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Yang J, Xiong Y, Barkema HW, Tong X, Lin Y, Deng Z, Kastelic JP, Nobrega DB, Wang Y, Han B, Gao J. Comparative genomic analyses of Klebsiella pneumoniae K57 capsule serotypes isolated from bovine mastitis in China. J Dairy Sci 2024; 107:3114-3126. [PMID: 37944808 DOI: 10.3168/jds.2023-23721] [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: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 11/12/2023]
Abstract
Klebsiella pneumoniae can cause severe clinical mastitis in dairy cows, with K. pneumoniae type K57 (K57-KP) being the most common capsular serotype. To identify virulence factors and antimicrobial-resistance (AMR) genes of K57-KP with varying virulence, Galleria mellonella (greater wax moth) larvae were infected as a screening model to characterize virulence of 90 K57-KP strains, with 10 and 11 strains defined as virulent or attenuated, respectively, based on larval survival rates. Next, virulence of these 21 isolates was subsequently confirmed in adhesion and lactate dehydrogenase release assays, using bovine mammary epithelial cells cultured in vitro. Finally, genes associated with virulence and AMR were characterize with whole-genome sequencing. These 21 K57-KP strains were designated into 16 sequence types based on multi-locus sequence typing and allocated in phylogenetic analysis based on single nucleotide polymorphisms. We found great genetic diversity among isolates. In addition, adhesion-associated genes (e.g., fimA, sfaA, and focA) aminoglycoside-resistance genes (aph(6)-Id, strAB) were associated with virulence. This study provided new knowledge regarding virulence of K57-KP associated with bovine mastitis, which may inform development of novel diagnostic tools and prevention strategies for bovine mastitis.
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Affiliation(s)
- Jingyue Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yindi Xiong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Herman W Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Xiaofang Tong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yushan Lin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhaoju Deng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - John P Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Diego B Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Yue Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Kabui S, Kimani J, Ngugi C, Kagira J. Prevalence and antimicrobial resistance profiles of mastitis causing bacteria isolated from dairy goats in Mukurweini Sub-County, Nyeri County, Kenya. Vet Med Sci 2024; 10:e1420. [PMID: 38546016 PMCID: PMC10976424 DOI: 10.1002/vms3.1420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 02/16/2024] [Accepted: 03/01/2024] [Indexed: 05/03/2024] Open
Abstract
BACKGROUND Ruminant mastitis continues to be a cause of economic losses in the dairy industry and remains a major public health hazard globally. OBJECTIVES This cross-sectional study was carried out in Mukurweini Sub-County of Nyeri County, Kenya, to investigate the prevalence of bacteria causing mastitis, risk factors associated with goat mastitis and the antibiotic resistance profiles of bacteria isolated from the goat milk. METHODS Farm level data on risk factors for mastitis was obtained from 56 farmers using a semi structured questionnaire. A total of 189 goat milk samples were collected. The goat's udder was observed for signs of clinical mastitis and the California Mastitis Test (CMT) used to test the milk for sub-clinical mastitis. All samples were then cultured for morphological identification of bacteria and strain typing by Matrix Assisted Laser Desorption/Ionization (MALDI)-Time of Flight (ToF) technique. Antimicrobial susceptibility of the isolated Staphylococcus aureus, coagulase-negative Staphylococcus (CoNS), Escherichia coli, Klebsiella oxytoca, Pseudomonas spp., Enterobacter spp., Proteus vulgaris and Escherichia vulneris to eight commonly used antibiotics was done by the disc diffusion method and validated by determining the presence of antibiotic resistance genes (mecA and blaTEM) using polymerase chain reaction method. RESULTS The prevalence of clinical mastitis was 1.1% (2/189) while that of sub-clinical mastitis was 84.7% (160/189). Higher (p < 0.05) prevalence of mastitis was observed in goats whose houses were cleaned fortnightly and in cases where farmers used same towel to dry different does' udders during the milking process. Thirteen different bacterial species were isolated from the milk samples and identified by MALDI-ToF, and these included S. aureus (22.0%), CoNS (20.3%), E. coli (18.1%), Pseudomonas spp. (14.3%), Enterobacter spp. (10.4%), K. oxytoca (6.0%), E. vulneris (1.7%), P. vulgaris (1.7%), Raoutella ornithinolytica (1.7%), Stenotrophomonas maltophilia (1.1%), Pantoea agglomerans (1.1%), Serratia marcescens (1.1%) and Cedeceas spp. (0.6%). One hundred pathogenic bacterial isolates were randomly selected and tested for antibiotic sensitivity to eight antibiotics out of which S. aureus were 97.5% resistant to Oxacillin and 100% sensitive to Ciprofloxacin. The CoNSs were 100% resistant to Oxacillin and 100% sensitive to Ciprofloxacin. E. coli were 93.9% resistant to Oxacillin, 69.7% sensitive to Ciprofloxacin and 87.9% sensitive to both Amoxicillin/Clavulanic acid and Meropenem. The antimicrobial resistant genes detected in S. aureus and E. coli were mecA [66.7%, 0%], and blaTEM [20% and 78.3%], respectively. CONCLUSION In conclusion, the study showed that most of the does were affected by subclinical mastitis with the main causative bacteria being Staphylococci spp. and coliforms. Farmers need to be trained on improved control of mastitis by adoption of good milking practices and use of CMT kit for early detection of mastitis. Occurrence of multidrug resistance by key mastitis causing pathogens was shown to be prevalent and therefore there is need for development of intervention strategies.
