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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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Kao CY, Zhang YZ, Bregente CJB, Kuo PY, Chen PK, Chao JY, Duong TTT, Wang MC, Thuy TTD, Hidrosollo JH, Tsai PF, Li YC, Lin WH. A 24-year longitudinal study of Klebsiella pneumoniae isolated from patients with bacteraemia and urinary tract infections reveals the association between capsular serotypes, antibiotic resistance, and virulence gene distribution. Epidemiol Infect 2023; 151:e155. [PMID: 37675569 PMCID: PMC10548544 DOI: 10.1017/s0950268823001486] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/20/2023] [Accepted: 08/26/2023] [Indexed: 09/08/2023] Open
Abstract
Longitudinal studies on the variations of phenotypic and genotypic characteristics of K. pneumoniae across two decades are rare. We aimed to determine the antimicrobial susceptibility and virulence factors for K. pneumoniae isolated from patients with bacteraemia or urinary tract infection (UTI) from 1999 to 2022. A total of 699 and 1,267 K. pneumoniae isolates were isolated from bacteraemia and UTI patients, respectively, and their susceptibility to twenty antibiotics was determined; PCR was used to identify capsular serotypes and virulence-associated genes. K64 and K1 serotypes were most frequently observed in UTI and bacteraemia, respectively, with an increasing frequency of K20, K47, and K64 observed in recent years. entB and wabG predominated across all isolates and serotypes; the least frequent virulence gene was htrA. Most isolates were susceptible to carbapenems, amikacin, tigecycline, and colistin, with the exception of K20, K47, and K64 where resistance was widespread. The highest average number of virulence genes was observed in K1, followed by K2, K20, and K5 isolates, which suggest their contribution to the high virulence of K1. In conclusion, we found that the distribution of antimicrobial susceptibility, virulence gene profiles, and capsular types of K. pneumoniae over two decades were associated with their clinical source.
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Affiliation(s)
- Cheng-Yen Kao
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Yen-Zhen Zhang
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Carl Jay Ballena Bregente
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pei-Yun Kuo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pek Kee Chen
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jo-Yen Chao
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tran Thi Thuy Duong
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Ming-Cheng Wang
- Division of Nephrology, Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tran Thi Dieu Thuy
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jazon Harl Hidrosollo
- Institute of Microbiology and Immunology, College of Life Sciences, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Pei-Fang Tsai
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chi Li
- Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Hung Lin
- Department of Internal Medicine, College of Medicine, National Cheng Kung University Hospital, National Cheng Kung University, Tainan, Taiwan
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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4
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Arcari G, Carattoli A. Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones. Pathog Glob Health 2023; 117:328-341. [PMID: 36089853 PMCID: PMC10177687 DOI: 10.1080/20477724.2022.2121362] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success is attributable to the introduction and extensive use in the clinical practice of antibiotics over the course of the last seven decades. In hospital settings, Klebsiella pneumoniae represents a well-known and commonly described opportunistic pathogen, typically characterized by resistance to several antibiotic classes. On the other hand, the broad wedge of population living in Low and/or Middle Income Countries is increasing rapidly, allowing the spread of several commensal bacteria which are transmitted via human contact. Community transmission has been the original milieu of K. pneumoniae isolates characterized by an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged as different pathways in the evolutionary history of K. pneumoniae. For a long time, the Sequence Type (ST), which is defined by the combination of alleles of the 7 housekeeping genes of the Multi-Locus Sequence Typing, has been a reliable marker of the pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) in the Western world and hypervirulent clones (e.g. ST23, ST65, ST86) in the Eastern. Currently, the boundaries separating the two pathotypes are fading away due to several factors, and we are witnessing a worrisome convergence in certain high-risk clones. Here we review the evidence available on confluence of multidrug-resistance and hypervirulence in specific K. pneumoniae clones.
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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5
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Shrestha R, Luterbach CL, Dai W, Komarow L, Earley M, Weston G, Herc E, Jacob JT, Salata R, Wong D, Anderson D, Rydell KB, Arias CA, Chen L, van Duin D. Characteristics of community-acquired carbapenem-resistant Enterobacterales. J Antimicrob Chemother 2022; 77:2763-2771. [PMID: 36179278 PMCID: PMC9989732 DOI: 10.1093/jac/dkac239] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 06/24/2022] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Community-acquired carbapenem-resistant Enterobacterales (CA-CRE) are an important threat. METHODS In CRACKLE-2, we defined patients with CA-CRE as admitted from home, without pre-existing conditions, and a positive culture within 48 h of admission. Healthcare-associated CRE (HA-CRE) were those with the lowest likelihood of community acquisition, not admitted from home and cultured >48 h after admission. Specific genetic markers in carbapenemase-producing Klebsiella pneumoniae were evaluated through random forest modelling. RESULTS CA-CRE and HA-CRE were detected in 83 (10%) and 208 (26%) of 807 patients. No significant differences were observed in bacterial species or strain type distribution. K. pneumoniae (204/291, 70%) was the most common CRE species, of these 184/204 (90%) were carbapenemase producers (CPKP). The top three genetic markers in random forest models were kpi_SA15, fimE, and kpfC. Of these, kpi_SA15 (which encodes a chaperone/usher system) was positively associated (OR 3.14, 95% CI 1.13-8.87, P = 0.026), and kpfC negatively associated (OR 0.21, 95% CI 0.05-0.72, P = 0.015) with CA-CPKP. CONCLUSIONS Ten percent of CDC-defined CRE were CA. The true proportion of CA-CRE in hospitalized patients is likely lower as patients may have had unrecorded prior healthcare exposure. The kpi_SA15 operon was associated with the CA phenotype.
