.7%), Meropenem (79%), and Amikacin (78.3%). The overall proportion of MDR K. pneumoniae isolates accounted for 57.1%. CONCLUSION The magnitude of MDR K. pneumoniae was very alarming. Therefore, strengthening antimicrobial stewardship programs and antimicrobial surveillance practices is strongly recommended in the study area.
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Affiliation(s)
- Minichil Worku
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Solomon Belay
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Tigist Molla
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Melak Aynalem
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| | - Muluneh Assefa
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia.
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Fleeman R, Beckman R, Cella E, Azarian T, Rendueles O. Diverse polysaccharide production and biofilm formation abilities of clinical Klebsiella pneumoniae. RESEARCH SQUARE 2024:rs.3.rs-4630973. [PMID: 39149462 PMCID: PMC11326372 DOI: 10.21203/rs.3.rs-4630973/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
Klebsiella pneumoniae infections have become a growing threat for human health. The lack of understanding of the relationship between antibiotic resistance, mucoviscosity, and biofilm formation in clinical isolates impedes our abilities to effectively predict K. pneumoniae infection outcomes. These traits are also associated with fitness in natural populations and more specifically within a host. The Multidrug-Resistant Organism Repository and Surveillance Network offers a unique opportunity into the genetic and phenotypic variabilities in the K. pneumoniae isolates encountered in the clinics today. To this end, we compared the genetic profiles of these isolates with the phenotypic biofilm formation abilities, percent mucoviscosity, and growth rates. We found most isolates formed limited biofilm, although a select group of isolates could form extremely robust biofilms. Variation in biofilm formation could not be explained by difference in growth rate, suggesting specific genetic and physical determinants. Interestingly, the most mucoid strains in the populations were lacking the genetic element regulating the mucoid phenotype and three of these isolates were able to form robust biofilms. There was a significant phenotype-genotype correlation with decreased biofilm formation and an insertion sequence in the transcriptional activator of the type III fimbrial system. Finally, confocal microscopy highlighted the structural and spatial heterogeneity of biofilm among the most robust biofilm formers not detected by traditional methods. The combination of phenotypic, genomic and image analyses allowed us to reveal an unexpected phenotypic diversity and an intricate relation between growth, mucoviscosity and specific virulence-associated genetic determinants.
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6
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Jomehzadeh N, Rahimzadeh M, Ahmadi B. Molecular detection of extended-spectrum β-lactamase- and carbapenemase-producing Klebsiella pneumoniae isolates in southwest Iran. Trop Med Int Health 2024. [PMID: 39095950 DOI: 10.1111/tmi.14043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
OBJECTIVE The global emergence of carbapenem-resistant Klebsiella pneumoniae is considered a significant contemporary concern., as carbapenems are the last resort for treating infections caused by multidrug-resistant Gram-negative bacteria. This study aimed to investigate the carbapenem-resistance genes in extended-spectrum β-lactamase producing K. pneumoniae isolates. METHODS Seventy-five non-duplicate clinical K. pneumoniae strains were isolated from urine, blood, sputum, and wound samples. Antimicrobial susceptibility tests for 12 different antibiotics were performed using the disk diffusion method, followed by determining minimum inhibitory concentrations of imipenem and meropenem. Phenotypic detection of extended-spectrum β-lactamase and carbapenemase enzymes was performed by double-disc synergy test and modified Hodge test, respectively. PCR assay further investigated resistant isolates for extended-spectrum β-lactamase and carbapenemase-encoding genes. RESULTS The highest and lowest resistance rates were observed against ampicillin (93.3%) and tigecycline (9.3%). According to phenotypic tests, 46.7% of isolates were positive for extended-spectrum β-lactamase enzymes and 52.8% for carbapenemase. A total of 11 isolates contained carbapenemase genes, with blaOXA-48 (19.4%; 7/36) being the predominant gene, followed by blaNDM (8.3%; 3/36). CONCLUSION The study's findings reveal the alarming prevalence of beta-lactamase enzymes in K. pneumoniae strains. Early detection of carbapenem-resistant isolates and effective infection control measures are necessary to minimise further spread, as carbapenem resistance has become a public health concern.
