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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Tootla HD, Prentice E, Moodley C, Marais G, Nyakutira N, Reddy K, Bamford C, Niehaus A, Whitelaw A, Brink A. Carbapenem-resistant Enterobacterales among hospitalized patients in Cape Town, South Africa: clinical and microbiological epidemiology. JAC Antimicrob Resist 2024; 6:dlae051. [PMID: 38523732 PMCID: PMC10959510 DOI: 10.1093/jacamr/dlae051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/03/2024] [Indexed: 03/26/2024] Open
Abstract
Background Carbapenem-resistant Enterobacterales (CRE) are a substantial problem in Cape Town. CRE epidemiology is largely unknown and mortality remains high. Objectives To describe and characterize the clinical and microbiological epidemiology of CRE within Cape Town hospitals to better inform therapy with regard to current and novel antibiotics, as well as improve antimicrobial stewardship (AMS), and infection prevention and control (IPC). Methods This prospective, multicentre study performed between 1 November 2020 and 30 November 2022, across three public and three private hospitals included hospitalized participants with CRE from clinical cultures. Participant demographics, clinical information and microbiology results were collected and analysed. Results Ninety percent of participants were from public hospitals. The age distribution ranged from 7 days to 88 years. Notable risk factors for CRE infection included recent exposure to antibiotics, medical devices and surgery. The most prevalent species was Klebsiella pneumoniae. However, a higher proportion of Serratia marcescens compared with previous reports was identified. The detected carbapenemases were blaOXA-48-like (80%) and blaNDM (11%). With the exception of amikacin (63%), tigecycline (65%), colistin (95%) and ceftazidime/avibactam (87%), susceptibility to antibiotics was low. Conclusions This study identified common risk factors for CRE infection and generated a description of carbapenemase enzymes, species distribution and antibiograms, enabling a better understanding of CRE epidemiology. This provides insights into transmission patterns and resistance determinants of CREs, beneficial to informing data-driven regional patient management, AMS and IPC strategies.
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Affiliation(s)
- Hafsah Deepa Tootla
- Division of Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Gert Marais
- Division of Medical Microbiology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Nyasha Nyakutira
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Microbiology, Pathcare, Cape Town, South Africa
| | - Abraham Niehaus
- Division of Medical Microbiology, Ampath, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Division of Medical Microbiology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Faculty of Health Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
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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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Kedišaletše M, Phumuzile D, Angela D, Andrew W, Mae NF. Epidemiology, risk factors, and clinical outcomes of carbapenem-resistant Enterobacterales in Africa: A systematic review. J Glob Antimicrob Resist 2023; 35:297-306. [PMID: 37879456 DOI: 10.1016/j.jgar.2023.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/16/2023] [Accepted: 10/18/2023] [Indexed: 10/27/2023] Open
Abstract
OBJECTIVES Carbapenem-resistant Enterobacterales (CRE) commonly cause hospital-acquired infections and hospital outbreaks worldwide, with an alarming increase in Africa, necessitating review of regional CRE epidemiological trends. METHODS A systematic review was conducted using PRISMA guidelines, searching PubMed, Scopus and Web of Science databases for studies describing CRE distribution, risk factors for CRE acquisition and clinical outcome of CRE infections in Africa. RESULTS One-hundred and sixty-nine studies were included, with the majority from North Africa (92/169, 54.4%). Most studies (136/169; 80.4%) focused only on infection, with a total of 15666 CRE isolates (97.4% clinical infection, 2.6% colonisation). The leading bacterial species included Klebsiella (72.2%), Escherichia coli (13.5%), and Enterobacter (8.3%). The most frequently detected carbapenemases were NDM (43.1%) and OXA-48-like (42.9%). Sequence types were reported in 44 studies, with ST101 and ST147 most commonly reported in K. pneumoniae, and ST410, ST167 and ST38 in E. coli. Previous antibiotic use, prior hospitalisation, surgical procedures, indwelling devices, intensive care unit admission and prolonged hospital stay, were the most frequent factors associated with CRE infection/colonisation. Crude mortality for CRE infection was 37%. CONCLUSION Although K. pneumoniae and E. coli remain the most frequent CRE in Africa, observed sequence types are not the commonly reported global 'high-risk' clones. The distribution of species and carbapenemases differs across African regions, while risk factors for CRE colonisation/infection, and patient outcomes are similar to those reported globally. There are limited data on CREs from parts of Africa, highlighting the need to strengthen epidemiologic surveillance programmes in the region.
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Affiliation(s)
- Moloto Kedišaletše
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
| | - Dube Phumuzile
- Synthetic Biology Center, NextGeneration Health, Council for Scientific and Industrial Research, Pretoria, South Africa
| | - Dramowski Angela
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Whitelaw Andrew
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Newton-Foot Mae
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
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Jafari-Sales A, Al-Khafaji NSK, Al-Dahmoshi HOM, Sadeghi Deylamdeh Z, Akrami S, Shariat A, Judi HK, Nasiri R, Bannazadeh Baghi H, Saki M. Occurrence of some common carbapenemase genes in carbapenem-resistant Klebsiella pneumoniae isolates collected from clinical samples in Tabriz, northwestern Iran. BMC Res Notes 2023; 16:311. [PMID: 37924149 PMCID: PMC10623837 DOI: 10.1186/s13104-023-06558-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 10/09/2023] [Indexed: 11/06/2023] Open
Abstract
OBJECTIVES This study aimed to evaluate the antibiotic resistance patterns and prevalence of carbapenemase genes in Klebsiella pneumoniae isolates in different clinical samples from Tabriz city, northwestern Iran. RESULTS This cross-sectional study was conducted in the Department of Microbiology, Islamic Azad University, Ahar Branch, Iran, in 2020. K. pneumoniae isolates were collected from different clinical samples, including blood, wounds, sputum, and urine. The isolates were identified using a series of standard bacteriological tests. Antibiotic resistance was determined by the disc diffusion method. The presence of blaVIM, blaNDM, blaKPC, blaOXA, and blaIMP genes were screened by polymerase chain reaction (PCR). A total of 100 non-duplicated K. pneumoniae isolates were collected from 57 urine samples, 27 blood samples, 13 wound samples, and 3 sputum samples. Overall, 70.0% of the samples were from inpatients, while 30.0% were from outpatients. The most resistance rate was related to ampicillin (94.0%), while the lowest resistance rate was related to imipenem (18.0%) and meropenem (20.0%). Overall, 25.0% of the isolates were carbapenem-resistant, of which 13.0% were resistant to both imipenem and meropenem. The PCR showed the total prevalence of 23.0% for carbapenemase genes, including 18.0% for blaKPC, 3.0% for blaVIM, 1.0% for blaIMP, and 1.0% for blaOXA gene. The blaNDM gene was not detected in any isolate. The prevalence of carbapenemase-producing K. pneumoniae isolates was relatively lower in northwestern Iran than in other regions of the country. However, special attention should be paid to the proper use of antibiotics, particularly carbapenems, to prevent further spread of antibiotic resistance and its related genes.
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Affiliation(s)
- Abolfazl Jafari-Sales
- Department of Microbiology, School of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Noor S K Al-Khafaji
- Department of Biology, College of Science, University of Babylon, Babylon, Hilla City, Iraq
| | | | - Zahra Sadeghi Deylamdeh
- Department of Biology, Faculty of Sciences, Malayer Branch, Islamic Azad University, Malayer, Iran
| | - Sousan Akrami
- Students' Scientific Research Center (SSRC), Tehran University of Medical Sciences, Tehran, Iran.
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
| | - Afsoon Shariat
- Department of Microbiology, School of Basic Sciences, Kazerun Branch, Islamic Azad University, Kazerun, Iran
| | - Hawraa K Judi
- Department of Medical Physics, Hilla University College, Babylon, Iraq
| | - Rozita Nasiri
- Iran National Elite Foundation, 93111-14578, Tehran, Iran
| | - Hossein Bannazadeh Baghi
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Morteza Saki
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran.