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Affiliation(s)
- Rima Shrestha
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Courtney L Luterbach
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
- Division of Pharmacotherapy and Experimental Therapeutics, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Weixiao Dai
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Michelle Earley
- The Biostatistics Center, The George Washington University, Rockville, Maryland, USA
| | - Gregory Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Erica Herc
- Division of Infectious Diseases, Department of Medicine, Henry Ford Hospital, Detroit, Michigan, USA
| | - Jesse T Jacob
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory Antibiotic Resistance Center, Atlanta, Georgia, USA
| | - Robert Salata
- Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Darren Wong
- Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Deverick Anderson
- Division of Infectious Diseases, Duke University, School of Medicine, Durham, North Carolina, USA
- Duke Center for Antimicrobial Stewardship and Infection Prevention, Durham, North Carolina, USA
| | - Kirsten B Rydell
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
| | - Cesar A Arias
- Division of Infectious Diseases, Houston Methodist Hospital, Houston, Texas, USA
- Center for Infectious Diseases Research at Houston Methodist Research Institute and Weill Cornell Medical College, Houston, Texas, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, USA
- Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, USA
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6
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Nucci A, Rocha EPC, Rendueles O. Adaptation to novel spatially-structured environments is driven by the capsule and alters virulence-associated traits. Nat Commun 2022; 13:4751. [PMID: 35963864 PMCID: PMC9376106 DOI: 10.1038/s41467-022-32504-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Accepted: 08/02/2022] [Indexed: 12/14/2022] Open
Abstract
The extracellular capsule is a major virulence factor, but its ubiquity in free-living bacteria with large environmental breadths suggests that it shapes adaptation to novel niches. Yet, how it does so, remains unexplored. Here, we evolve three Klebsiella strains and their capsule mutants in parallel. Their comparison reveals different phenotypic and genotypic evolutionary changes that alter virulence-associated traits. Non-capsulated populations accumulate mutations that reduce exopolysaccharide production and increase biofilm formation and yield, whereas most capsulated populations become hypermucoviscous, a signature of hypervirulence. Hence, adaptation to novel environments primarily occurs by fine-tuning expression of the capsular locus. The same evolutionary conditions selecting for mutations in the capsular gene wzc leading to hypermucoviscosity also result in increased susceptibility to antibiotics by mutations in the ramA regulon. This implies that general adaptive processes outside the host can affect capsule evolution and its role in virulence and infection outcomes may be a by-product of such adaptation. Phenotypic and genotypic evolution in worrisome Klebsiella spp. is influenced by the capsule. Here the authors show that adaptation outside the host can impact virulence-associated traits, including de novo emergence of hypermucoviscosity.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université de Paris, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France.
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7
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Klebsiella pneumoniae Complex Harboring mcr-1, mcr-7, and mcr-8 Isolates from Slaughtered Pigs in Thailand. Microorganisms 2021; 9:microorganisms9122436. [PMID: 34946038 PMCID: PMC8703602 DOI: 10.3390/microorganisms9122436] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/05/2021] [Accepted: 11/22/2021] [Indexed: 11/29/2022] Open
Abstract
Dissemination of the mobile colistin resistance gene mcr in Enterobacterales among humans, animals, and the environment is a public health issue. We characterized mcr genes in the Klebsiella pneumoniae complex (KpnC) isolated from slaughtered pigs in Thailand. The 280 KpnCs consisted of K. pneumoniae (85%), Klebsiella quasipneumoniae (8.21%), and Klebsiella variicola (6.79%). mcr genes were detected in 6.79% (19/280) of KpnC isolates, consisting of mcr-8 (n = 9; 3.21%), mcr-7 (n = 7; 2.50%), mcr-7 + mcr-8 (n = 2; 0.71%), and mcr-1 + mcr-7 (n = 1; 0.36%). K. pneumoniae predominantly carried the mcr-7 and mcr-8 genes, while K. variicola and K. quasipneumoniae harbored mcr-7 and mcr-8, respectively. Six of the nineteen mcr-harboring KpnC isolates exhibited colistin resistance, and five had mcr-1 or mcr-8 transferable to an Escherichia coli recipient. Antimicrobial susceptibility analysis revealed that all mcr-carrying KpnC isolates were susceptible to carbapenems, cefotaxime, cefepime, amoxicillin/clavulanic acid, piperacillin/tazobactam, amikacin, and fosfomycin, and had high resistance to azithromycin. Multilocus sequence analysis demonstrated that the mcr-harboring KpnC isolates were genetically diverse. A ‘One-Health’ approach is useful to combat antimicrobial-resistant bacteria through coordinating the human, animal, and environmental sectors. Hence, continuous monitoring and surveillance of mcr-carrying KpnCs throughout the pork supply chain is crucial for ensuring public health.
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8
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Ribeiro S, Mourão J, Novais Â, Campos J, Peixe L, Antunes P. From farm to fork: Colistin voluntary withdrawal in Portuguese farms reflected in decreasing occurrence of mcr-1-carrying Enterobacteriaceae from chicken meat. Environ Microbiol 2021; 23:7563-7577. [PMID: 34327794 DOI: 10.1111/1462-2920.15689] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/27/2021] [Indexed: 11/27/2022]
Abstract
Expansion of mcr-carrying Enterobacteriaceae (MCR-E) is a well-recognized problem affecting animals, humans and the environment. Ongoing global control actions involve colistin restrictions among food-animal production, but their impact on poultry-derived products is largely unknown, justifying comprehensive farm-to-fork studies. Occurrence of MCR-E among 53 chicken-meat batches supplied from 29 Portuguese farms shortly after colistin withdrawal was evaluated. Strains (FT-IR/MLST/WGS), mcr plasmids and their adaptive features were characterized by cultural, molecular and genomic approaches. We found high rates of chicken-meat batches (80%-100% - 4 months; 12% - the last month) with multiple MDR + mcr-1-carrying Escherichia coli (Ec-including ST117 and ST648-Cplx) and Klebsiella pneumoniae (Kp-ST147-O5:K35) clones, some of them persisting over time. The mcr-1 was located in the chromosome (Ec-ST297/16-farms) or dispersed IncX4 (Ec-ST602/ST6469/5-farms), IncHI2-ST2/ST4 (Ec-ST533/ST6469/5 farms and Kp-ST147/6-farms) or IncI2 (Ec-ST117/1-farm) plasmids. WGS revealed high load and diversity in virulence, antibiotic resistance and metal tolerance genes. This study supports colistin withdrawal potential efficacy in poultry production and highlights both poultry-production chain as a source of mcr-1 and the risk of foodborne transmission to poultry-meat consumers. Finally, in the antibiotic reduction/replacement context, other potential co-selective pressures (e.g., metals-Cu as feed additives) need to be further understood to guide concerted, effective and durable actions under 'One Health' perspective.