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Affiliation(s)
- Nabi Jomehzadeh
- Department of Basic Medical Sciences, Faculty of Medicine, Abadan University of Medical Sciences, Abadan, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | | | - Bahare Ahmadi
- Department of Basic Medical Sciences, Faculty of Medicine, Abadan University of Medical Sciences, Abadan, Iran
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El Naggar NM, Shawky RM, Serry FME, Emara M. The Increased Prevalence of rmpA Gene in Klebsiella pneumoniae Isolates Coharboring blaNDM and blaOXA-48-like Genes. Microb Drug Resist 2024; 30:317-324. [PMID: 38770796 DOI: 10.1089/mdr.2023.0296] [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] [Indexed: 05/22/2024] Open
Abstract
The emergence of carbapenemase-producing Klebsiella pneumoniae poses a substantial risk to public health. It is essential to comprehend the influence of carbapenemase on the virulence characteristics of K. pneumoniae in order to devise successful strategies for combating these infections. In this study, we explored the distribution disparity of virulence determinants between carbapenemase-producing (CP-Kp, n = 52) and carbapenemase-nonproducing (CN-Kp, n = 43) isolates. The presence of carbapenemases was detected via the modified carbapenem inactivation method and confirmed by PCR. The New Delhi metallo-β-lactamase (blaNDM) and Oxacillinase-48-like (blaOXA-48-like) genes were the most prevalent (94.23% and 76.92%, respectively) in CP-Kp isolates. Coexistence of blaNDM and blaOXA-48-like was observed in 71.15% of isolates, whereas 5.77% coharbored blaNDM and blaKPC. PCR analysis revealed the presence of several virulence genes, including adhesins (fimH, 92.63%, mrkD, 97.89%), capsule-associated virulence (uge, 90.53%), the K2 capsule serotype (k2, 6.32%), the iron acquisition system (kfu, 23.16%), and the regulator of mucoid phenotype (rmpA, 28.42%). A significantly higher prevalence of rmpA was detected in the CP-Kp compared with the CN-Kp (24/52 vs. 3/43, p < 0.0001), indicating a potential association between rmpA and carbapenemase acquisition. In addition, the majority of rmpA (22/24) positive isolates in the CP-Kp isolates coharbored blaNDM and either blaOXA-48-like or blaKPC.
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Affiliation(s)
- Nora M El Naggar
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Riham M Shawky
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
| | - Fathy M E Serry
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
| | - Mohamed Emara
- Department of Microbiology and Immunology, Faculty of Pharmacy, Helwan University, Cairo, Egypt
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Jiang M, Zhang H, Lu W, Qiu X, Lin C, Zhao R, Li Q, Wu Q. Molecular Characteristics of Virulence Genes in Carbapenem-Resistant and Carbapenem-Sensitive Klebsiella Pneumoniae in Relation to Different Capsule Serotypes in Ningbo, China. Infect Drug Resist 2024; 17:2109-2120. [PMID: 38828374 PMCID: PMC11141717 DOI: 10.2147/idr.s461666] [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: 03/01/2024] [Accepted: 04/29/2024] [Indexed: 06/05/2024] Open
Abstract
Background Klebsiella pneumoniae (KP) is a common nosocomial pathogen. Capsules are an important component of KP's virulence, among which the K1, K2, K5, K20, K54, and K57 serotypes are predominant and exhibit varying degrees of virulence. Methods The capsule and virulence genes of 150 carbapenem-resistant Klebsiella pneumoniae (CRKP) and 213 carbapenem-sensitive Klebsiella pneumoniae (CSKP) isolates were examined by polymerase chain reaction (PCR). The isolates were tested for hypermucoviscosity by string tests. Phylogenetic relationships between KP isolates were analyzed using multilocus sequence typing (MLST) and a Galleria mellonella infection model confirmed the differences in virulence. Results A total of 111 of 363 isolates of KP were detected, the highest detected serotypes were K1, K5, and K2, and CSKP was detected more frequently than CRKP. There was a greater prevalence of K1 and K2 serotypes in CSKP, while in CRKP, K5 serotypes were more prevalent. K1 isolates had the highest detection rates for hypermucoviscosity Klebsiella pneumoniae (hmKP) and hypervirulent Klebsiella pneumoniae (hvKP), and carried the most virulence genes. K54 isolates had the lowest detection rate of hmKP while K5 isolates had the lowest detection rate of hvKP and carried the fewest virulence genes. MLST results for serotypes K1, K20, and K57 showed significant homogeneity, while those for serotypes K2, K5, and K54 showed diversity. The Galleria mellonella infection model showed that the K1 serotype was the most virulent and the K54 serotype was the weakest. Conclusion CSKP isolates were detected more frequently than CRKP isolates for capsular serotype detection. K1 isolates had the most virulence gene and strongest virulence, K5 isolates carried the fewest virulence genes, and K54 isolates had the weakest virulence. Furthermore, significant homogeneity was observed among K1, K20, and K57 isolates.