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Sampah J, Owusu-Frimpong I, Aboagye FT, Owusu-Ofori A. Prevalence of carbapenem-resistant and extended-spectrum beta-lactamase-producing Enterobacteriaceae in a teaching hospital in Ghana. PLoS One 2023; 18:e0274156. [PMID: 37903118 PMCID: PMC10615269 DOI: 10.1371/journal.pone.0274156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 09/18/2023] [Indexed: 11/01/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Enterobacteriaceae (CRE) and Extended-spectrum beta-lactamase (ESBL) production among Gram-negative Enterobacteriaceae is an increasing global challenge due to the high morbidity and mortality associated with their infections, especially in developing countries where there are little antibiotic treatment options. Despite these challenges, few studies in Ghana have described the burden of CRE. Therefore, this study aimed to determine the prevalence of carbapenem-resistant Enterobacteriaceae isolated from patients at the Cape Coast Teaching Hospital (CCTH) in the Central region of Ghana. METHODOLOGY/PRINCIPAL FINDINGS Enterobacteriaceae isolates were collected from April to July 2019 at the bacteriology unit of CCTH using a consecutive sampling method. Isolates were identified by standard microbiological techniques and confirmed using API 20E. Kirby Bauer disc diffusion method was used to determine the antibiogram of isolates. Isolates were also subjected to ESBL testing using the single-disc combination method. Carbapenem-resistant isolates were identified by the Kirby Bauer disc diffusion method and then examined genotypically for the presence of blaKPC-1, blaIMP-1, blaVIM-1, blaNDM-1, and blaOXA-48 genes via polymerase chain reaction (PCR). Of the 230 isolates comprising E. coli (40.9%), Citrobacter spp. (32.6%), K. pneumoniae (9.1%), P. mirabilis (6.1%), P. vulgaris (5.2%), Enterobacter spp (3.5%)., K. oxytoca (2.2%), and Serratia marcenses (0.4%). Most isolates were from urine 162(70.4%) and wound samples. The isolates showed high resistance to ampicillin 171 (74.3%) and cefuroxime 134(58.3%). The prevalence of MDR was 35.2% (81), with E. coli 40(42.6%) being the majority that exhibited MDR. Of the 230 isolates, 113(49.1%) were ESBL producers, with E. coli 54(57.5%) accounting for the majority, while Serratia marcenses was the least. Of the 13 (5.7%) CRE isolates that showed resistance towards carbapenem in the disc diffusion method, 11 showed the presence of the blaNDM-1 gene, while all isolates showed the presence of the blaOXA-48 gene. CONCLUSION The prevalence of carbapenem resistance and ESBL-producing Enterobacteriaceae pathogens among patients at the Cape Coast Teaching Hospital is high and alarming. Therefore, it is imperative to consider effective infection prevention and control measures should be implemented at the hospital to prevent the rapid spread of these dangerous organisms.
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Affiliation(s)
- James Sampah
- Department of Clinical Microbiology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Laboratory Department, St. Patrick’s Hospital, Offinso, Ghana
| | - Isaac Owusu-Frimpong
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Frank Twum Aboagye
- CSIR-Water Research Institute, Biomedical and Public Health Research Unit, Accra, Ghana
| | - Alex Owusu-Ofori
- Department of Clinical Microbiology, School of Medicine and Dentistry, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Clinical Microbiology Unit, Laboratory Services Directorate Komfo Anokye Teaching Hospital, Kumasi, Ghana
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Overmeyer AJ, Prentice E, Brink A, Lennard K, Moodley C. The genomic characterization of carbapenem-resistant Serratia marcescens at a tertiary hospital in South Africa. JAC Antimicrob Resist 2023; 5:dlad089. [PMID: 37497336 PMCID: PMC10368080 DOI: 10.1093/jacamr/dlad089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 06/26/2023] [Indexed: 07/28/2023] Open
Abstract
Background Serratia marcescens is an opportunistic nosocomial pathogen, and recent reports have highlighted the rapid increase in multidrug resistance in this organism. There is a paucity in genomic data for carbapenem-resistant S. marcescens (CRSM). Methods A retrospective cohort study describing laboratory-confirmed CRSM from a tertiary academic hospital in Cape Town, South Africa, for the period 2015-20, was performed. Stored CRSM and contemporary isolates were submitted for WGS using Illumina MiSeq, with the Nextera DNA Flex Library Preparation Kit. Sequence data were analysed in-house using srst2 and Tychus, and CRSM and contemporary isolates were compared. Results Twenty-one CRSM and four contemporary isolates were sequenced and analysed. Twenty-four different resistance genes were identified, with all isolates having at least two resistance genes, and seventeen isolates harbouring three or more genes. This correlated well with phenotypic results. The blaOXA-48-like carbapenemase was the most common carbapenemase identified, in 86% (18/21) of CRSM. A core SNP difference tree indicated that the CRSM could be grouped into three clusters. Eleven isolates had shared plasmids. Several genes and SNPs were identified in the CRSM, which may putatively augment virulence, but this requires further functional characterization. Conclusions A diverse resistome was observed in CRSM, which was also reflected phenotypically, with blaOXA-48-like the most commonly carbapenemase. Though distinct clusters were observed, no clonality was noted, and a limited number of isolates shared plasmids. This study provides genomic data for emerging CRSM and highlights the importance of ongoing genomic surveillance to inform infection prevention control and antimicrobial stewardship initiatives.
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Affiliation(s)
| | - Elizabeth Prentice
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Katie Lennard
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Groote Schuur Hospital, Cape Town, South Africa
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Perovic O, Singh-Moodley A, Lowe M. In Vitro Activity of Ceftolozane-Tazobactam against Escherichia coli, Klebsiella pneumoniae and Pseudomonas aeruginosa Obtained from Blood Cultures from Sentinel Public Hospitals in South Africa. Antibiotics (Basel) 2023; 12:antibiotics12030453. [PMID: 36978322 PMCID: PMC10044232 DOI: 10.3390/antibiotics12030453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/16/2023] [Accepted: 02/22/2023] [Indexed: 03/02/2023] Open
Abstract
Multidrug-resistant (MDR) Gram-negative bacteria are responsible for the majority of healthcare-associated infections and pose a serious threat as they complicate and prolong clinical care. A novel cephalosporin-β-lactamase-inhibitor combination, ceftolozane-tazobactam (C/T) was introduced in 2014, which improved the treatment of MDR pathogens. This study aimed to evaluate the activity of C/T against Escherichia coli (n = 100), Klebsiella pneumoniae (n = 100), and Pseudomonas aeruginosa (n = 100) blood culture isolates in South Africa (SA). Isolates were sequentially selected (2010 to 2020) from the Group for Enteric, Respiratory, and Meningeal Diseases Surveillance (GERMS) programme in SA. Organism identification was performed using the matrix-assisted laser desorption/ionisation-time of flight mass spectrometry (MALDI-TOF MS) instrument (Microflex, Bruker Daltonics, Bremen, Germany), and antibiotic susceptibility was performed using the Sensititre instrument (Trek Diagnostic Systems, East Grinstead, UK). C/T resistance was reported in 16 E. coli, 28 K. pneumoniae and 13 P. aeruginosa isolates. Fifty percent of the C/T resistant isolates were subjected to whole-genome sequencing (WGS). According to the whole genome multilocus sequence typing (MLST) analysis, the E. coli isolates (n = 8) belonged to sequence type (ST)10, ST131, ST405, and ST410, the K. pneumoniae isolates (n = 14) belonged to ST1, ST37, ST73, ST101, ST231, ST307, ST336 and ST6065 (novel ST), and the P. aeruginosa isolates (n = 7) belonged to ST111, ST233, ST273, and ST815. The WGS data also showed that all the E. coli isolates harboured aminoglycoside (aph (3′′)-Ib, aph (6)-Id), macrolide (mdfA, mphA), and sulphonamide (sul2) antibiotic resistance genes, all the K. pneumoniae isolates harboured β-lactam (blaCTX-M-15), and sulphonamide (sul2) antibiotic resistance genes, and all the P. aeruginosa isolates harboured aminoglycoside (aph (3′)-IIb), β-lactam (PAO), fosfomycin (fosA), phenicol (catB7), quinolone (crpP), and disinfectant (qacE) antibiotic resistance genes. It is evident that E. coli, K. pneumoniae and P. aeruginosa can adapt pre-existing resistance mechanisms to resist newer β-lactam molecules and inhibitors, since these isolates were not exposed to ceftolozane-tazobactam previously.