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Affiliation(s)
- Sarah Kabui
- Department of BiochemistryJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Josephine Kimani
- Department of BiochemistryJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - Caroline Ngugi
- Department of Medical MicrobiologyJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
| | - John Kagira
- Department of Animal SciencesJomo Kenyatta University of Agriculture and TechnologyNairobiKenya
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Chelaru EC, Muntean AA, Hogea MO, Muntean MM, Popa MI, Popa GL. The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden. Antibiotics (Basel) 2024; 13:295. [PMID: 38666971 PMCID: PMC11047529 DOI: 10.3390/antibiotics13040295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.
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Affiliation(s)
- Edgar-Costin Chelaru
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Andrei-Alexandru Muntean
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
- Department of Microbiology, Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania
| | - Mihai-Octav Hogea
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Mădălina-Maria Muntean
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Mircea-Ioan Popa
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
- Department of Microbiology, Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania
| | - Gabriela-Loredana Popa
- Department of Microbiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Parasitic Disease Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Ofosu-Appiah F, Acquah EE, Mohammed J, Sakyi Addo C, Agbodzi B, Ofosu DAS, Myers CJ, Mohktar Q, Ampomah OW, Ablordey A, Amissah NA. Klebsiella pneumoniae ST147 harboring blaNDM-1, multidrug resistance and hypervirulence plasmids. Microbiol Spectr 2024; 12:e0301723. [PMID: 38315028 PMCID: PMC10913492 DOI: 10.1128/spectrum.03017-23] [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: 08/03/2023] [Accepted: 12/17/2023] [Indexed: 02/07/2024] Open
Abstract
The spread of hypervirulent (hv) and carbapenem-/multidrug-resistant Klebsiella pneumoniae is an emerging problem in healthcare settings. The New Delhi metallo-β-lactamase-1 (blaNDM-1) is found in Enterobacteriaceae including K. pneumoniae. The blaNDM-1 is capable of hydrolyzing β-lactam antibiotics which are used for treatment of severe infections caused by multidrug-resistant Gram-negative bacteria. This is associated with the unacceptably high mortality rate in immunocompromised burn injury patients. This study reports on the characterization of blaNDM-1 gene and virulence factors in hv carbapenem-/multidrug-resistant K. pneumoniae ST147 in the burns unit of a tertiary teaching hospital during routine surveillance. Two K. pneumoniae strains were obtained from wounds of burn-infected patients from May 2020 to July 2021. The hypervirulence genes and genetic context of the blaNDM-1 gene and mobile genetic elements potentially involved in the transposition of the gene were analyzed. We identified a conserved genetic background and an IS26 and open reading frame flanking the blaNDM-1 gene that could suggest its involvement in the mobilization of the gene. The plasmid harbored additional antibiotic resistance predicted regions that were responsible for resistance to almost all the routinely used antibiotics. To ensure the identification of potential outbreak strains during routine surveillance, investigations on resistance genes and their environment in relation to evolution are necessary for molecular epidemiology.IMPORTANCEData obtained from this study will aid in the prompt identification of disease outbreaks including evolving resistance and virulence of the outbreak bacteria. This will help establish and implement antimicrobial stewardship programs and infection prevention protocols in fragile health systems in countries with limited resources. Integration of molecular surveillance and translation of whole-genome sequencing in routine diagnosis will provide valuable data for control of infection. This study reports for the first time a high-risk clone K. pneumoniae ST147 with hypervirulence and multidrug-resistance features in Ghana.