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Affiliation(s)
- Min Jiang
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Hui Zhang
- Clinical Laboratory, Ninghai County Chengguan Hospital, Ningbo, Zhejiang Province, People’s Republic of China
| | - Wenjun Lu
- Intensive Care Units, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Xuedan Qiu
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Chenyao Lin
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Rongqing Zhao
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Qingcao Li
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
| | - Qiaoping Wu
- Clinical Laboratory, The Affiliated LiHuiLi Hospital of Ningbo University, Ningbo, Zhejiang Province, People’s Republic of China
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Marzouk E, Abalkhail A, ALqahtani J, Alsowat K, Alanazi M, Alzaben F, Alnasser A, Alasmari A, Rawway M, Draz A, Abu-Okail A, Altwijery A, Moussa I, Alsughayyir S, Alamri S, Althagafi M, Almaliki A, Elmanssury AE, Elbehiry A. Proteome analysis, genetic characterization, and antibiotic resistance patterns of Klebsiella pneumoniae clinical isolates. AMB Express 2024; 14:54. [PMID: 38722429 PMCID: PMC11082098 DOI: 10.1186/s13568-024-01710-7] [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: 02/10/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is a member of the ESKAPE group and is responsible for severe community and healthcare-associated infections. Certain Klebsiella species have very similar phenotypes, which presents a challenge in identifying K. pneumoniae. Multidrug-resistant K. pneumoniae is also a serious global problem that needs to be addressed. A total of 190 isolates were isolated from urine (n = 69), respiratory (n = 52), wound (n = 48) and blood (n = 21) samples collected from various hospitals in the Al-Qassim, Saudi Arabia, between March 2021 and October 2022. Our study aimed to rapidly and accurately detect K. pneumoniae using the Peptide Mass Fingerprinting (PMF) technique, confirmed by real-time PCR. Additionally, screening for antibiotic susceptibility and resistance was conducted. The primary methods for identifying K. pneumoniae isolates were culture, Gram staining, and the Vitek® 2 ID Compact system. An automated MALDI Biotyper (MBT) instrument was used for proteome identification, which was subsequently confirmed using SYBR green real-time polymerase chain reaction (real-time PCR) and microfluidic electrophoresis assays. Vitek® 2 AST-GN66 cards were utilized to evaluate the antimicrobial sensitivity of K. pneumoniae isolates. According to our results, Vitek® 2 Compact accurately identified 178 out of 190 (93.68%) K. pneumoniae isolates, while the PMF technique correctly detected 188 out of 190 (98.95%) isolates with a score value of 2.00 or higher. Principal component analysis was conducted using MBT Compass software to classify K. pneumoniae isolates based on their structure. Based on the analysis of the single peak intensities generated by MBT, the highest peak values were found at 3444, 5022, 5525, 6847, and 7537 m/z. K. pneumoniae gene testing confirmed the PMF results, with 90.53% detecting entrobactin, 70% detecting 16 S rRNA, and 32.63% detecting ferric iron uptake. The resistance of the K. pneumoniae isolates to antibiotics was as follows: 64.75% for cefazolin, 62.63% for trimethoprim/sulfamethoxazole, 59.45% for ampicillin, 58.42% for cefoxitin, 57.37% for ceftriaxone, 53.68% for cefepime, 52.11% for ampicillin-sulbactam, 50.53% for ceftazidime, 52.11% for ertapenem, and 49.47% for imipenem. Based on the results of the double-disk synergy test, 93 out of 190 (48.95%) K. pneumoniae isolates were extended-spectrum beta-lactamase. In conclusion, PMF is a powerful analytical technique used to identify K. pneumoniae isolates from clinical samples based on their proteomic characteristics. K. pneumoniae isolates have shown increasing resistance to antibiotics from different classes, including carbapenem, which poses a significant threat to human health as these infections may become difficult to treat.
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Affiliation(s)
- Eman Marzouk
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia.