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Affiliation(s)
- Olga Perovic
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg 2193, South Africa
- Correspondence:
| | - Ashika Singh-Moodley
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg 2193, South Africa
| | - Michelle Lowe
- Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases a Division of the National Health Laboratory Service, Johannesburg 2192, South Africa
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg 2193, South Africa
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Eltahlawi RA, Jiman-Fatani A, Gad NM, Ahmed SH, Al-Rabia MW, Zakai S, Kharaba A, El-Hossary D. Detection of Carbapenem-resistance in CRE by Comparative Assessment of RAPIDEC ® CARBA NP and Xpert™Carba-R Assay. Infect Drug Resist 2023; 16:1123-1131. [PMID: 36855392 PMCID: PMC9968435 DOI: 10.2147/idr.s393739] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 02/02/2023] [Indexed: 02/24/2023] Open
Abstract
Introduction Carbapenem-resistant Enterobacteriaceae (CRE) infections resist nearly most available antimicrobials, resulting in poor clinical outcomes. Saudi Arabia has a relatively high CRE prevalence. This study aims to evaluate the sensitivity of Rapidec Carba NP test and GeneXpert Carba-R assay compared with conventional manners for detection of carbapenemase-producing Enterobacteriaceae. Methods This is a cross-sectional study including a total of 90 CRE isolates examined at two tertiary hospitals in KSA from October 2020 to December 2021. Gram-negative Enterobacteriaceae were identified by using Vitek 2 system and were furtherly tested for imipenem and meropenem susceptibility by E- test strips, followed by Rapidec Carba NP test and the Xpert™Carba-R assay. Results Carbapenem-resistant K. pneumoniae (78.9%) and carbapenem-resistant E. coli (14.4%) were the two most common isolates species. Colistin (98.9%) and tigecycline (88.9%) were the most effective antibiotics against CRE isolates, followed by amikacin (52.2%), gentamicin (33.3%), cotrimoxazole (15.6%), and ciprofloxacin (8.9%). blaOXA-48 was the predominant carbapenemase gene (44.4%), followed by blaNDM (32.2%). blaKPC gene was not detected. The Rapidec Carba NP and the Xpert™Carba-R demonstrated an overall sensitivity of 69.3% and 88%, respectively, in comparison to gold standard detection of meropenem and imipenem resistance by Vitek 2 system and E- test strips. Discussion RAPIDEC® CARBA NP may be a beneficial screening test for detecting CRE, but for confirmation of the results, Xpert Carba-R assay is more sensitive, significantly lowering the turnaround time compared to reference traditional methods. The information on carbapenemase genes may be used for epidemiologic purposes and outbreak management.
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Affiliation(s)
- Rehab A Eltahlawi
- Department of Microbiology, College of Medicine, Taibah University, Taibah, Saudi Arabia,Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt
| | - Asif Jiman-Fatani
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Clinical and Molecular Microbiology Laboratory, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Niveen M Gad
- Clinical Microbiology Laboratory, King Fahd Hospital, Medina, Saudi Arabia,Medical Microbiology and Immunology Department, Faculty of Medicine, Benha University, Benha, Egypt
| | - Shereen H Ahmed
- Medical Microbiology and Immunology Department, Faculty of Medicine, Benha University, Benha, Egypt
| | - Mohammed W Al-Rabia
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia,Health Promotion Center, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shadi Zakai
- Department of Medical Microbiology and Parasitology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Ayman Kharaba
- Intensive Care Unit, King Fahad Hospital, Madinah, Saudi Arabia
| | - Dalia El-Hossary
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Zagazig University, Zagazig, Egypt,Correspondence: Dalia El-Hossary, Email
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10
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Abrahams I, Dramowski A, Moloto K, Lloyd L, Whitelaw A, Bekker A. Colistin use in a carbapenem-resistant Enterobacterales outbreak at a South African neonatal unit. S Afr J Infect Dis 2023; 38:487. [PMID: 36756243 PMCID: PMC9900379 DOI: 10.4102/sajid.v38i1.487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/05/2022] [Indexed: 02/04/2023] Open
Abstract
Background Colistin is increasingly prescribed for neonates with carbapenem-resistant Enterobacterales (CRE) infections. Objectives We described patient demographics, infection episodes, treatment and clinical outcomes, colistin related adverse events and relatedness of isolates in neonates with clinically confirmed or clinically suspected CRE infections. Method The authors retrospectively reviewed culture-confirmed and clinically suspected culture-negative CRE infections at a South African neonatal unit during a CRE outbreak. Results Fifty-three neonates (median gestational age 29 weeks and birth weight 1185 g) were included. Twenty-three of 53 neonates (43%) had culture-confirmed CRE (17 received colistin; 6 died without receiving colistin) and 30 (57%) received colistin for clinically suspected CRE infection but were ultimately culture-negative. Prior respiratory support and surgical conditions were present in 37/53 (70%) and 19/53 (36%) neonates, respectively. Crude mortality was high (20/53; 38%) with no significant difference between culture-confirmed CRE versus clinically suspected culture-negative CRE groups (10/23 [44%] vs 10/30 [33%]; p = 0.45). Hypomagnesaemia (10/38; 26%) and hypokalaemia (15/38; 40%) were frequent; acute kidney injury was rare (1/44; 2%). Three CRE infection clusters were identified by genotypic analysis of 20 available isolates (18 [90%] bla NDM-1 [New Delhi metallo-beta-lactamase], 2 [10%] bla OXA [oxacillinase]-48). Conclusion Neonates receiving colistin therapy were predominantly preterm, with multiple risk factors for infection. Colistin-associated electrolyte derangement was frequent. Over one-third of neonates died. Bla NDM-1 was the most frequent carbapenemase gene identified in the outbreak isolates. Contribution Colistin was safely used during an Enterobacterales outbreak in predominantly premature and surgical neonates. The mortality was high.
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Affiliation(s)
- Ilhaam Abrahams
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Kedisaletse Moloto
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Lizel Lloyd
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Department of Pathology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa,National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Adrie Bekker
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
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11
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Taha MS, Hagras MM, Shalaby MM, Zamzam YA, Elkolaly RM, Abdelwahab MA, Maxwell SY. Genotypic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Isolated from an Egyptian University Hospital. Pathogens 2023; 12:121. [PMID: 36678469 PMCID: PMC9866858 DOI: 10.3390/pathogens12010121] [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: 12/12/2022] [Revised: 01/04/2023] [Accepted: 01/09/2023] [Indexed: 01/13/2023] Open
Abstract
Globally, Klebsiella pneumoniae (K. pneumoniae) has been identified as a serious source of infections. The objectives of our study were to investigate the prevalence of multidrug-resistant (MDR) K. pneumoniae in Tanta University Hospitals, Gharbia Governorate, Egypt; characterize their carbapenem resistance profiles; and identify their different capsular serotypes. We identified and isolated 160 (32%) K. pneumoniae from 500 different clinical samples, performed antimicrobial susceptibility testing, and then used multiplex PCR to detect carbapenemase genes and capsular serotypes K1, K2, K3, K5, K20, K54, and K57. We detected phenotypic carbapenem resistance in 31.3% (50/160) of the isolates; however, molecular assays revealed that 38.75% (62/160) of isolates were carrying carbapenemase-encoding genes. Generally, blaOXA-48 was the prevalent gene (15.5%), followed by blaVIM (15%), blaIMP (7.5%), blaKPC (4%), and blaNDM (3.8%). BlaVIM and blaOXA-48 correlated with phenotypic resistance in 91.67% and 88% of the isolates that harbored them, respectively. Capsular typing showed that the most prevalent pathotype was K1 (30.6%), followed by K57 (24.2%), K54 (19.35%), K20 (9.67%), and K2 (6.45%). A critical risk to community health is posed by the high incidence of multidrug-resistant (MDR) virulent K. pneumoniae isolates from our hospital, and our study examines this pathogen's public health and epidemiological risks.
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Affiliation(s)
- Marwa S. Taha
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Maha M. Hagras
- Department of Clinical Pathology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Marwa M. Shalaby
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | | | - Reham M. Elkolaly
- Department of Chest Diseases, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Marwa A. Abdelwahab
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
| | - Sara Youssef Maxwell
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Tanta University, Tanta 31527, Egypt
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12
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Duze ST, Thomas T, Pelego T, Jallow S, Perovic O, Duse A. Evaluation of Xpert Carba-R for detecting carbapenemase-producing organisms in South Africa. Afr J Lab Med 2023; 12:1898. [PMID: 36756217 PMCID: PMC9900380 DOI: 10.4102/ajlm.v12i1.1898] [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: 03/24/2022] [Accepted: 09/15/2022] [Indexed: 12/27/2022] Open
Abstract
This study evaluated the performance of the Xpert Carba-R assay for detecting the five common carbapenemases in carbapenemase-producing organisms in Johannesburg, South Africa between April 2021 and September 2021. The assay demonstrated 98% sensitivity and 97% specificity. It was also able to detect all the carbapenemases in double carbapenemase producers, as well as carbapenemases in non-fermenter organisms. The Xpert Carba-R assay, therefore, allows the rapid (< 1 h) and accurate identification of the common carbapenemases in pure bacterial cultures and rectal swabs. This assay can aid in the timeous institution of appropriate treatment and infection prevention and control measures.