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Affiliation(s)
- Sofia Ribeiro
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Mourão
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Center for Neuroscience and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Ângela Novais
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Joana Campos
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,INEB-Institute of Biomedical Engineering, i3S-Institute for Research & Innovation in Health, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal
| | - Patrícia Antunes
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, 4050-313, Portugal.,Faculty of Nutrition and Food Sciences, University of Porto, Porto, 4150-180, Portugal
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9
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Saxenborn P, Baxter J, Tilevik A, Fagerlind M, Dyrkell F, Pernestig AK, Enroth H, Tilevik D. Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden. Front Microbiol 2021; 12:640408. [PMID: 33995300 PMCID: PMC8120268 DOI: 10.3389/fmicb.2021.640408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/13/2021] [Indexed: 02/02/2023] Open
Abstract
Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.
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Affiliation(s)
- Patricia Saxenborn
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - John Baxter
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Andreas Tilevik
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Magnus Fagerlind
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | | | - Anna-Karin Pernestig
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Helena Enroth
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden.,Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden
| | - Diana Tilevik
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
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10
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Parrott AM, Shi J, Aaron J, Green DA, Whittier S, Wu F. Detection of multiple hypervirulent Klebsiella pneumoniae strains in a New York City hospital through screening of virulence genes. Clin Microbiol Infect 2020; 27:583-589. [PMID: 32461145 DOI: 10.1016/j.cmi.2020.05.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 05/09/2020] [Accepted: 05/13/2020] [Indexed: 12/28/2022]
Abstract
OBJECTIVES The 'hypervirulent' variant of Klebsiella pneumoniae (hvKp) is a predominant cause of community-acquired pyogenic liver abscess in Asia, and is an emerging pathogen in Western countries. hvKp infections have demonstrated 'metastatic' dissemination in immunocompetent hosts, an unusual mode of infection associated with severe complications. Two cases alerted us to the possible presence of hvKp at our hospital, both involving elderly Hispanic males who presented with recurrent fever, bacteraemia, epigastric pain and liver abscesses/phlegmon, thus prompting an assessment of hvKp prevalence. METHODS A surveillance of K. pneumoniae blood, body fluid and wound isolates was conducted using real-time PCR to detect virulence-associated genes (uni-rmpA, iucA and peg344). Positive isolates were further characterized by wzi gene sequencing to determine capsular types (K-type) and by multilocus sequence typing and pulsed-field gel electrophoresis to determine strain relatedness. RESULTS Four-hundred and sixty-three K. pneumoniae isolates, derived from 412 blood, 21 body fluids and 30 abdominal wound specimens, were screened over a 3-year period. Isolates included 98 multidrug-resistant strains. Eighteen isolates from 17 patients, including two from the index patient, screened positive for all three virulence genes. Sixteen of 18 positive isolates had K-types associated with hvKp, and isolates from different patients were unrelated strains, indicating likely community acquisition. Of 13 patients with significant morbidity, five died; eight patients had co-existing hepatobiliary disease, and six had diabetes mellitus. CONCLUSIONS Multiple strains of hvKp are emerging in New York City and are associated with high mortality relative to multidrug-resistant and classical Klebsiella infections. Co-existing hepatobiliary disease appears to be a potential risk factor for these infections.
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Affiliation(s)
- A M Parrott
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA.
| | - J Shi
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - J Aaron
- Department of Medicine, Division of Infectious Diseases, Columbia University Irving Medical Center, New York, NY, USA
| | - D A Green
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - S Whittier
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
| | - F Wu
- Department of Pathology & Cell Biology, Columbia University Irving Medical Center, New York, NY, USA
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11
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The determination of gyrA and parC mutations and the prevalence of plasmid-mediated quinolone resistance genes in carbapenem resistant Klebsiella pneumonia ST11 and ST76 strains isolated from patients in Heilongjiang Province, China. INFECTION GENETICS AND EVOLUTION 2020; 82:104319. [PMID: 32278145 DOI: 10.1016/j.meegid.2020.104319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/17/2020] [Accepted: 04/07/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND There is increasing resistance to carbapenems among Klebsiella pneumoniae,and fluoroquinolones (FQ) are increasingly used to treat infections from extended-spectrum β- lactamase(ESBLs) and carbapenemase-producing Klebsiella pneumoniae. However, the acquisition of plasmid-mediated quinolone resistance (PMQR) or the spontaneous mutation of the quinolone resistance-determining regions (QRDR) of the gyrA and parC genes can severely affect the therapeutic effect of quinolones. The goal of this study was to investigate the molecular determinants of FQ resistance(FQ-R) in carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from Heilongjiang Province,China. MATERIALS AND METHODS We isolated 40 strains of CRKP from a treatment center in the eastern part of Heilongjiang Province from January 2016 to December 2018. The VITEK2 Compact analyzer was used to identify and detect drug sensitivity. Different types of drug resistance genes were detected by polymerase chain reaction (PCR). PCR and DNA sequencing were used to assess the presence of qnrA, qnrB, qnrS,qepA and acc(6') Ib-cr genes,which are plasmid-encode genes that can contribute to resistance. The sequences of gyrA and parC genes were sequenced and compared with the sequences of standard strains to determine if mutations were present.Multi-site sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE) were performed on the strains to assess homology. RESULTS The isolated CRKP strains showed rates of resistance to fluoroquinolones of 22.5% to 42.5%. The resistance rate of ciprofloxacin was significantly higher than that of levofloxacin.Nine CRKP strains (22.5%) showed co-resistance to ciprofloxacin and levofloxacin.The quinolone resistant strains were screened for plasmid-encoded genes that can contribute to resistance (PMQR genes).Among the 17 quinolone resistant strains,one strain contained no PMQR genes,twelve strains contained two PMQR genes,and four strains contained four PMQR genes.Acc (6') Ib-cr was the most frequently detected PMQR gene, detected in 95% of strains tested (38 of 40) and in 94.1% of the quinolone-resistant strains (16 of 17). The qepA gene encoding an efflux pump was not detected in any strains.No isolate carried five different PMQRs simultaneously.Changes of S83I and D87G changes in gyrA, and the S80I change in parC,which were mediated by QRDR,were identified in two isolates,which showed resistance to both ciprofloxacin and levofloxacin.Most of the FQ-R strains(58.8%,10/17) belong to ST(sequence type) 76, which is dominant in the local area, while all the mutant strains (100%,2/2),that differ in at least one site from standard bacteria, belong to the ST11 group. The strains were isolated from a hospital where there had been a recent outbreak of ST76 type CRKP in the neurosurgery ward and intensive care unit. CONCLUSION CRKP strains were identified that were insensitive or even resistant to quinolones,and this resistance is common in Heilongjiang Province of eastern China;fluoroquinolone-resistance in these clinical CRKP strains is a complex interplay between PMQR determinants and mutations in gyrA and parC.The resistance level caused by QRDR mutation is higher than that caused by PMQR, however, the high frequency of PMQR genes in the isolated CRKP strains suggests the potential for impact of these genes.PMQR determinants are often found in carbapenemase-producing or ESBLs-producing Klebsiella pneumoniae,and some resistance genes,such as:SHV,TEM, CTX-M-15,and OXA-1 are closely associated with FQ-R. Finally, geographical factors can affect the emergence and spread of PMQR and QRDR.Some genetic lineages have higher potential risks, and continuous close monitoring is required.