| | - Adil Abalkhail
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
| | - Jamaan ALqahtani
- Family Medicine Department, King Fahad Armed Hospital, 23311, Jeddah, Saudi Arabia
| | - Khalid Alsowat
- Pharmacy Department, Prince Sultan Armed Forces Hospital, 42375, Medina, Saudi Arabia
| | - Menwer Alanazi
- Dental Department, King Salman Armed Forces Hospital, 47521, Tabuk, Saudi Arabia
| | - Feras Alzaben
- Department of Food Service, King Fahad Armed Forces Hospital, 23311, Jeddah, Saudi Arabia
| | - Abdulaziz Alnasser
- Psychiatry Department, Prince Sultan Military Medical City, 11632, Riyadh, Saudi Arabia
| | - Anas Alasmari
- Neurology department, king Fahad military hospital, 23311, Jeddah, Saudi Arabia
| | - Mohammed Rawway
- Biology Department, College of Science, Jouf University, 42421, Sakaka, Saudi Arabia
- Botany and Microbiology Department, Faculty of Science, Al-Azhar University, 71524, Assiut, Egypt
| | - Abdelmaged Draz
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
| | - Akram Abu-Okail
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, Qassim University, 52571, Buraydah, Saudi Arabia
| | | | - Ihab Moussa
- Department of Botany and Microbiology, College of Science, King Saud University, 11451, Riyadh, Saudi Arabia
| | - Sulaiman Alsughayyir
- Medical Administration, Armed Forces Medical Services, 12426, Riyadh, Saudi Arabia
| | - Saleh Alamri
- Prince Sultan Military Medical City, 13525, Riyadh, Saudi Arabia
| | - Mohammed Althagafi
- Laboratory Department, Armed Forces Center for Health Rehabilitation, 21944, Taif, Saudi Arabia
| | - Abdulrahman Almaliki
- Physiotherapy Department, Armed Forces Center for Health Rehabilitation, 21944, Taif, Saudi Arabia
| | - Ahmed Elnadif Elmanssury
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
| | - Ayman Elbehiry
- Department of Public Health, College of Applied Medical Sciences, Qassim University, Buraydah, 51452 , P.O. Box 6666, Saudi Arabia
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10
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De los Santos L, Beckman RL, DeBarro C, Keener JE, Torres MD, de la Fuente-Nunez C, Brodbelt JS, Fleeman RM. Polyproline peptide targets Klebsiella pneumoniae polysaccharides to collapse biofilms. CELL REPORTS. PHYSICAL SCIENCE 2024; 5:101869. [PMID: 38605913 PMCID: PMC11008256 DOI: 10.1016/j.xcrp.2024.101869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
Hypervirulent Klebsiella pneumoniae is known for its increased extracellular polysaccharide production. Biofilm matrices of hypervirulent K. pneumoniae have increased polysaccharide abundance and are uniquely susceptible to disruption by peptide bactenecin 7 (bac7 (1-35)). Here, using confocal microscopy, we show that polysaccharides within the biofilm matrix collapse following bac7 (1-35) treatment. This collapse led to the release of cells from the biofilm, which were then killed by the peptide. Characterization of truncated peptide analogs revealed that their interactions with polysaccharide were responsible for the biofilm matrix changes that accompany bac7 (1-35) treatment. Ultraviolet photodissociation mass spectrometry with the parental peptide or a truncated analog bac7 (10-35) reveal the important regions for bac7 (1-35) complexing with polysaccharides. Finally, we tested bac7 (1-35) using a murine skin abscess model and observed a significant decrease in the bacterial burden. These findings unveil the potential of bac7 (1-35) polysaccharide interactions to collapse K. pneumoniae biofilms.
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Affiliation(s)
- Laura De los Santos
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Robert L. Beckman
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - Christina DeBarro
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
| | - James E. Keener
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Marcelo D.T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA 19104, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Renee M. Fleeman
- Division of Immunity and Pathogenesis, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32827, USA
- X (formerly Twitter): @FleemanLab
- Lead contact
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11
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Abdulkadir N, Saraiva JP, Zhang J, Stolte S, Gillor O, Harms H, Rocha U. Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater. Microbiol Spectr 2024; 12:e0291823. [PMID: 38289113 PMCID: PMC10913551 DOI: 10.1128/spectrum.02918-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 11/25/2023] [Indexed: 03/06/2024] Open
Abstract
Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species ( average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities. IMPORTANCE Antimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.