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Affiliation(s)
- Sanelisiwe T. Duze
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Teena Thomas
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa,Infection Control Services Laboratory, National Health Laboratory Services, Charlotte Maxeke Academic Hospital, Johannesburg, South Africa
| | - Tshegofatso Pelego
- Infection Control Services Laboratory, National Health Laboratory Services, Charlotte Maxeke Academic Hospital, Johannesburg, South Africa
| | - Sabelle Jallow
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa,Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Olga Perovic
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa,Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Adriano Duse
- Department of Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, School of Pathology, University of the Witwatersrand, Johannesburg, South Africa,Infection Control Services Laboratory, National Health Laboratory Services, Charlotte Maxeke Academic Hospital, Johannesburg, South Africa
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13
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Abraham V, Meyer JC, Godman B, Helberg E. Perceptions of managerial staff on the patient safety culture at a tertiary hospital in South Africa. Int J Qual Stud Health Well-being 2022; 17:2066252. [PMID: 35445629 PMCID: PMC9037162 DOI: 10.1080/17482631.2022.2066252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Affiliation(s)
- Veena Abraham
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Science University, South Africa
| | - Johanna C Meyer
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Science University, South Africa
| | - Brian Godman
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Science University, South Africa
- Strathclyde Institute of Pharmacy and Biomedical Sciences, Strathclyde University, Glasgow, UK
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, UAE
| | - Elvera Helberg
- Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Science University, South Africa
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14
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Mmatli M, Leshaba TMS, Skosana LB, Mbelle NM, Osei Sekyere J. Molecular Screening of Clinical Multidrug-Resistant Gram-Negative Bacteria Shows Endemicity of Carbapenemases, Coexistence of Multiple Carbapenemases, and Rarity of mcr in South Africa. Microb Drug Resist 2022; 28:1028-1036. [PMID: 36251876 DOI: 10.1089/mdr.2022.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Extensive use of carbapenems to treat multidrug-resistant (MDR) Gram-negative bacteria (GNB) facilitates the wide dissemination of carbapenemase-producing carbapenem-resistant GNB. Colistin was reintroduced into clinical settings to manage these GNB infections. However, there is currently an increase in the dissemination of mobile colistin resistance (mcr)-producing colistin-resistant GNB isolates in clinical settings. The epidemiology of carbapenemases and mcr in Pretoria was evaluated. Methods: Clinical MDR GNB were collected and screened for carbapenemases and mcr using polymerase chain reaction (PCR); their antibiotic susceptibility profiles were elucidated using the Vitek® 2 automated system (Biomerieux, France) and microbroth dilution (for colistin). Results and Discussion: A total of 306 isolates were collected; a majority of these were Klebsiella pneumoniae (n = 208) and were collected from males (n = 158). The isolates were retrieved from a variety of infection sites, including urine, blood cultures, and rectal swabs. The Vitek 2 system found that these isolates were largely resistant to β-lactams, where 217 (70.9%) had reduced susceptibility to at least one carbapenem (ertapenem, meropenem, or imipenem), and 81 isolates (26.5%) were resistant to colistin. PCR screening identified 201 (65.7%) isolates harboring carbapenemase genes consisting of blaOXA-48 (170, 84.2%), blaNDM (31, 15.4%), blaIMP (5, 2%), blaKPC (4, 1%), and blaVIM (5, 2%). Furthermore, 14 blaOXA-48-producing isolates were coharboring blaVIM (2), blaNDM (9), blaKPC (1), and blaIMP (2) genes. Only one isolate harbored the mobile colistin resistance (mcr)-1 gene, and this is the first report of an mcr-1-producing Acinetobacter baumannii isolate in South Africa. Conclusion: There is high endemicity of carbapenemase genes and a low prevalence of mcr genes in GNB, particularly in K. pneumoniae, in health care facilities in Pretoria and surrounding regions of South Africa. Significance: Health care facilities in Pretoria are becoming breeding grounds for MDR infections that threaten public health. Careful use of carbapenems and other antibiotics is necessary to prevent further escalation and outbreak of these MDR strains that can claim several lives.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | | | - Lebogang B Skosana
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Tshwane Academic Division, Department of Medical Microbiology, National Health Laboratory Service, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
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15
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Ma J, Song X, Li M, Yu Z, Cheng W, Yu Z, Zhang W, Zhang Y, Shen A, Sun H, Li L. Global Spread of Carbapenem-Resistant Enterobacteriaceae: Epidemiological Features, Resistance Mechanisms, Detection and Therapy. Microbiol Res 2022; 266:127249. [DOI: 10.1016/j.micres.2022.127249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 10/25/2022] [Accepted: 10/28/2022] [Indexed: 11/06/2022]
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16
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Brink AJ, Coetzee J, Richards GA, Feldman C, Lowman W, Tootla HD, Miller MGA, Niehaus AJ, Wasserman S, Perovic O, Govind CN, Schellack N, Mendelson M. Best practices: Appropriate use of the new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam in South Africa. S Afr J Infect Dis 2022; 37:453. [PMID: 36338193 PMCID: PMC9634826 DOI: 10.4102/sajid.v37i1.453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023] Open
Abstract
Antibiotic stewardship of hospital-acquired infections because of difficult-to-treat resistant (DTR) Gram-negative bacteria is a global challenge. Their increasing prevalence in South Africa has required a shift in prescribing in recent years towards colistin, an antibiotic of last resort. High toxicity levels and developing resistance to colistin are narrowing treatment options further. Recently, two new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam were registered in South Africa, bringing hope of new options for management of these life-threatening infections. However, with increased use in the private sector, increasing levels of resistance to ceftazidime-avibactam are already being witnessed, putting their long-term viability as treatment options of last resort, in jeopardy. This review focuses on how these two vital new antibiotics should be stewarded within a framework that recognises the resistance mechanisms currently predominant in South Africa's multi-drug and DTR Gram-negative bacteria. Moreover, the withholding of their use for resistant infections that can be treated with currently available antibiotics is a critical part of stewardship, if these antibiotics are to be conserved in the long term.
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Affiliation(s)
- Adrian J Brink
- Division of Medical Microbiology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jennifer Coetzee
- Division of Microbiology, Ampath National Reference Laboratory, Centurion, South Africa
| | - Guy A Richards
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Warren Lowman
- Department of Clinical Microbiology, Pathcare/Vermaak Pathologists, Gauteng, South Africa, South Africa
- Department Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- Department of Clinical Microbiology and Infection Prevention and Control, Wits Donald Gordon Medical Centre, Johannesburg, South Africa
| | - Hafsah D Tootla
- Division of Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Malcolm G A Miller
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Abraham J Niehaus
- Department of Medical Microbiology, Ampath Laboratory Services, Cape Town, South Africa
| | - Sean Wasserman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Olga Perovic
- National Institute for Communicable Disease, National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chetna N Govind
- Department of Medical Microbiology, Lancet Laboratories, KwaZulu-Natal, Durban, South Africa
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Natalie Schellack
- Department of Pharmacology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
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17
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Kashkouri N, Tabarsi P, Pourabdollah Toutkaboni M, Kazempour Dizaji M, Bahrami N, Narimani A, Mohamadnia A, Askari E. The Prevalence of Carbapenemase Genes in Carbapenem-resistant Gram-negative Bacilli, Masih Daneshvari Hospital, Tehran, Iran, 2019-2020. IRANIAN JOURNAL OF MEDICAL MICROBIOLOGY 2022. [DOI: 10.30699/ijmm.16.6.573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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18
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Carbapenem-resistant Enterobacterales in patients with bacteraemia at tertiary academic hospitals in South Africa, 2019 - 2020: An update. S Afr Med J 2022; 112:542-552. [DOI: 10.7196/samj.2022.v112i8.16351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Indexed: 11/08/2022] Open
Abstract
Background. The emergence of carbapenem-resistant Enterobacterales (CRE) has become a serious and significant public health threat worldwide, owing to the limited antimicrobial therapy options, and the elevated mortality rates associated with these infections.Objectives. To present an update on the epidemiology of CRE bloodstream infections among hospitalised patients reported under the Group for Enteric, Respiratory and Meningeal Diseases Surveillance in South Africa (GERMS-SA) between January 2019 and December 2020. Methods. Patients of all ages with CRE bacteraemia were included and isolates, when available, were sent to the reference laboratory for confirmatory testing and molecular characterisation. Multivariable logistic regression analysis was performed to assess factors associated with in-hospital mortality.