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12
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Pajand O, Darabi N, Arab M, Ghorbani R, Bameri Z, Ebrahimi A, Hojabri Z. The emergence of the hypervirulent Klebsiella pneumoniae (hvKp) strains among circulating clonal complex 147 (CC147) harbouring bla NDM/OXA-48 carbapenemases in a tertiary care center of Iran. Ann Clin Microbiol Antimicrob 2020; 19:12. [PMID: 32234050 PMCID: PMC7110786 DOI: 10.1186/s12941-020-00349-z] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 02/12/2020] [Indexed: 11/14/2022] Open
Abstract
Background Klebsiella pneumoniae is a public health concern because of its ability to develop multidrug resistance and hypervirulent genotypes, of those capsular types K1 and K2 cause community and nosocomial life-threatening infections. This study aimed to determine the antibiotic susceptibility patterns and genotypic traits of a collection of Klebsiella spp. isolates. Furthermore, the clonal relatedness of blaNDM producing strains was investigated. Methods During a 19-months surveillance study, 122 Klebsiella spp. isolates were cultured from extraintestinal specimens of patients admitted to the tertiary referral hospital in Semnan, Iran. Isolates were identified using biochemical tests and subjected to determination of phylogroups, capsular types and virulence/resistance genes content. Hypervirulent K. pneumoniae (hvKp) strains were detected genotypically, and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR fingerprinting was used to determine the clonality of blaNDM producing strains. Results Multidrug resistant phenotype was detected in 75 (61.5%) isolates and amikacin was found as the most potent antibiotic with the susceptibility rate of 85.2%. The carbapenemase genes were detected in 45 (36.8%) strains, including 21 (17.2%) blaOXA-48, 7 (5.6%) blaNDM-1, 14 (11.4%) blaNDM-1/OXA-48 and 3 (2.4%) blaIMP- carrying strains, while 55 (45.08%) isolates showed carbapenem resistant phenotype. The first blaNDM-1 carrying strain was cultured from a sputum specimen on March 2015, while the last positive one was recovered from blood culture on September 2016. Most of the isolates (80.3%) belonged to phylogroup I, and blaNDM-1 was identified among all three phylogroups. The ERIC-PCR clustered the 101 blaNDM negative and 21 blaNDM-1 positive isolates into 25 and five clusters, respectively, and the latter group belonged to clonal complex 147 (CC147). One K1 and 15 K2 blaNDM-1 negative isolates were detected, of those three strains were identified as hvKp. Five K2 positive strains, including four blaOXA-48 producer and one hvKp sequence type 86 (ST86) were carbapenem resistant. Among carbapenem resistant isolates, CC147 strains harboured higher rates of siderophores iutA and ybtS. Conclusion The present findings showed a hospital circulation of CC147 blaNDM-1 or blaNDM-1/OXA-48 producing strains, disseminated in different wards. The hvKp/ST86 strain expressing K2 capsular type and carbapenem resistant phenotype wasn’t reported from Iran so far. So, it seems that we must be aware of the emergence and spread of new K. pneumoniae clones associated with resistant and hypermucoviscous phenotypes.
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Affiliation(s)
- Omid Pajand
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Student Research Committee, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Narges Darabi
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Maedeh Arab
- Student Research Committee, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Raheb Ghorbani
- Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Zakaria Bameri
- Infectious Disease and Tropical Medicine Research Center, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Ebrahimi
- Student Research Committee, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Zoya Hojabri
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran. .,Student Research Committee, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran.
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13
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The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples. Appl Environ Microbiol 2020; 86:AEM.02711-19. [PMID: 32005732 PMCID: PMC7082575 DOI: 10.1128/aem.02711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources. Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10−1 CFU g−1 after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 103 to 1.5 × 104 CFU g−1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates. IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.
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14
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Alghoribi MF, Binkhamis K, Alswaji AA, Alhijji A, Alsharidi A, Balkhy HH, Doumith M, Somily A. Genomic analysis of the first KPC-producing Klebsiella pneumoniae isolated from a patient in Riyadh: A new public health concern in Saudi Arabia. J Infect Public Health 2020; 13:647-650. [PMID: 32067931 DOI: 10.1016/j.jiph.2020.01.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 11/25/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have been isolated from human patients in many countries across the globe but rarely in Saudi Arabia. Here we provide the genomic characterization of the first KPC-producing K. pneumoniae isolated from the urine of a patient in Riyadh, Saudi Arabia, who had a recent travel history to Egypt involving a medical procedure. Presence of KPC-encoding gene initially detected with the Xpert Carba-R assay was confirmed by traditional PCR. Susceptibility testing using the VITEK 2 system, E-test and microbroth dilution methods showed that the K. pneumoniae isolate, namely SA01_KPC-2, was resistant to all antibiotics except colistin and ceftazidime/avibactam. Whole-genome sequencing (WGS), performed on the Illumina Miseq instrument, identified the isolate as sequence type (ST) 383 and serotype KL30-D1 O1v2. Genome assembly of SA01_KPC-2 indicated the presence of two plasmids. Plasmid pSA01_KPC-2, of approximately 45.9 kb in size, harbored the blaKPC-2 flanked by ISKpn27 and ISKpn6 and had a backbone similar to published KPC-carrying IncX6 plasmids. The second plasmid pSA01_incHIB1, a derivative of published 372-kb plasmid pKpvST383, carried genes encoding virulence factors and resistance to five classes of antibiotics. The isolation of the first KPC producer in Saudi Arabia requires high attention and rapid interventions to prevent further spread.