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Affiliation(s)
- Nafi’u Abdulkadir
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Joao Pedro Saraiva
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
| | - Junya Zhang
- Department of Isotope Biogeochemistry, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Stefan Stolte
- Institute of Water Chemistry, Technical University of Dresden, Dresden, Germany
| | - Osnat Gillor
- Zuckerberg Institute for Water Research, J. Blaustein Institutes for Desert Research, Ben Gurion University, Midreshet Ben Gurion, Israel
| | - Hauke Harms
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
- Department of Biochemistry, Faculty of Natural Science, University of Leipzig, Leipzig, Germany
| | - Ulisses Rocha
- Department of Environmental Microbiology, Helmholtz Center for Environmental Research-UFZ, Leipzig, Germany
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12
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Russo TA, Alvarado CL, Davies CJ, Drayer ZJ, Carlino-MacDonald U, Hutson A, Luo TL, Martin MJ, Corey BW, Moser KA, Rasheed JK, Halpin AL, McGann PT, Lebreton F. Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance. mBio 2024; 15:e0286723. [PMID: 38231533 PMCID: PMC10865842 DOI: 10.1128/mbio.02867-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Distinguishing hypervirulent (hvKp) from classical Klebsiella pneumoniae (cKp) strains is important for clinical care, surveillance, and research. Some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g., siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Furthermore, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49 K. pneumoniae strains that possessed some combinations of iucA, iroB, peg-344, rmpA, and rmpA2 and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N = 16) or cKp (N = 33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid's Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression, the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49), respectively. These findings can be used to inform the identification of hvKp.IMPORTANCEHypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistant K. pneumoniae isolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all five of the biomarkers iucA, iroB, peg-344, rmpA, and rmpA2 was most accurate (94%); the presence of ≥4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which, in turn, would assist in optimizing patient care.
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Affiliation(s)
- Thomas A. Russo
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
- Department of Microbiology and Immunology, University at Buffalo, Buffalo, New York, USA
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo, State University of New York, Buffalo, New York, USA
| | - Cassandra L. Alvarado
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Connor J. Davies
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Zachary J. Drayer
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Ulrike Carlino-MacDonald
- Veterans Administration Western New York Healthcare System, University at Buffalo, Buffalo, New York, USA
- Department of Medicine, University at Buffalo, Buffalo, New York, USA
| | - Alan Hutson
- Department of Biostatistics and Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, New York, USA
| | - Ting L. Luo
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Melissa J. Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Brendan W. Corey
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Kara A. Moser
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - J. Kamile Rasheed
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Alison L. Halpin
- Division of Healthcare Quality Promotion, U.S. Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Patrick T. McGann
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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13
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Bai R, Guo J. Interactions and Implications of Klebsiella pneumoniae with Human Immune Responses and Metabolic Pathways: A Comprehensive Review. Infect Drug Resist 2024; 17:449-462. [PMID: 38333568 PMCID: PMC10849896 DOI: 10.2147/idr.s451013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/26/2024] [Indexed: 02/10/2024] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae), a significant contributor to the global challenge of antibiotic resistance, is not only a ubiquitous component of the human microbiome but also a potent pathogen capable of causing a spectrum of diseases. This review provides a thorough analysis of the intricate interactions between K. pneumoniae and the human immune system, elucidating its substantial impact on metabolic processes. We explore the mechanisms employed by K. pneumoniae to evade and manipulate immune responses, including molecular mimicry, immune modulation, and biofilm formation. The review further investigates the bacterium's influence on metabolic pathways, particularly glycolysis, highlighting how these interactions exacerbate disease severity. The emergence of multidrug-resistant and extremely drug-resistant strains within the Enterobacteriaceae family has heightened the public health crisis, underscoring the urgency for comprehensive research. We investigate the roles of the host's complement system, autophagy, cell death mechanisms, and various cytokines in combating K. pneumoniae infections, shedding light on areas that warrant further academic investigation. Additionally, the review discusses the challenges posed by K1- and K2-capsule polysaccharides in vaccine development due to their complex molecular structures and adhesive properties. Acknowledging the limited availability of effective antimicrobials, this review advocates for exploring alternative approaches such as immunotherapeutics, vaccinations, and phage therapy. We consolidate current knowledge on K. pneumoniae, covering classical and non-classical subtypes, antimicrobial resistance-mediated genes, virulence factors, and epidemiological trends in isolation and antibiotic resistance rates. This comprehensive review not only advances our understanding of K. pneumoniae but also underscores the imperative for ongoing research and collaborative efforts to develop new prevention and treatment strategies against this formidable pathogen.