Results. We included 2 144 patients with CRE bacteraemia with a median age of 33 (interquartile range 1 - 51) years, of whom 1 145 (54.2%) were male. Klebsiella pneumoniae accounted for 79.8% of infections (n=863/1 082), of which 89.5% (n=611/683) were healthcare associated (HA). The most common carbapenemase genes were carbapenem-hydrolysing oxacillinase-48 (blaOXA-48-like) (76.8%; n=761/991), New Delhi metallo-β-lactamase (blaNDM) (21.1%; n=209/991) and Verona integron-encoded metallo-β-lactamase (blaVIM) (1.3%; n=13/991). None of the screened isolates with a colistin minimum inhibitory concentration >2 μg/mL harboured the mobilised colistin resistance (mcr)-1 to mcr-5 genes. The crude in-hospital mortality rate was 36.6% (n=377/1 029). Patients aged ≥60 years (v. 1.6 - 9 years) (adjusted odds ratio (aOR) 4.53; 95% confidence interval (CI) 2.21 - 9.28), those with comorbidities (diabetes, malignancy, renal and/or cardiovascular failure) (aOR 1.72; 95% CI 1.17 - 2.52), those with altered mental state (aOR 5.36; 95% CI 3.21 - 8.92) and those with previous antimicrobial use (aOR 1.88; 95% CI 1.27 - 2.77) had increased odds of in-hospital mortality.
Conclusion. The epidemiology of CRE bloodstream infections remained similar compared with the previous surveillance report. Most infections were HA and caused by OXA-48-like carbapenemase-producing K. pneumoniae with no plasmid-mediated colistin resistance. Standard infection control measures should be strengthened.
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19
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Nana T, Perovic O, Chibabhai V. Comparison of carbapenem minimum inhibitory concentrations of OXA-48-like Klebsiella pneumoniae by Sensititre, Vitek 2, MicroScan and Etest. Clin Microbiol Infect 2022; 28:1650.e1-1650.e5. [PMID: 35811020 DOI: 10.1016/j.cmi.2022.06.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 06/15/2022] [Accepted: 06/21/2022] [Indexed: 11/25/2022]
Abstract
OBJECTIVES The aim of this laboratory-based study was to compare carbapenem minimum inhibitory concentrations (MICs) yielded by Sensititre, Vitek 2, MicroScan WalkAway plus and Etest for OXA-48-like Klebsiella pneumoniae isolates. METHODS Analysis was performed for categorical agreement for ertapenem, meropenem and imipenem, and the proportion of isolates with MICs ≤8μg/mL and the MIC50/MIC90 for meropenem and imipenem, from a convenience sample of 82 deduplicated blood culture OXA-48-like K. pneumoniae isolates. RESULTS The proportion of isolates testing susceptible to ertapenem by Etest (19/82, 23.1%) differed from Sensititre/Vitek (0/82) and MicroScan (2/82, 2.4%) (p<0.001 for all). For meropenem the proportion of isolates susceptible by Etest (31/82, 37.8%) differed from Sensititre/Vitek (16/82, 19.5%) (p=0.015). There was variation in the proportion of isolates that tested imipenem susceptible when comparing Sensititre (9/82, 11%) and Vitek (8/82, 9.8%) to MicroScan (27/82, 32.9%), p=0.001 and p<0.001, respectively, Sensititre and Vitek to Etest (45/82, 54.9%), p<0.001 for both, and MicroScan to Etest, p=0.007. The proportion of isolates with meropenem MICs ≤8μg/mL with Sensititre and Vitek differed significantly from Etest, 58.5% and 85.4%, respectively, p<0.001. A 2-fold difference between the Sensititre and Vitek meropenem and imipenem MIC at which ≥50% of isolates were inhibited compared to the MicroScan, and a 4-fold difference compared to Etest, was present. CONCLUSIONS Substantial variability in carbapenem MICs for OXA-48-like CPE isolates by the four methods was demonstrated. Performance characteristics verification of MIC methods in use for the predominant CPE type is required by laboratories to optimise accuracy of carbapenem reporting.
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Affiliation(s)
- Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg, South Africa; Charlotte Maxeke Johannesburg academic Hospital Microbiology Laboratory, National Health Laboratory Services, South Africa.
| | - Olga Perovic
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg, South Africa; Centre for Healthcare-Associated Infections, Antimicrobial Resistance and Mycoses, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, South Africa
| | - Vindana Chibabhai
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, University of Witwatersrand, Johannesburg, South Africa; Charlotte Maxeke Johannesburg academic Hospital Microbiology Laboratory, National Health Laboratory Services, South Africa
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20
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Nogbou ND, Ramashia M, Nkawane GM, Allam M, Obi CL, Musyoki AM. Whole-Genome Sequencing of a Colistin-Resistant Acinetobacter baumannii Strain Isolated at a Tertiary Health Facility in Pretoria, South Africa. Antibiotics (Basel) 2022; 11:594. [PMID: 35625238 PMCID: PMC9138137 DOI: 10.3390/antibiotics11050594] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii's (A. baumannii) growing resistance to all available antibiotics is of concern. The study describes a colistin-resistant A. baumannii isolated at a clinical facility from a tracheal aspirate sample. Furthermore, it determines the isolates' niche establishment ability within the tertiary health facility. METHODS An antimicrobial susceptibility test, conventional PCR, quantitative real-time PCR, phenotypic evaluation of the efflux pump, and whole-genome sequencing and analysis were performed on the isolate. RESULTS The antimicrobial susceptibility pattern revealed a resistance to piperacillin/tazobactam, ceftazidime, cefepime, cefotaxime/ceftriaxone, imipenem, meropenem, gentamycin, ciprofloxacin, trimethoprim/sulfamethoxazole, tigecycline, and colistin. A broth microdilution test confirmed the colistin resistance. Conventional PCR and quantitative real-time PCR investigations revealed the presence of adeB, adeR, and adeS, while mcr-1 was not detected. A MIC of 0.38 µg/mL and 0.25 µg/mL was recorded before and after exposure to an AdeABC efflux pump inhibitor. The whole-genome sequence analysis of antimicrobial resistance-associated genes detected beta-lactam: blaOXA-66; blaOXA-23; blaADC-25; blaADC-73; blaA1; blaA2, and blaMBL; aminoglycoside: aph(6)-Id; aph(3″)-Ib; ant(3″)-IIa and armA) and a colistin resistance-associated gene lpsB. The whole-genome sequence virulence analysis revealed a biofilm formation system and cell-cell adhesion-associated genes: bap, bfmR, bfmS, csuA, csuA/B, csuB, csuC, csuD, csuE, pgaA, pgaB, pgaC, and pgaD; and quorum sensing-associated genes: abaI and abaR and iron acquisition system associated genes: barA, barB, basA, basB, basC, basD, basF, basG, basH, basI, basJ, bauA, bauB, bauC, bauD, bauE, bauF, and entE. A sequence type classification based on the Pasteur scheme revealed that the isolate belongs to sequence type ST2. CONCLUSIONS The mosaic of the virulence factors coupled with the resistance-associated genes and the phenotypic resistance profile highlights the risk that this strain is at this South African tertiary health facility.
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Affiliation(s)
- Noel-David Nogbou
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Mbudzeni Ramashia
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Granny Marumo Nkawane
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
| | - Mushal Allam
- Department of Genetics and Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain 15551, United Arab Emirates;
| | - Chikwelu Lawrence Obi
- School of Sciences and Technology, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa;
| | - Andrew Munyalo Musyoki
- Microbiological Pathology Department, School of Medicine, Sefako Makgatho Health Sciences University, Pretoria 0204, South Africa; (N.-D.N.); (M.R.); (G.M.N.)