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Affiliation(s)
- Majed F Alghoribi
- King Abdullah International Medical Research Center, Infectious Diseases Research Department, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.
| | - Khalifa Binkhamis
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman A Alswaji
- King Abdullah International Medical Research Center, Infectious Diseases Research Department, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ali Alhijji
- Department of Medicine, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Aynaa Alsharidi
- Department of Medicine, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
| | - Hanan H Balkhy
- King Abdullah International Medical Research Center, Infectious Diseases Research Department, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Michel Doumith
- King Abdullah International Medical Research Center, Infectious Diseases Research Department, Riyadh, Saudi Arabia; King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Ali Somily
- Department of Pathology and Laboratory Medicine, College of Medicine, King Saud University Medical City, King Saud University, Riyadh, Saudi Arabia
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15
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Kudo M, Matono T, Morita M, Izumiya H, Ohnishi M, Hasegawa J, Izumi M, Yoshino M, Arai K, Imura H. Molecular analysis of virulence factors of hypermucoviscous Klebsiella pneumoniae in a diabetes patient with multifocal intramuscular and musculoskeletal abscesses. J Infect Chemother 2019; 26:110-114. [PMID: 31266705 DOI: 10.1016/j.jiac.2019.06.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Revised: 05/18/2019] [Accepted: 06/04/2019] [Indexed: 11/26/2022]
Abstract
Unusual community-acquired invasive Klebsiella pneumoniae infection has been reported worldwide, particularly in Asia. Recently, several virulence-associated genes of the isolates have been investigated. We report a case of multifocal intramuscular and musculoskeletal abscesses caused by K. pneumoniae in a 61-year-old male diabetes patient. A string test of the K. pneumoniae isolate, which was recovered from abscesses obtained by surgical debridement and drainage, was positive. We used whole-genome sequencing to analyze the virulence-associated gene profile of the isolate. The isolate belonged to the K2 genotype with sequence type 375. The isolate harbored rmpA and rmpA2, which induce serum resistance (hypermucoviscosity). The isolate also carried siderophores, i.e., aerobactin and salmochelin, which are associated with enhanced bacterial growth. The isolate did not harbor K1-unique virulence factors, such as colibactin, microcin, and yersiniabactin. Our K2 strain harbored a combination of virulence plasmid-associated genes-rmpA/A2 and siderophores (aerobactin and salmochelin). Hence, we advocate that essential molecular virulence factors of isolates that cannot be identified by a string test and capsular serotyping alone may exist.
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Affiliation(s)
- Masataka Kudo
- Department of General Internal Medicine, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
| | - Takashi Matono
- Department of Infectious Diseases, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan.
| | - Masatomo Morita
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Hidemasa Izumiya
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku-ku, Tokyo, 162-8640, Japan
| | - Junichi Hasegawa
- Department of General Internal Medicine, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
| | - Migiwa Izumi
- Department of General Internal Medicine, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
| | - Mai Yoshino
- Department of General Internal Medicine, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
| | - Ken Arai
- Department of Orthopedics, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
| | - Hiroshi Imura
- Department of General Internal Medicine, Iizuka Hospital, 3-83 Yoshio-machi, Iizuka, Fukuoka, 820-8505, Japan
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16
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Roe CC, Vazquez AJ, Esposito EP, Zarrilli R, Sahl JW. Diversity, Virulence, and Antimicrobial Resistance in Isolates From the Newly Emerging Klebsiella pneumoniae ST101 Lineage. Front Microbiol 2019; 10:542. [PMID: 31001209 PMCID: PMC6454207 DOI: 10.3389/fmicb.2019.00542] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 03/01/2019] [Indexed: 11/13/2022] Open
Abstract
The global dissemination of Klebsiella pneumoniae and Klebsiella pneumoniae carbapenemase (KPC) has been largely attributed to a few high-risk sequence types (STs) (ST258, ST11, ST512) associated with human disease. ST101 is an emerging clone that has been identified in different parts of the world with the potential to become a global, persistent public health threat. Recent research suggests the ST101 lineage is associated with an 11% increase in mortality rate in comparison to non-ST101 infections. In this study, we generated a high-quality, near-finished genome assembly of a multidrug-resistant (MDR) isolate from Italy (isolate 4743) that is a single locus variant of ST101 (ST1685). We demonstrate that the 4743 genome contains virulence features such as an integrative conjugative element carrying the yersiniabactin siderophore (ICEKp3), the mannose-resistant Klebsiella-like (type III) fimbriae cluster (mrkABCDFHIJ), the ferric uptake system (kfuABC), the yersiniabactin receptor gene fyuA, a capsular K type K17, and an O antigen type of O1. K. pneumoniae 4743 carries the blaKPC-2 carbapenemase gene along with genes conferring resistance to aminoglycosides, beta-lactams, fluoroquinolones, fosfomycin, macrolides, lincosamides, and streptogramin B. A comparative genomics analysis of 44 ST101 genomes as well as newly sequenced isolate 4743 identified variable antimicrobial resistance (AMR) resistance profiles and incompatibility plasmid types, but similar virulence factor profiles. Using Bayesian methodologies, we estimate the common ancestor for the ST101 lineage emerged in 1990 (95% HPD: 1965 to 2007) and isolates within the lineage acquired bla KPC after the divergence from its parental clonal group and dissemination. The identification of virulence factors and antibiotic resistance genes acquired by this newly emerging clone provides insight into the reported increased mortality rates and highlights its potential success as a persistent nosocomial pathogen. With a combination of both colistin resistance, carbapenem resistance, and several known virulence factors, the ST101 genetic repertoire may be a "perfect storm" allowing for a newly emerging, high-risk, extensively antibiotic resistant clone. This high-risk clone appears adept at acquiring resistance and may perpetuate the dissemination of extensive antimicrobial resistance. Greater focus on the acquisition of virulence factors and antibiotic resistance genes is crucial for understanding the spread of antibiotic resistance.