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Affiliation(s)
- Frederick Ofosu-Appiah
- West African Centre for Cell Biology of Infectious Pathogens, University of Ghana, Accra, Ghana
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ezra E. Acquah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Jibril Mohammed
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Comfort Sakyi Addo
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Bright Agbodzi
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Dorcas A. S. Ofosu
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Charles J. Myers
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Quaneeta Mohktar
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Opoku-Ware Ampomah
- The Burns Unit, Reconstructive Plastic Surgery and Burns Unit, Korle Bu Teaching Hospital, Accra, Ghana
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Nana Ama Amissah
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
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Dinda V, Kimang’a AN, Kariuki D, Sifuna AW, O’Brien TJ, Welch M, Reva ON. Whole genome sequencing and genotyping Klebsiella pneumoniae multi-drug resistant hospital isolates from Western Kenya. Access Microbiol 2024; 6:000667.v4. [PMID: 38361654 PMCID: PMC10866029 DOI: 10.1099/acmi.0.000667.v4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/08/2024] [Indexed: 02/17/2024] Open
Abstract
Objectives Klebsiella pneumoniae are a frequent cause of nosocomial infections worldwide. Sequence type 147 (ST147) has been reported as a major circulating high-risk lineage in many countries, and appears to be a formidable platform for the dissemination of antimicrobial resistance (AMR) determinants. However, the distribution of this pathogen in Western African hospitals has been scarcely studied. The main objective of this work was to perform whole genome sequencing of K. pneumoniae isolates from a referral hospital in Kakamega (Kenya) for genotyping and identification of AMR and virulence determinants. Methods In total, 15 K. pneumoniae isolates showing a broad spectrum antimicrobial resistance were selected for whole genome sequencing by Illumina HiSeq 2500 platform. Results ST147 was the dominant lineage among the highly-resistant K. pneumoniae isolates that we sequenced. ST147 was associated with both community- and the hospital-acquired infections, and with different infection sites, whereas other STs were predominantly uropathogens. Multiple antibiotic resistance and virulence determinants were detected in the genomes including extended-spectrum β-lactamases (ESBL) and carbapenemases. Many of these genes were plasmid-borne. Conclusions Our data suggest that the evolutionary success of ST147 may be linked with the acquisition of broad host-range plasmids, and their propensity to accrue AMR and virulence determinants. Although ST147 is a dominant lineage in many countries worldwide, it has not been previously reported as prevalent in Africa. Our data suggest an influx of new nosocomial pathogens with new virulence genes into African hospitals from other continents.
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Affiliation(s)
- Victor Dinda
- Department of Medical Laboratory Science, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Andrew Nyerere Kimang’a
- Department of Medical Microbiology, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Daniel Kariuki
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Anthony Wawire Sifuna
- Department of Medical Biochemistry, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Thomas James O’Brien
- Department of Biochemistry, University of Cambridge, Hopkins Building, Cambridge, UK
| | - Martin Welch
- Department of Biochemistry, University of Cambridge, Hopkins Building, Cambridge, UK
| | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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Zhao Y, Qian C, Ye J, Li Q, Zhao R, Qin L, Mao Q. Convergence of plasmid-mediated Colistin and Tigecycline resistance in Klebsiella pneumoniae. Front Microbiol 2024; 14:1221428. [PMID: 38282729 PMCID: PMC10813211 DOI: 10.3389/fmicb.2023.1221428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 11/15/2023] [Indexed: 01/30/2024] Open
Abstract
Objective The co-occurrence of colistin and tigecycline resistance genes in Klebsiella pneumoniae poses a serious public health problem. This study aimed to characterize a K. pneumoniae strain, K82, co-harboring a colistin resistance gene (CoRG) and tigecycline resistance gene (TRG), and, importantly, investigate the genetic characteristics of the plasmid with CoRG or TRG in GenBank. Methods K. pneumoniae strain K82 was subjected to antimicrobial susceptibility testing, conjugation assay, and whole-genome sequencing (WGS). In addition, comparative genomic analysis of CoRG or TRG-harboring plasmids from K82 and GenBank was conducted. K. pneumoniae strain K82 was resistant to all the tested antimicrobials including colistin and tigecycline, except for carbapenems. Results WGS and bioinformatic analysis showed that K82 belonged to the ST656 sequence type and carried multiple drug resistance genes, including mcr-1 and tmexCD1-toprJ1, which located on IncFIA/IncHI2/IncHI2A/IncN/IncR-type plasmid pK82-mcr-1 and IncFIB/IncFII-type plasmid pK82-tmexCD-toprJ, respectively. The pK82-mcr-1 plasmid was capable of conjugation. Analysis of the CoRG/TRG-harboring plasmid showed that mcr-8 and tmexCD1-toprJ1 were the most common CoRG and TRG of Klebsiella spp., respectively. These TRG/CoRG-harboring plasmids could be divided into two categories based on mash distance. Moreover, we found an IncFIB/IncHI1B-type plasmid, pSYCC1_tmex_287k, co-harboring mcr-1 and tmexCD1-toprJ1. To the best of our knowledge, this is the first report on the co-occurrence of mcr-1 and tmexCD1-toprJ1 on a single plasmid. Conclusion Our research expands the known diversity of CoRG and TRG-harboring plasmids in K. pneumoniae. Effective surveillance should be implemented to assess the prevalence of co-harboring CoRG and TRG in a single K. pneumoniae isolate or even a single plasmid.