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21
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Wang M, Earley M, Chen L, Hanson BM, Yu Y, Liu Z, Salcedo S, Cober E, Li L, Kanj SS, Gao H, Munita JM, Ordoñez K, Weston G, Satlin M, Valderrama-Beltrán SL, Marimuthu K, Stryjewski ME, Komarow L, Luterbach C, Marshall S, Rudin SD, Manca C, Paterson DL, Reyes J, Villegas MV, Evans S, Hill C, Arias R, Baum K, Fries BC, Doi Y, Patel R, Kreiswirth BN, Bonomo RA, Chambers HF, Fowler VG, Arias CA, van Duin D. Clinical outcomes and bacterial characteristics of carbapenem-resistant Klebsiella pneumoniae complex among patients from different global regions (CRACKLE-2): a prospective, multicentre, cohort study. THE LANCET. INFECTIOUS DISEASES 2022; 22:401-412. [PMID: 34767753 PMCID: PMC8882129 DOI: 10.1016/s1473-3099(21)00399-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/05/2021] [Accepted: 07/02/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a global threat. We therefore analysed the bacterial characteristics of CRKP infections and the clinical outcomes of patients with CRKP infections across different countries. METHODS In this prospective, multicentre, cohort study (CRACKLE-2), hospitalised patients with cultures positive for CRKP were recruited from 71 hospitals in Argentina, Australia, Chile, China, Colombia, Lebanon, Singapore, and the USA. The first culture positive for CRKP was included for each unique patient. Clinical data on post-hospitalisation death and readmission were collected from health records, and whole genome sequencing was done on all isolates. The primary outcome was a desirability of outcome ranking at 30 days after the index culture, and, along with bacterial characteristics and 30-day all-cause mortality (a key secondary outcome), was compared between patients from China, South America, and the USA. The desirability of outcome ranking was adjusted for location before admission, Charlson comorbidity index, age at culture, Pitt bacteremia score, and anatomical culture source through inverse probability weighting; mortality was adjusted for the same confounders, plus region where relevant, through multivariable logistic regression. This study is registered at ClinicalTrials.gov, NCT03646227, and is complete. FINDINGS Between June 13, 2017, and Nov 30, 2018, 991 patients were enrolled, of whom 502 (51%) met the criteria for CRKP infection and 489 (49%) had positive cultures that were considered colonisation. We observed little intra-country genetic variation in CRKP. Infected patients from the USA were more acutely ill than were patients from China or South America (median Pitt bacteremia score 3 [IQR 2-6] vs 2 [0-4] vs 2 [0-4]) and had more comorbidities (median Charlson comorbidity index 3 [IQR 2-5] vs 1 [0-3] vs 1 [0-2]). Adjusted desirability of outcome ranking outcomes were similar in infected patients from China (n=246), South America (n=109), and the USA (n=130); the estimates were 53% (95% CI 42-65) for China versus South America, 50% (41-61) for the USA versus China, and 53% (41-66) for the USA versus South America. In patients with CRKP infections, unadjusted 30-day mortality was lower in China (12%, 95% CI 8-16; 29 of 246) than in the USA (23%, 16-30; 30 of 130) and South America (28%, 20-37; 31 of 109). Adjusted 30-day all-cause mortality was higher in South America than in China (adjusted odds ratio [aOR] 4·82, 95% CI 2·22-10·50) and the USA (aOR 3·34, 1·50-7·47), with the mortality difference between the USA and China no longer being significant (aOR 1·44, 0·70-2·96). INTERPRETATION Global CRKP epidemics have important regional differences in patients' baseline characteristics and clinical outcomes, and in bacterial characteristics. Research findings from one region might not be generalisable to other regions. FUNDING The National Institutes of Health.
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Affiliation(s)
- Minggui Wang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
| | - Michelle Earley
- The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, New Jersey, USA
| | - Blake M. Hanson
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, United States of America,Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, United States of America
| | - Yunsong Yu
- Sir Run Run Shaw Hospital, Zhejiang University-School of Medicine, Hangzhou, Zhejiang, China
| | - Zhengyin Liu
- Infectious Disease Section, Department of Internal Medicine, Peking Union Medical College Hospital, Beijing, China
| | - Soraya Salcedo
- Organizacion Clinica General del Norte, Barranquilla, Atlántico, Colombia,Universidad Simón Bolívar, Facultad de Ciencias de la Salud, Barranquilla, Colombia
| | - Eric Cober
- Department of Infectious Diseases, Cleveland Clinic, Cleveland, Ohio, United States of America
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital of Medical School of Zhejiang University, Hangzhou, Zhejiang, China
| | - Souha S. Kanj
- Division of Infectious Disease, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hainv Gao
- Shulan Hangzhou Hospital, Shulan Health, Hangzhou, Zhejiang Province, China
| | - Jose M. Munita
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, United States of America,Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R) and Instituto de Ciencias e Innovación en Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Karen Ordoñez
- E.S.E Hospital Universitario, San Jorge de Pereira, Pereira, Colombia
| | - Greg Weston
- Division of Infectious Diseases, Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York, United States of America
| | - Michael Satlin
- Division of Infectious Diseases, Weill Cornell Medicine, New York-Presbyterian Hospital, New York, New York, United States of America
| | - Sandra L. Valderrama-Beltrán
- Infectious Diseases Research Group, Hospital Universitario San Ignacio, Pontificia Universidad Javeriana, School of Medicine, Bogotá, Colombia
| | - Kalisvar Marimuthu
- Department of Infectious Diseases, Tan Tock Seng Hospital, Singapore,National Centre for Infectious Diseases, Singapore
| | - Martin E. Stryjewski
- Department of Medicine and Division of Infectious Diseases, Centro de Educación Médica e Investigaciones Clínicas (CEMIC), Buenos Aires, Argentina
| | - Lauren Komarow
- The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Courtney Luterbach
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Steve Marshall
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Susan D. Rudin
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America
| | - Claudia Manca
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America
| | - David L. Paterson
- University of Queensland Centre for Clinical Research, Royal Brisbane and Women’s Hospital Campus, Queensland, Australia
| | - Jinnethe Reyes
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque. Bogotá, Colombia,Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Maria V. Villegas
- Grupo de Resistencia Antimicrobiana y Epidemiología Hospitalaria, Universidad El Bosque. Bogotá, Colombia,Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Scott Evans
- The Biostatistics Center, The George Washington University, Rockville, Maryland, United States of America
| | - Carol Hill
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Rebekka Arias
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Keri Baum
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Bettina C. Fries
- Department of Medicine, Division of Infectious Diseases, Stony Brook University, Stony Brook, New York, United States of America
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, United States of America,Departments of Microbiology and Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, United States of America,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Barry N. Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, New Jersey, United States of America
| | - Robert A. Bonomo
- Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, United States of America,Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America,Departments of Pharmacology, Molecular Biology and Microbiology, Biochemistry, and Proteomics and Bioinformatics, Case Western Reserve University School of Medicine, Cleveland, Ohio, United States of America,CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, United States of America
| | - Henry F. Chambers
- Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Vance G. Fowler
- Duke Clinical Research Institute, Duke University Medical Center, Durham, North Carolina, United States of America
| | - Cesar A. Arias
- Division of Infectious Diseases and Center for Antimicrobial Resistance and Microbial Genomics, UTHealth, McGovern School of Medicine at Houston, Houston, Texas, United States of America,Center for Infectious Diseases, UTHealth School of Public Health, Houston, Texas, United States of America,Molecular Genetics and Antimicrobial Resistance Unit, International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA.