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Affiliation(s)
- Ruojing Bai
- Department of Geriatric Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People’s Republic of China
| | - Jun Guo
- Department of Geriatric Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, People’s Republic of China
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14
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Gauba A, Rahman KM. Evaluation of Antibiotic Resistance Mechanisms in Gram-Negative Bacteria. Antibiotics (Basel) 2023; 12:1590. [PMID: 37998792 PMCID: PMC10668847 DOI: 10.3390/antibiotics12111590] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 10/30/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Multidrug-resistant Gram-negative bacterial infections are exponentially increasing, posing one of the most urgent global healthcare and economic threats. Due to the lack of new therapies, the World Health Organization classified these bacterial species as priority pathogens in 2017, known as ESKAPE pathogens. This classification emphasizes the need for urgent research and development of novel targeted therapies. The majority of these priority pathogens are Gram-negative species, which possess a structurally dynamic cell envelope enabling them to resist multiple antibiotics, thereby leading to increased mortality rates. Despite 6 years having passed since the WHO classification, the progress in generating new treatment ideas has not been sufficient, and antimicrobial resistance continues to escalate, acting as a global ticking time bomb. Numerous efforts and strategies have been employed to combat the rising levels of antibiotic resistance by targeting specific resistance mechanisms. These mechanisms include antibiotic inactivating/modifying enzymes, outer membrane porin remodelling, enhanced efflux pump action, and alteration of antibiotic target sites. Some strategies have demonstrated clinical promise, such as the utilization of beta-lactamase inhibitors as antibiotic adjuvants, as well as recent advancements in machine-based learning employing artificial intelligence to facilitate the production of novel narrow-spectrum antibiotics. However, further research into an enhanced understanding of the precise mechanisms by which antibiotic resistance occurs, specifically tailored to each bacterial species, could pave the way for exploring narrow-spectrum targeted therapies. This review aims to introduce the key features of Gram-negative bacteria and their current treatment approaches, summarizing the major antibiotic resistance mechanisms with a focus on Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Additionally, potential directions for alternative therapies will be discussed, along with their relative modes of action, providing a future perspective and insight into the discipline of antimicrobial resistance.
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Affiliation(s)
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London SE1 9NH, UK;
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15
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Russo TA, Alvarado CL, Davies CJ, Drayer ZJ, Carlino-MacDonald U, Hutson A, Luo TL, Martin MJ, Corey BW, Moser KA, Rasheed JK, Halpin AL, McGann PT, Lebreton F. Differentiation of hypervirulent and classical Klebsiella pneumoniae with acquired drug resistance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.30.547231. [PMID: 37961280 PMCID: PMC10634668 DOI: 10.1101/2023.06.30.547231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Distinguishing hypervirulent (hvKp) from classical Klebsiella pneumoniae (cKp) strains is important for clinical care, surveillance, and research. Some combination of iucA, iroB, peg-344, rmpA, and rmpA2 are most commonly used, but it is unclear what combination of genotypic or phenotypic markers (e.g. siderophore concentration, mucoviscosity) most accurately predicts the hypervirulent phenotype. Further, acquisition of antimicrobial resistance may affect virulence and confound identification. Therefore, 49 K. pneumoniae strains that possessed some combination of iucA, iroB, peg-344, rmpA, and rmpA2 and had acquired resistance were assembled and categorized as hypervirulent hvKp (hvKp) (N=16) or cKp (N=33) via a murine infection model. Biomarker number, siderophore production, mucoviscosity, virulence plasmid's Mash/Jaccard distances to the canonical pLVPK, and Kleborate virulence score were measured and evaluated to accurately differentiate these pathotypes. Both stepwise logistic regression and a CART model were used to determine which variable was most predictive of the strain cohorts. The biomarker count alone was the strongest predictor for both analyses. For logistic regression the area under the curve for biomarker count was 0.962 (P = 0.004). The CART model generated the classification rule that a biomarker count = 5 would classify the strain as hvKP, resulting in a sensitivity for predicting hvKP of 94% (15/16), a specificity of 94% (31/33), and an overall accuracy of 94% (46/49). Although a count of ≥ 4 was 100% (16/16) sensitive for predicting hvKP, the specificity and accuracy decreased to 76% (25/33) and 84% (41/49) respectively. These findings can be used to inform the identification of hvKp. Importance Hypervirulent Klebsiella pneumoniae (hvKp) is a concerning pathogen that can cause life-threatening infections in otherwise healthy individuals. Importantly, although strains of hvKp have been acquiring antimicrobial resistance, the effect on virulence is unclear. Therefore, it is of critical importance to determine whether a given antimicrobial resistant K. pneumoniae isolate is hypervirulent. This report determined which combination of genotypic and phenotypic markers could most accurately identify hvKp strains with acquired resistance. Both logistic regression and a machine-learning prediction model demonstrated that biomarker count alone was the strongest predictor. The presence of all 5 of the biomarkers iucA, iroB, peg-344, rmpA, and rmpA2 was most accurate (94%); the presence of ≥ 4 of these biomarkers was most sensitive (100%). Accurately identifying hvKp is vital for surveillance and research, and the availability of biomarker data could alert the clinician that hvKp is a consideration, which in turn would assist in optimizing patient care.