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Affiliation(s)
- Chandler C. Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
| | - Eliana Pia Esposito
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Naples, Italy
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, United States
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17
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Remya PA, Shanthi M, Sekar U. Characterisation of virulence genes associated with pathogenicity in Klebsiella pneumoniae. Indian J Med Microbiol 2019; 37:210-218. [PMID: 31745021 DOI: 10.4103/ijmm.ijmm_19_157] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
Purpose This study was undertaken to characterise the virulence factors in clinical strains of Klebsiella pneumoniae and analyse their association with various infections caused and also to determine the association between virulence factors and antimicrobial resistance profile. Materials and Methods A total number of 370 clinically significant, non-duplicate isolates of K. pneumoniae isolated from both hospitalised patients and patients attending clinics were included in this study. Polymerase chain reaction (PCR) was carried out for the detection of various virulence genes such as mucoviscosity-associated gene A (magA), gene associated with allantoin metabolism (allS), Klebsiella ferric iron uptake(Kfu), capsule-associated gene A (K2A), regulator of mucoid phenotype A (rmpA), enterobactin (entB), yersiniabactin (YbtS), aerobactin, Fimbrial adhesin (FimH) and uridine-diphosphate galacturonate 4-epimerase (uge). Antimicrobial susceptibility testing and PCR-based detection of beta-lactamase-encoding genes such as extended-spectrum beta-lactamases, AmpCs and carbapenemases were performed. Univariate analysis was done to find the association between virulence genes and mortality. Results The siderophore, entB, was present in most (90.5%) of the isolates. Of the 370 isolates, 345 carried multiple virulence genes; 15 harboured single virulence genes and 10 did not harbour any of the studied virulence genes. The most common combination of occurrence was entB and FimH. A mortality rate of 12.75% (38/298) was observed among hospitalised patients. None of the virulence genes had any significant association with mortality. Conclusion Pathogenic K. pneumoniae can harbour single to multiple virulence genes. Invasive infection with even a single virulence gene-harbouring K. pneumoniae can lead to poor outcomes. Both multidrug-resistant (MDR) and non-MDR K. pneumoniae can harbour a variety of virulence genes. None of the virulence genes have a significant association with mortality.
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Affiliation(s)
- P A Remya
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - M Shanthi
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
| | - Uma Sekar
- Department of Microbiology, Sri Ramachandra Institute of Higher Education and Research, Chennai, Tamil Nadu, India
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18
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Rodrigues C, Passet V, Rakotondrasoa A, Brisse S. Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:3000. [PMID: 30581423 PMCID: PMC6294014 DOI: 10.3389/fmicb.2018.03000] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae (phylogroup Kp1), one of the most problematic pathogens associated with antibiotic resistance worldwide, is phylogenetically closely related to K. quasipneumoniae [subsp. quasipneumoniae (Kp2) and subsp. similipneumoniae (Kp4)], K. variicola (Kp3) and two unnamed phylogroups (Kp5 and Kp6). Together, Kp1 to Kp6 make-up the K. pneumoniae complex. Currently, the phylogroups can be reliably identified only based on gene (or genome) sequencing. Misidentification using standard laboratory methods is common and consequently, the clinical significance of K. pneumoniae complex members is imprecisely defined. Here, we evaluated and validated the potential of MALDI-TOF mass spectrometry (MS) to discriminate K. pneumoniae complex members. We detected mass spectrometry biomarkers associated with the phylogroups, with a sensitivity and specificity ranging between 80-100% and 97-100%, respectively. Strains within phylogroups Kp1, Kp2, Kp4, and Kp5 each shared two specific peaks not observed in other phylogroups. Kp3 strains shared a peak that was only observed otherwise in Kp5. Finally, Kp6 had a diagnostic peak shared only with Kp1. Kp3 and Kp6 could therefore be identified by exclusion criteria (lacking Kp5 and Kp1-specific peaks, respectively). Further, ranked Pearson correlation clustering of spectra grouped strains according to their phylogroup. The model was tested and successfully validated using different culture media. These results demonstrate the potential of MALDI-TOF MS for precise identification of K. pneumoniae complex members. Incorporation of spectra of all K. pneumoniae complex members into reference MALDI-TOF spectra databases, in which they are currently lacking, is desirable. MALDI-TOF MS may thereby enable a better understanding of the epidemiology, ecology, and pathogenesis of members of the K. pneumoniae complex.
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Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Andriniaina Rakotondrasoa
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
- Institut Pasteur Madagascar, Madagascar, Africa
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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19
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Becker L, Fuchs S, Pfeifer Y, Semmler T, Eckmanns T, Korr G, Sissolak D, Friedrichs M, Zill E, Tung ML, Dohle C, Kaase M, Gatermann S, Rüssmann H, Steglich M, Haller S, Werner G. Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario. Front Microbiol 2018. [PMID: 29527200 PMCID: PMC5829066 DOI: 10.3389/fmicb.2018.00322] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K. pneumoniae clones (ST15, n = 31; ST405, n = 7) and one CTX-M-15 producing Klebsiella quasipneumoniae strain (ST414, n = 8). Additionally, we determined sequence variations associated with antimicrobial resistance phenotypes in single isolates expressing carbapenem and colistin resistance, respectively. For rapid detection of the major K. pneumoniae outbreak clone (ST15), a selective triplex PCR was deduced from WGS data of the major outbreak strain and K. pneumoniae genome data deposited in central databases. Moreover, we introduce two novel open-source applications supporting reference genome selection (refRank; https://gitlab.com/s.fuchs/refRank) and alignment-based SNP-filtering (SNPfilter; https://gitlab.com/s.fuchs/snpfilter) in NGS analyses.