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22
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Ramsamy Y, Mlisana KP, Amoako DG, Abia ALK, Ismail A, Allam M, Mbanga J, Singh R, Essack SY. Mobile genetic elements-mediated Enterobacterales-associated carbapenemase antibiotic resistance genes propagation between the environment and humans: A One Health South African study. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150641. [PMID: 34606866 DOI: 10.1016/j.scitotenv.2021.150641] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 06/13/2023]
Abstract
We, (1) studied carbapenem-resistant Enterobacterales (CRE) in the environment, humans, and animals, within the same geographical area and, (2) delineated the isolates' resistome, mobilome, virulome, and phylogeny. Following ethical approval, 587 samples (humans = 230, pigs = 345, and water = 12) were collected and cultured on CRE selective media. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK 2 automated platform. The resistomes, virulomes, mobilomes, and phylogenies were ascertained by whole genome sequencing. Nineteen (3.2%), i.e., 15/19 humans and 4/19 environmental, but no pig, CRE were obtained. CREs included Klebsiella pneumoniae 9/19 (47%), Enterobacter hormaechei 6/19 (32%), Klebsiella quasipneumoniae 2/19 (11%), a novel ST498 Citrobacter freundii 1/19 (5%) and Serratia marcescens 1/19 (5%). Eleven isolates were extensively drug-resistant; eight were multidrug-resistant. Sixteen CRE harbored the blaOXA-181, blaOXA-48, blaOXA-484, blaNDM-1, and blaGES-5 genes. Multiple species/clones carried blaOXA-48 and blaNDM-1 carbapenemase-encoding genes with respective mobile genetic elements (MGEs). The IncFIB(K) plasmid replicon was found in most human K. pneumoniae strains (7/9) and all environmental K. quasipneumoniae isolates; most K. pneumoniae produced OXA-181 (5/9). The (Col440I) plasmid replicon, identified in 11 (26.82%) isolates, mainly E. hormaechei (n = 6), predominated both sectors. Most β-lactamase-encoding genes were associated with class 1 integrons IntI1, insertion sequences (IS) (IS91, IS5075, IS30, IS3000, IS3, IS19, ISKpn19, IS5075) and transposons (Tn3). The IncL/M(pMU407) and IncL/M(pOXA48) plasmid replicons were found exclusively in K. pneumoniae; all but one of these strains produced OXA-181. Also, the Klebsiella spp. harbored 80 virulence genes. Phylogenomic clustered identified isolates with other carbapenemase-producing K. pneumoniae, E. hormaechei, S. marcescens, and C. freundii from different South African sources (animals, environment, and humans). We delineated the resistome, mobilome, virulome, and phylogeny of carbapenemase-producing Enterobacterales in humans and environment, highlighting antibiotic resistance genes propagation via MGEs across sectors, emphasizing a One Health approach to AMR.
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Affiliation(s)
- Yogandree Ramsamy
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa; Medical Microbiology, National Health Laboratory Services, Durban, South Africa; Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Koleka P Mlisana
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Daniel G Amoako
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Joshua Mbanga
- Department of Applied Biology and Biochemistry, National University of Science and Technology, Bulawayo, Zimbabwe
| | - Ravesh Singh
- Medical Microbiology, National Health Laboratory Services, Durban, South Africa
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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23
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Treatment of Severe Infections Due to Metallo-Betalactamases Enterobacterales in Critically Ill Patients. Antibiotics (Basel) 2022; 11:antibiotics11020144. [PMID: 35203747 PMCID: PMC8868391 DOI: 10.3390/antibiotics11020144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/19/2022] [Accepted: 01/21/2022] [Indexed: 02/06/2023] Open
Abstract
Metallo-beta-lactamases-producing (MBL) Enterobacterales is a growing problem worldwide. The optimization of antibiotic therapy is challenging. The pivotal available therapeutic options are either the combination of ceftazidime/avibactam and aztreonam or cefiderocol. Colistin, fosfomycin, tetracyclines and aminoglycosides are also frequently effective in vitro, but are associated with less bactericidal activity or more toxicity. Prior to the availability of antibiotic susceptibility testing, severe infections should be treated with a combination therapy. A careful optimization of the pharmacokinetic/pharmacodynamic properties of antimicrobials is instrumental in severe infections. The rules of antibiotic therapy are also reported and discussed. To conclude, treatment of severe MBL infections in critically ill patients is difficult. It should be individualized with a close collaboration of intensivists with microbiologists, pharmacists and infection control practitioners.
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24
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Simeon P, Godman B, Kalemeera F. Antibiotics' susceptibility patterns of bacterial isolates causing lower respiratory tract infections in ICU patients at referral hospitals in Namibia. Hosp Pract (1995) 2021; 49:356-363. [PMID: 34436942 DOI: 10.1080/21548331.2021.1973825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lower respiratory tract infections (LRTIs) are a particular public health concern especially among sub-Saharan African countries. This is especially the case in Namibia, where LRTIs are currently the third leading cause of death, 300 deaths in children under 5 years of age. To reduce the burden of LRTIs on health systems and ensure appropriate patient management, it is critical to know the most prevalent pathogens leading to LRTIs and their susceptibility patterns in the local setting. Consequently, the objective of this study was to formulate cumulative antibiograms for Intensive Care Units (ICUs) of referral hospitals in Namibia to guide future antibiotic use. METHODS A retrospective analytical cross-sectional study was conducted over 2 years. The cumulative antibiograms were constructed in accordance with current guidelines. RESULTS A total of 976 first isolate cultures were obtained from ICUs of the different referral hospitals. K. pneumoniae (8.8%, 8.1%) was a predominant pathogen in Windhoek Central hospital ICU in 2017 and 2018. In Oshakati intermediate hospital ICU, Enterobacter sp. (22.2%) and P. aeruginosa (37.5%) were the common pathogens in 2017 and 2018, respectively. A. baumannii isolates were >90% susceptibility to colistin, carbapenems, and tigecycline in 2017. In 2017, K. pneumoniae isolates were more susceptible to carbapenems (94% and 93.8% among isolates), amikacin (89.3%), and tigecycline (88.7%). In 2018, K. pneumoniae isolates were 100% susceptible amikacin, colistin, and carbapenems. S. maltophilia isolates were more than 80% susceptible to all the tested antibiotics. S. aureus isolates were 100% susceptible to linezolid, rifampicin, teicoplanin, and vancomycin in 2017 and in 2018. Its susceptibility to these antibiotics did not change. CONCLUSION The susceptibility patterns of the common isolated gram-negative pathogens were highly variable. Meropenem in combination with gentamicin is now the recommended antibiotic combination for empiric therapy for patients with LRTIs in Windhoek Central Hospital ICU.
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Affiliation(s)
- Pia Simeon
- School of Pharmacy, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
| | - Brian Godman
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, UK.,Division of Public Health Pharmacy and Management, School of Pharmacy, Sefako Makgatho Health Sciences University, Pretoria, South Africa.,School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Francis Kalemeera
- School of Pharmacy, Faculty of Health Sciences, University of Namibia, Windhoek, Namibia
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25
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Rule R, Paruk F, Becker P, Neuhoff M, Chausse J, Said M. Diagnostic accuracy of the BioFire FilmArray blood culture identification panel when used in critically ill patients with sepsis. J Microbiol Methods 2021; 189:106303. [PMID: 34411640 DOI: 10.1016/j.mimet.2021.106303] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 08/12/2021] [Accepted: 08/13/2021] [Indexed: 12/29/2022]
Abstract
Sepsis accounts for high mortality rates in critical care units. Prompt and accurate identification of causative pathogens and initiation of appropriate antimicrobial therapy is critical for the appropriate management of patients in order to optimise clinical outcomes. The BioFire FilmArray blood culture identification (BCID) panel is a US Food and Drug Administration (FDA) approved rapid, multiplex polymerase chain reaction (PCR) assay that is able to identify a variety of bacteria, fungi and antimicrobial resistance determinants directly from positive blood cultures. The aim of this study was to evaluate the diagnostic performance of the BioFire FilmArray BCID panel against the gold standard of blood cultures. Seventy-eight positive blood cultures obtained from critically ill patients suspected of having sepsis were included in the study. Each bottle was processed with the BioFire FilmArray BCID panel as well as conventional culture methods. Diagnostic accuracy of the BioFire FilmArray BCID panel was determined. The assay demonstrated a high sensitivity and specificity for pathogen identification of 96.5% (95% CI, 91.3-99.0) and 99.7% (95% CI, 99.3-99.9), respectively. The findings of this study support the role of the BioFire FilmArray BCID panel in the management of critically ill patients with sepsis.