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Affiliation(s)
- Yujie Zhao
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Changrui Qian
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Ye
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Qingcao Li
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Rongqing Zhao
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Ling Qin
- Department of Clinical Laboratory, The Affiliated Li Huili Hospital, Ningbo University, Ningbo, China
| | - Qifeng Mao
- Department of Clinical Laboratory, Ningbo No. 2 Hospital, Ningbo, China
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Miliotis G, McDonagh F, Singh NK, O'Connor L, Tuohy A, Morris D, Venkateswaran K. Genomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station. Microbiol Spectr 2023; 11:e0189723. [PMID: 37966203 PMCID: PMC10715203 DOI: 10.1128/spectrum.01897-23] [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: 05/05/2023] [Accepted: 09/27/2023] [Indexed: 11/16/2023] Open
Abstract
IMPORTANCE The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the "high-risk" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.
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Affiliation(s)
- Georgios Miliotis
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Francesca McDonagh
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Nitin Kumar Singh
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
| | - Louise O'Connor
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Alma Tuohy
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, University of Galway, Galway, Ireland
| | - Kasthuri Venkateswaran
- Biotechnology and Planetary Protection Group, NASA Jet Propulsion Laboratory, California Institute of Technology, Pasadena, California, USA
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Emeraud C, Mahamat A, Jousset AB, Bernabeu S, Goncalves T, Pommier C, Girlich D, Birer A, Rodriguez C, Pawlotsky JM, Naas T, Bonnin RA, Dortet L. Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022. Euro Surveill 2023; 28:2300095. [PMID: 37855905 PMCID: PMC10588306 DOI: 10.2807/1560-7917.es.2023.28.42.2300095] [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: 02/06/2023] [Accepted: 06/26/2023] [Indexed: 10/20/2023] Open
Abstract
BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Aba Mahamat
- Corsica Centre for Healthcare-Associated Infections Control and Prevention, Hôpital Eugénie, Ajaccio, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Tania Goncalves
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Camille Pommier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Aurélien Birer
- Centre National de Référence de la Résistance aux antibiotiques, Service de Bactériologie, CHU Gabriel-Montpied, Clermont-Ferrand, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
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9
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Kigen C, Muraya A, Kyanya C, Kingwara L, Mmboyi O, Hamm T, Musila L. Enhancing capacity for national genomics surveillance of antimicrobial resistance in public health laboratories in Kenya. Microb Genom 2023; 9:mgen001098. [PMID: 37646415 PMCID: PMC10483422 DOI: 10.1099/mgen.0.001098] [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: 02/24/2023] [Accepted: 08/06/2023] [Indexed: 09/01/2023] Open
Abstract
Genomic surveillance is vital for detecting outbreaks and understanding the epidemiology and transmission of bacterial strains, yet it is not integrated into many national antimicrobial resistance (AMR) surveillance programmes. Key factors are that few scientists in the public health sector are trained in bacterial genomics, and the diverse sequencing platforms and bioinformatic tools make it challenging to generate reproducible outputs. In Kenya, these gaps were addressed by training public health scientists to conduct genomic surveillance on isolates from the national AMR surveillance repository and produce harmonized reports. The 2-week training combined theory and laboratory and bioinformatic experiences with Klebsiella pneumoniae isolates from the surveillance repository. Whole-genome sequences generated on Illumina and Nanopore sequencers were analysed using publicly available bioinformatic tools, and a harmonized report was generated using the HAMRonization tool. Pre- and post-training tests and self-assessments were used to assess the effectiveness of the training. Thirteen scientists were trained and generated data on the K. pneumoniae isolates, summarizing the AMR genes present consistently with the reported phenotypes and identifying the plasmid replicons that could transmit antibiotic resistance. Ninety per cent of the participants demonstrated an overall improvement in their post-training test scores, with an average increase of 14 %. Critical challenges were experienced in delayed delivery of equipment and supplies, power fluctuations and internet connections that were inadequate for bioinformatic analysis. Despite this, the training built the knowledge and skills to implement bacterial genomic surveillance. More advanced and immersive training experiences and building supporting infrastructure would solidify these gains to produce tangible public health outcomes.