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16
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Noreika A, Stankevičiūtė J, Rutkienė R, Meškys R, Kalinienė L. Exploring the enzymatic activity of depolymerase gp531 from Klebsiella pneumoniae jumbo phage RaK2. Virus Res 2023; 336:199225. [PMID: 37741345 PMCID: PMC10550766 DOI: 10.1016/j.virusres.2023.199225] [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: 07/19/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Klebsiella pneumoniae poses a major global challenge due to its virulence, multidrug resistance, and nosocomial nature. Thus, bacteriophage-derived proteins are extensively being investigated as a means to combat this bacterium. In this study, we explored the enzymatic specificity of depolymerase gp531, encoded by the jumbo bacteriophage vB_KleM_RaK2 (RaK2). We used two different methods to modify the reducing end of the oligosaccharides released during capsule hydrolysis with gp531. Subsequent acidic cleavage with TFA, followed by TLC and HPLC-MS analyses, revealed that RaK2 gp531 is a β-(1→4)-endoglucosidase. The enzyme specifically recognizes and cleaves the capsular polysaccharide (CPS) of the Klebsiella pneumoniae K54 serotype, releasing K-unit monomers (the main product), dimers, and trimers. Depolymerase gp531 remains active from 10 to 50 °C and in the pH 3-8 range, indicating its stability and versatility. Additionally, we demonstrated that gp531's activity is not affected by CPS acetylation, which is influenced by the growth conditions of the bacterial culture. Overall, our findings provide valuable insights into the enzymatic activity of the first characterized depolymerase targeting the capsule of the clinically relevant K54 serotype of K. pneumoniae.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Laura Kalinienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
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17
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Zhang QB, Zhu P, Zhang S, Rong YJ, Huang ZA, Sun LW, Cai T. Hypervirulent Klebsiella pneumoniae detection methods: a minireview. Arch Microbiol 2023; 205:326. [PMID: 37672079 DOI: 10.1007/s00203-023-03665-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/15/2023] [Accepted: 08/18/2023] [Indexed: 09/07/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp), characterized by high virulence and epidemic potential, has become a global public health challenge. Therefore, improving the identification of hvKp and enabling earlier and faster detection in the community to support subsequent effective treatment and prevention of hvKp are an urgent issue. To address these issues, a number of assays have emerged, such as String test, Galleria mellonella infection test, PCR, isothermal exponential amplification, and so on. In this paper, we have collected articles on the detection methods of hvKp and conducted a retrospective review based on two aspects: traditional detection technology and biomarker-based detection technology. We summarize the advantages and limitations of these detection methods and discuss the challenges as well as future directions, hoping to provide new insights and references for the rapid detection of hvKp in the future. The aim of this study is to focus on the research papers related to Hypervirulent Klebsiella pneumoniae involving the period from 2012 to 2022. We conducted searches using the keywords "Hypervirulent Klebsiella pneumoniae, biomarkers, detection techniques" on ScienceDirect and Google Scholar. Additionally, we also searched on PubMed, using MeSH terms associated with the keywords (such as Klebsiella pneumoniae, Klebsiella Infections, Virulence, Biomarkers, diagnosis, etc.).
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Affiliation(s)
- Qi-Bin Zhang
- The Affiliated People's Hospital of Ningbo University, Ningbo, China
| | - Peng Zhu
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Shun Zhang
- Ningbo No. 2 Hospital, Ningbo, China
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Yan-Jing Rong
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | - Zuo-An Huang
- Ningbo No. 2 Hospital, Ningbo, China
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China
| | | | - Ting Cai
- Ningbo No. 2 Hospital, Ningbo, China.
- Ningbo Institute of Life and Health Industry, University of Chinese Academy of Sciences, Ningbo, China.
- Key Laboratory of Diagnosis and Treatment of Digestive System Tumors of Zhejiang Province, Ningbo, China.