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Affiliation(s)
- Laura Becker
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Yvonne Pfeifer
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Tim Eckmanns
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Gerit Korr
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.,Postgraduate Training for Applied Epidemiology, Robert Koch Institute, Affiliated to the European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dagmar Sissolak
- Department of Infection Control, Medical Disaster Control and Environmental Health Control, Department of Public Health, Berlin, Germany
| | | | - Edith Zill
- Medical Care Centre Labor 28 GmbH, Berlin, Germany
| | | | | | - Martin Kaase
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, Germany
| | - Holger Rüssmann
- Immunology and Laboratory Medicine, Institute for Microbiology, HELIOS Klinikum Emil von Behring, Berlin, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Culture, Braunschweig, Germany
| | - Sebastian Haller
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
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20
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Turton JF, Payne Z, Coward A, Hopkins KL, Turton JA, Doumith M, Woodford N. Virulence genes in isolates of Klebsiella pneumoniae from the UK during 2016, including among carbapenemase gene-positive hypervirulent K1-ST23 and ‘non-hypervirulent’ types ST147, ST15 and ST383. J Med Microbiol 2018; 67:118-128. [DOI: 10.1099/jmm.0.000653] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Jane F. Turton
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Zoë Payne
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Amy Coward
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Katie L. Hopkins
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
| | | | - Michel Doumith
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
| | - Neil Woodford
- Antimicrobial Resistance and Healthcare Associated Infections (AMRHAI) Reference Unit, Public Health England, London NW9 5EQ, UK
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21
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Obasi A, Nwachukwu S, Ugoji E, Kohler C, Göhler A, Balau V, Pfeifer Y, Steinmetz I. Extended-Spectrum β-Lactamase-Producing Klebsiella pneumoniae from Pharmaceutical Wastewaters in South-Western Nigeria. Microb Drug Resist 2017; 23:1013-1018. [PMID: 28375698 DOI: 10.1089/mdr.2016.0269] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Emergence and spread of Klebsiella pneumoniae isolates producing extended-spectrum β-lactamases (ESBLs) present a major threat to public health. In this study, we characterized β-lactam-resistant K. pneumoniae isolates from six wastewater samples obtained from two pharmaceutical industries located in Lagos and Ogun States, Nigeria. Bacteria were isolated by using MacConkey agar; species identification and antibacterial susceptibility testing were performed by Vitek 2. Etest was used for ESBL phenotype confirmation. The presence of β-lactamase genes was investigated by PCR and sequencing. Bacterial strain typing was done by XbaI-macrorestriction and subsequent pulsed-field gel electrophoresis (PFGE) as well as multilocus sequence typing (MLST). Thirty-five bacterial species were isolated from the six samples; among them, we identified seven K. pneumoniae isolates with resistance to β-lactams and co-resistance to fluoroquinolones, aminoglycosides, and folate pathway inhibitors. The ESBL phenotype was confirmed in six K. pneumoniae isolates that harbored ESBL genes blaCTX-M-15 (n = 5), blaSHV-2 (n = 1), and blaSHV-12 (n = 1). PFGE and MLST analysis revealed five clones belonging to four sequence types (ST11, ST15, ST37, ST101), and clone K. pneumoniae-ST101 was present in the wastewater samples from two different pharmaceutical industries. Additionally performed conjugation assays confirmed the location of β-lactamase genes on conjugative plasmids. This is the first confirmation of K. pneumoniae isolates producing CTX-M-15-ESBL from pharmaceutical wastewaters in Nigeria. The co-resistance observed might be a reflection of the different drugs produced by these industries. Continuous surveillance of the environmental reservoirs of multidrug-resistant bacteria is necessary to prevent their further spread.
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Affiliation(s)
- Avemaria Obasi
- 1 Department of Microbiology, University of Lagos , Lagos, Nigeria
| | | | - Esther Ugoji
- 1 Department of Microbiology, University of Lagos , Lagos, Nigeria
| | - Christian Kohler
- 2 Department of Medical Microbiology, Friedrich Loeffler Institute for Medical Microbiology, University of Greifswald , Greifswald, Germany
| | - André Göhler
- 2 Department of Medical Microbiology, Friedrich Loeffler Institute for Medical Microbiology, University of Greifswald , Greifswald, Germany
| | - Veronica Balau
- 2 Department of Medical Microbiology, Friedrich Loeffler Institute for Medical Microbiology, University of Greifswald , Greifswald, Germany
| | - Yvonne Pfeifer
- 3 FG13 Nosocomial Pathogens and Antibiotic Resistance, Robert Koch Institute , Wernigerode, Germany
| | - Ivo Steinmetz
- 2 Department of Medical Microbiology, Friedrich Loeffler Institute for Medical Microbiology, University of Greifswald , Greifswald, Germany
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22
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Melot B, Brisse S, Breurec S, Passet V, Malpote E, Lamaury I, Thiery G, Hoen B. Community-acquired meningitis caused by a CG86 hypervirulent Klebsiella pneumoniae strain: first case report in the Caribbean. BMC Infect Dis 2016; 16:736. [PMID: 27923372 PMCID: PMC5142283 DOI: 10.1186/s12879-016-2065-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 11/24/2016] [Indexed: 11/18/2022] Open
Abstract
Background Community-acquired bacterial meningitis due to Klebsiella pneumoniae has mainly been described in Southeast Asia and has a poor prognosis. Severe invasive infections caused by K. pneumoniae, including meningitis, are often due to hypervirulent strains (hvKP), which are characterized by capsular serotypes K1 and K2, a gene responsible for hypermucoviscosity, and the cluster for synthesis of the siderophore aerobactin. Case presentation A 55 year old man with a history of essential hypertension, benign prostate hyperplasia, hyperlipidemia, obstructive sleep apnea, and chronic alcoholism was admitted for meningitis due to Klebsiella pneumoniae with a wild-type susceptibility profile. Its genomic features were consistent with a capsular K2 strain belonging to clonal group 86 (CG86) displaying the large virulence of Klebsiella plasmid (pLVPK) with heavy metal resistance gene clusters, aerobactin, rmpA. Conclusion This is the first case of community-acquired meningitis caused by a hypervirulent strain of hvKP ever reported in the Caribbean.