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Affiliation(s)
- Roxanne Rule
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa.
| | - Fathima Paruk
- Department of Critical Care, Steve Biko Academic Hospital, Pretoria, South Africa; Department of Critical Care, University of Pretoria, Pretoria, South Africa
| | - Piet Becker
- Department of Biostatics, University of Pretoria, South Africa
| | - Matthew Neuhoff
- Department of Critical Care, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Julian Chausse
- Department of Critical Care, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Mohamed Said
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa; Tshwane Academic Division, National Health Laboratory Service, Pretoria, South Africa
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26
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Zhang H, Guo Z, Chai Y, Fang YP, Mu X, Xiao N, Guo J, Wang Z. Risk Factors for and Clinical Outcomes of Carbapenem-Resistant Klebsiella pneumoniae Nosocomial Infections: A Retrospective Study in a Tertiary Hospital in Beijing, China. Infect Drug Resist 2021; 14:1393-1401. [PMID: 33880044 PMCID: PMC8053504 DOI: 10.2147/idr.s298530] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/18/2021] [Indexed: 11/23/2022] Open
Abstract
Purpose Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections have been increasingly reported worldwide. We aimed to identify the risk factors for nosocomial CRKP infections and assess the clinical outcomes. Patients and Methods We conducted a case-control study with data collected from January 2016 to December 2018 in China. Controls were selected at a ratio of 1:1 from patients with nosocomial carbapenem-susceptible Klebsiella pneumonia (CSKP) infections. Risk factors for nosocomial CRKP infections and clinical outcomes were assessed with univariate and multivariate analyses. Results A total of one hundred forty-two patients with CRKP infections and one hundred forty-two patients with CSKP infections were enrolled in this study. Multivariate analysis showed that exposure to antibiotics within 3 months prior to admission (odds ratio OR, 2.585; 95% confidence interval [CI], 1.425–4.691; P=0.002), exposure to carbapenems (OR, 2.532; 95% CI, 1.376–4.660; P=0.003), exposure to fluoroquinolones (OR, 3.309; 95% CI, 1.326–8.257; P=0.010), and the presence of a nasogastric tube (OR, 2.796; 95% CI, 1.369–5.712; P=0.005) were independent risk factors for CRKP infections. The 30-day mortality rate in the CRKP group was 19.7%, while the in-hospital mortality rate was 28.9%. In the CRKP group, a higher creatinine level (OR, 1.009; 95% CI, 1.002–1.016; P = 0.013), being in shock at the time of a positive culture (OR, 4.454; 95% CI, 1.374–14.443; P = 0.013), and co-infection with other resistant bacteria (OR, 4.799; 95% CI, 1.229–18.740; P = 0.024) were independent predictors of in-hospital mortality in patients with CRKP infections. Kaplan–Meier curves showed that the CRKP group had a shorter survival time than the CSKP group. Conclusion Nosocomial CRKP infection was associated with exposure to carbapenems and fluoroquinolones within 3 months prior to hospitalization and the presence of a nasogastric tube. Patients infected with CRKP had higher 30-day and in-hospital mortality rates. A higher creatinine level, shock and co-infection with other resistant bacteria were independent predictors of in-hospital mortality in patients with CRKP infections.
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Affiliation(s)
- Huijuan Zhang
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Zhe Guo
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China.,Department of Liver Intensive Care Unit, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Yan Chai
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Yi-Peng Fang
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China
| | - Xiangdong Mu
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Nan Xiao
- Department of Laboratory Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Jun Guo
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China.,Department of Pulmonary and Critical Care Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Zhong Wang
- School of Clinical Medicine, Tsinghua University, Beijing, 100084, People's Republic of China.,Department of General Practice Medicine, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
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27
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Ssekatawa K, Byarugaba DK, Nakavuma JL, Kato CD, Ejobi F, Tweyongyere R, Eddie WM. Prevalence of pathogenic Klebsiella pneumoniae based on PCR capsular typing harbouring carbapenemases encoding genes in Uganda tertiary hospitals. Antimicrob Resist Infect Control 2021; 10:57. [PMID: 33736698 PMCID: PMC7977577 DOI: 10.1186/s13756-021-00923-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 03/02/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is an opportunistic pathogen that has been implicated as one of commonest cause of hospital and community acquired infections. The K. pneumoniae infections have considerably contributed to morbidity and mortality in patients with protracted ailments. The capacity of K. pneumoniae to cause diseases depends on the presence of an array virulence factors. Coexistence and expression of virulence factors and genetic determinants of antibiotic resistance complicates treatment outcomes. Thus, emergence of pathogenic MDR K. pneumoniae poses a great threat to the healthcare system. However, the carriage of antibiotic resistance among pathogenic K. pneumoniae is yet to be investigated in Uganda. We sought to investigate the carbapenem resistance profiles and pathogenic potential based on capsular serotypes of K. pneumoniae clinical isolates. METHODS This was a cross sectional study involving use of archived Klebsiella pneumoniae isolates collected between January and December, 2019 at four tertiary hospitals in Uganda. All isolates were subject to antimicrobial susceptibility assays to determine phenotypic antibiotic resistance, pentaplex PCR to detect carbapenemases encoding genes and heptaplex PCR to identify capsular serotypes K1, K2, K3, K5, K20, K54 and K57. RESULTS The study found an overall phenotypic carbapenem resistance of 23.3% (53/227) and significantly higher genotypic resistance prevalence of 43.1% (98/227). Over all, the most prevalent gene was blaOXA-48-like (36.4%), followed by blaIMP-type (19.4%), blaVIM-type (17.1%), blaKPC-type (14.0%) and blaNDM-type (13.2%). blaVIM-type and blaOXA-48-like conferred phenotypic resistance in all isolates and 38.3% of isolates that harbored them respectively. Capsular multiplex PCR revealed that 46.7% (106/227) isolates were pathogenic and the predominantly prevalent pathotype was K5 (18.5%) followed by K20 (15.1%), K3 (7.1%), K2 (3.1%) and K1 (2.2%). Of the 106 capsular serotypes, 37 expressed phenotypic resistance; thus, 37 of the 53 carbapenem resistant K. pneumoniae were pathogenic. CONCLUSION The high prevalence of virulent and antibiotic resistant K. pneumoniae among clinical isolates obtained from the four tertiary hospital as revealed by this study pose a great threat to healthcare. Our findings underline the epidemiological and public health risks and implications of this pathogen.
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Affiliation(s)
- Kenneth Ssekatawa
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
- Department of Biochemistry, Faculty of Biomedical Sciences, Kampala International University-Western Campus, P. O. Box 71, Bushenyi, Uganda
- Africa Center Excellence in Materials Product Development and Nanotechnology (MAPRONANO ACE), College of Engineering Design Art and Technology, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Denis K. Byarugaba
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Jesca L. Nakavuma
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Charles D. Kato
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Francis Ejobi
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Robert Tweyongyere
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Wampande M. Eddie
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, P. O. Box 7062, Kampala, Uganda
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Tshitshi L, Manganyi MC, Montso PK, Mbewe M, Ateba CN. Extended Spectrum Beta-Lactamase-Resistant Determinants among Carbapenem-Resistant Enterobacteriaceae from Beef Cattle in the North West Province, South Africa: A Critical Assessment of Their Possible Public Health Implications. Antibiotics (Basel) 2020; 9:E820. [PMID: 33213050 PMCID: PMC7698526 DOI: 10.3390/antibiotics9110820] [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: 10/23/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/27/2022] Open
Abstract
Carbapenems are considered to be the last resort antibiotics for the treatment of infections caused by extended-spectrum beta-lactamase (ESBL)-producing strains. The purpose of this study was to assess antimicrobial resistance profile of Carbapenem-resistant Enterobacteriaceae (CRE) isolated from cattle faeces and determine the presence of carbapenemase and ESBL encoding genes. A total of 233 faecal samples were collected from cattle and analysed for the presence of CRE. The CRE isolates revealed resistance phenotypes against imipenem (42%), ertapenem (35%), doripenem (30%), meropenem (28%), cefotaxime, (59.6%) aztreonam (54.3%) and cefuroxime (47.7%). Multidrug resistance phenotypes ranged from 1.4 to 27% while multi antibiotic resistance (MAR) index value ranged from 0.23 to 0.69, with an average of 0.40. Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), Proteus mirabilis (P. mirabilis) and Salmonella (34.4, 43.7, 1.3 and 4.6%, respectively) were the most frequented detected species through genus specific PCR analysis. Detection of genes encoding carbapenemase ranged from 3.3% to 35% (blaKPC, blaNDM, blaGES, blaOXA-48, blaVIM and blaOXA-23). Furthermore, CRE isolates harboured ESBL genes (blaSHV (33.1%), blaTEM (22.5%), blaCTX-M (20.5%) and blaOXA (11.3%)). In conclusion, these findings indicate that cattle harbour CRE carrying ESBL determinants and thus, proper hygiene measures must be enforced to mitigate the spread of CRE strains to food products.
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Affiliation(s)
- Lungisile Tshitshi
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
- Faculty of Agriculture and Natural Sciences, University of Mpumalanga, Private Bag X11283, Mbombela 1200, South Africa;
| | - Madira Coutlyne Manganyi
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa;
| | - Peter Kotsoana Montso
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
| | - Moses Mbewe
- Faculty of Agriculture and Natural Sciences, University of Mpumalanga, Private Bag X11283, Mbombela 1200, South Africa;
| | - Collins Njie Ateba
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
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