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Affiliation(s)
- Collins Kigen
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
| | - Angela Muraya
- Jomo Kenyatta University of Agriculture and Technology, P. O. Box 62000-00200, Nairobi, Kenya
| | - Cecilia Kyanya
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
| | - Leonard Kingwara
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Onesmus Mmboyi
- National Public Health Laboratory Services, Kenyatta National Hospital Grounds, Hospital Road, P.O Box 20750 -00202, Nairobi, Kenya
| | - Tiffany Hamm
- Henry M. Jackson Foundation for the Advancement of Military Medicine, 6720A Rockledge Drive, Bethesda, Maryland, USA
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, P. O. Box 606-00621, Village Market, Nairobi, Kenya
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10
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Altayb HN, Hosawi S, Baothman O, Kazmi I, Chaieb K, Abu Zeid IM, Elbadawi HS, Lopes BS, Moglad E. Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes. Front Public Health 2023; 10:1068888. [PMID: 36711372 PMCID: PMC9878601 DOI: 10.3389/fpubh.2022.1068888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae. Methods Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools. Results Six strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, bla OKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of bla SHV-1, bla OXA-1, aac(6')-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3")-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH). Conclusion Our study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.
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Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Hisham N. Altayb ✉
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M. Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom,National Horizons Centre, Teesside University, Darlington, United Kingdom,Bruno Silvester Lopes ✉
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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11
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Long-Read Whole Genome Sequencing Elucidates the Mechanisms of Amikacin Resistance in Multidrug-Resistant Klebsiella pneumoniae Isolates Obtained from COVID-19 Patients. Antibiotics (Basel) 2022; 11:antibiotics11101364. [PMID: 36290022 PMCID: PMC9598329 DOI: 10.3390/antibiotics11101364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/28/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative, encapsulated, non-motile bacterium, which represents a global challenge to public health as one of the major causes of healthcare-associated infections worldwide. In the recent decade, the World Health Organization (WHO) noticed a critically increasing rate of carbapenem-resistant K. pneumoniae occurrence in hospitals. The situation with extended-spectrum beta-lactamase (ESBL) producing bacteria further worsened during the COVID-19 pandemic, due to an increasing number of patients in intensive care units (ICU) and extensive, while often inappropriate, use of antibiotics including carbapenems. In order to elucidate the ways and mechanisms of antibiotic resistance spreading within the K. pneumoniae population, whole genome sequencing (WGS) seems to be a promising approach, and long-read sequencing is especially useful for the investigation of mobile genetic elements carrying antibiotic resistance genes, such as plasmids. We have performed short- and long read sequencing of three carbapenem-resistant K. pneumoniae isolates obtained from COVID-19 patients in a dedicated ICU of a multipurpose medical center, which belonged to the same clone according to cgMLST analysis, in order to understand the differences in their resistance profiles. We have revealed the presence of a small plasmid carrying aph(3′)-VIa gene providing resistance to amikacin in one of these isolates, which corresponded perfectly to its phenotypic resistance profile. We believe that the results obtained will facilitate further elucidating of antibiotic resistance mechanisms for this important pathogen, and highlight the need for continuous genomic epidemiology surveillance of clinical K. pneumoniae isolates.
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