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Affiliation(s)
- Bénédicte Melot
- Inserm-CIC 1424 et Service de Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, France
| | - Sylvain Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France. .,UMR3525, CNRS, Paris, France.
| | - Sébastien Breurec
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France.,Unité Environnement et Santé, Institut Pasteur de Pointe-à-Pitre, Pointe-à-Pitre, Guadeloupe, France.,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France
| | - Virginie Passet
- Microbial Evolutionary Genomics, Institut Pasteur, 28 rue du Dr Roux, 75724, Paris, France.,UMR3525, CNRS, Paris, France
| | - Edith Malpote
- Laboratoire de Microbiologie clinique et environnementale, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Isabelle Lamaury
- Inserm-CIC 1424 et Service de Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, France
| | - Guillaume Thiery
- Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France.,Service de Réanimation, Centre Hospitalier Universitaire de Pointe-à-Pitre/les Abymes, Pointe-à-Pitre, France
| | - Bruno Hoen
- Inserm-CIC 1424 et Service de Maladies Infectieuses et Tropicales, Centre Hospitalier Universitaire de Pointe-à-Pitre, Pointe-à-Pitre, France. .,Faculté de Médecine Hyacinthe Bastaraud, Université des Antilles et de la Guyane, Pointe-à-Pitre, Guadeloupe, France. .,Centre Hospitalier Universitaire de Pointe-à-Pitre, Service de Maladies Infectieuses et Tropicales, BP 465, 97159, Pointe-à-Pitre Cedex, France.
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23
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Development of a Colloidal Gold-Based Immunochromatographic Strip for Rapid Detection of Klebsiella pneumoniae Serotypes K1 and K2. J Clin Microbiol 2016; 54:3018-3021. [PMID: 27707941 DOI: 10.1128/jcm.01608-16] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 09/26/2016] [Indexed: 11/20/2022] Open
Abstract
In this study, a novel colloidal gold-based immunochromatographic strip (ICS) containing anti-Klebsiella pneumoniae capsular polysaccharide polyclonal antibodies was developed to specifically detect K. pneumoniae serotypes K1 and K2. Capsular polysaccharide K1 and K2 antigens were first used to produce polyclonal anti-K1 and anti-K2 antibodies. Reference strains with different serotypes, nontypeable K. pneumoniae strains, and other bacterial species were then used to assess the sensitivity and specificity of these test strips. The detection limit was found to be 105 CFU, and the ICSs were stable for 6 months when stored at room temperature. No false-positive or false-negative results were observed, and equivalent results were obtained compared to those of more conventional test methods, such as PCR or serum agglutination. In conclusion, the ICS developed here requires no technical expertise and allows for the specific, rapid, and simultaneous detection of K. pneumoniae serotypes K1 and K2.
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24
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Sun Y, Wu H, Shen D. Clinical and Molecular Analysis of Klebsiella pneumoniae Causing Liver Abscess in China. J Mol Microbiol Biotechnol 2016; 26:245-51. [PMID: 27073997 DOI: 10.1159/000444367] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 01/27/2016] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE Hypervirulent Klebsiella pneumoniae (hvKP) has been characterized as the major pathogen associated with the development of liver abscesses. Although the prevalence of K. pneumoniae in liver abscesses in Chinese patients is on the rise, methods for the early laboratory identification and recognition of hvKP are lacking, and hvKP detection and surveillance are thus limited. METHODS A retrospective study was conducted in 240 patients with cultures that were positive for K. pneumoniae, who were hospitalized in the Hospital of Beijing area from May 2013 to August 2014. The clinical and molecular characteristics of K. pneumoniae strains that cause liver abscesses were studied. Thirty-eight (16.7%) of 240 patients positive for K. pneumoniae cultures had liver abscesses. RESULTS Among these K. pneumoniae isolates, 92.1% (35/38) and 84.2% (32/38) were rmpA and aerobactin (abc) positive, respectively, as indicated by multiplex PCR, while 81.6% (31/38) were string test positive. Intriguingly, K. pneumoniae isolates that were positive for rmpA, abc, or string test accounted for almost all isolates (97.3%; n = 37/38) and thus were defined as hvKP in this study. Based on the new criteria for hvKP, none of these hvKP strains were positive for extended spectrum β-lactamases. CONCLUSIONS Compared to the string test alone, integrating rmpA and abc detection with the string test is robuster and more extensive in the identification of liver abscess-causing hvKP strains. Multiplex PCR assays may therefore accelerate the early laboratory detection of hvKP.
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Affiliation(s)
- Yunfang Sun
- Department of Microbiology, Chinese General Hospital of People's Liberation Army, Beijing, China
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25
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Transfer of CMY-2 Cephalosporinase from Escherichia coli to Virulent Klebsiella pneumoniae Causing a Recurrent Liver Abscess. Antimicrob Agents Chemother 2015; 59:5000-2. [PMID: 25987637 DOI: 10.1128/aac.00492-15] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2015] [Accepted: 05/09/2015] [Indexed: 11/20/2022] Open
Abstract
A CMY-2-producing capsular type K2 Klebsiella pneumoniae strain (TVGHKP93) with multidrug resistance was isolated from a recurrent liver abscess in a patient who also carried a CMY-2-producing Escherichia coli strain (TVGHEC01) in the stool. TVGHKP93 retained its high virulence compared with that of the isogenic strain (TVGHKP60) with wild-type resistance from the first liver abscess. Our conjugation experiment showed the successful transfer of the blaCMY-2-carrying plasmid from TVGHEC01 into TVGHKP60. The transconjugant showed both high virulence and the multidrug-resistant phenotype, as did TVGHKP93.
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26
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Association of tellurite resistance with hypervirulent clonal groups of Klebsiella pneumoniae. J Clin Microbiol 2015; 53:1380-2. [PMID: 25631812 DOI: 10.1128/jcm.03053-14] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Tellurite-based selective growth media are used for several bacterial pathogens. We found that, in Klebsiella pneumoniae, tellurite resistance is strongly associated with hypervirulent clonal group 23 (CG23), CG65, and CG86, providing a novel approach for screening environmental or carriage samples. The terW gene was also associated with these groups.
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27
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Multiplex PCR for detection of seven virulence factors and K1/K2 capsular serotypes of Klebsiella pneumoniae. J Clin Microbiol 2014; 52:4377-80. [PMID: 25275000 DOI: 10.1128/jcm.02316-14] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
A single multiplex PCR assay targeting seven virulence factors and the wzi gene specific for the K1 and K2 capsular serotypes of Klebsiella pneumoniae was developed and tested on 65 clinical isolates, which included 45 isolates responsible for community-acquired severe human infections. The assay is useful for the surveillance of emerging highly virulent strains.
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