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18
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Adukauskiene D, Ciginskiene A, Adukauskaite A, Koulenti D, Rello J. Clinical Features and Outcomes of VAP Due to Multidrug-Resistant Klebsiella spp.: A Retrospective Study Comparing Monobacterial and Polybacterial Episodes. Antibiotics (Basel) 2023; 12:1056. [PMID: 37370375 DOI: 10.3390/antibiotics12061056] [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: 05/10/2023] [Revised: 06/10/2023] [Accepted: 06/13/2023] [Indexed: 06/29/2023] Open
Abstract
VAP due to multidrug-resistant (MDR) bacteria is a frequent infection among patients in ICUs. Patient characteristics and mortality in mono- and polybacterial cases of VAP may differ. A single-centre, retrospective 3-year study was conducted in the four ICUs of a Lithuanian referral university hospital, aiming to compare both the clinical features and the 60-day ICU all-cause mortality of monobacterial and polybacterial MDR Klebsiella spp. VAP episodes. Of the 86 MDR Klebsiella spp. VAP episodes analyzed, 50 (58.1%) were polybacterial. The 60-day mortality was higher (p < 0.05) in polybacterial episodes: overall (50.0 vs. 27.8%), in the sub-group with less-severe disease (SOFA < 8) at VAP onset (45.5 vs. 15.0%), even with appropriate treatment (41.7 vs. 12.5%), and the sub-group of extended drug-resistant (XDR) Klebsiella spp. (46.4 vs. 17.6%). The ICU mortality (44.0 vs. 22.5%) was also higher in the polybacterial episodes. The monobacterial MDR Klebsiella spp. VAP was associated (p < 0.05) with prior hospitalization (61.1 vs. 40.0%), diabetes mellitus (30.6 vs. 5.8%), obesity (30.6 vs. 4.7%), prior antibiotic therapy (77.8 vs. 52.0%), prior treatment with cephalosporins (66.7 vs. 36.0%), and SOFA cardiovascular ≥ 3 (44.4 vs. 10.0%) at VAP onset. Patients with polybacterial VAP were more likely (p < 0.05) to be comatose (22.2 vs. 52.0%) and had a higher SAPS II score (median [IQR] 45.0 [35.25-51.1] vs. 50.0 [40.5-60.75]) at VAP onset. Polybacterial MDR Klebsiella spp. VAP had distinct demographic and clinical characteristics compared to monobacterial, and was associated with poorer outcomes.
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Affiliation(s)
- Dalia Adukauskiene
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Ausra Ciginskiene
- Medical Academy, Lithuanian University of Health Sciences, 44307 Kaunas, Lithuania
| | - Agne Adukauskaite
- Department of Cardiology and Angiology, University Hospital of Innsbruck, 6020 Innsbruck, Austria
| | - Despoina Koulenti
- Second Critical Care Department, Attikon University Hospital, 12462 Athens, Greece
- UQ Centre for Clinical Research (UQCCR), Faculty of Medicine, The Univesrity of Queensland, 4029 Brisbane, Australia
| | - Jordi Rello
- Vall d'Hebron Institute of Research, Vall d'Hebron Campus Hospital, 08035 Barcelona, Spain
- Clinical Research, CHU Nîmes, 30900 Nîmes, France
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Lucena ACR, Ferrarini MG, de Oliveira WK, Marcon BH, Morello LG, Alves LR, Faoro H. Modulation of Klebsiella pneumoniae Outer Membrane Vesicle Protein Cargo under Antibiotic Treatment. Biomedicines 2023; 11:1515. [PMID: 37371610 PMCID: PMC10294825 DOI: 10.3390/biomedicines11061515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 04/14/2023] [Accepted: 05/14/2023] [Indexed: 06/29/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen and an important propagator of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains. Like other Gram-negative bacteria, they secrete outer membrane vesicles (OMVs) that distribute virulence and resistance factors. Here, we subjected a K. pneumoniae-XDR to subinhibitory concentrations of meropenem, amikacin, polymyxin B, and a combination of these agents to evaluate changes in the protein cargo of OMVs through liquid chromatography-tandem mass spectrometry (LC-MS/MS). Genome sequencing of the clinical isolate K. pneumoniae strain HCD1 (KpHCD1) revealed the presence of 41 resistance genes and 159 virulence factors. We identified 64 proteins in KpHCD1-OMVs modulated with different antibiotic treatments involved in processing genetic information, environmental information, cell envelope formation, energy metabolism, and drug resistance. The OMV proteome expression profile suggests that OMVs may be associated with pathogenicity, survival, stress response, and resistance dissemination.
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Affiliation(s)
- Aline Castro Rodrigues Lucena
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Mariana Galvão Ferrarini
- Laboratoire de Biométrie et Biologie Évolutive, UMR 5558, CNRS, Université de Lyon, Université Lyon 1, 69622 Villeurbanne, France
| | - Willian Klassen de Oliveira
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Bruna Hilzendeger Marcon
- Laboratory for Basic Biology of Stem Cells, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Luis Gustavo Morello
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
| | - Lysangela Ronalte Alves
- Gene Expression Regulation Laboratory, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
| | - Helisson Faoro
- Laboratory for Applied Science and Technology in Health, Carlos Chagas Institute, FIOCRUZ, Curitiba 81350-010, PR, Brazil
- CHU de Quebec Research Center, Department of Microbiology, Infectious Disease and Immunology, University Laval, Quebec, QC G1V 0A6, Canada
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