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Ibrahim K, Thwood D, ELgheriani H, Salem M, Elgadiym Z, Zaghdani A, Alhudiri I, Habibi A, Elfahem A, Belaid S, Ermithi O, Almaghrabi M, ELmaryul A, Almadah S, Rayes A, El Meshri SE, El Salabi A, Elzagheid A. Prevalence of multi-drug resistant bacteria in intensive care units at Tripoli University Hospital, Tripoli, Libya. Libyan J Med 2024; 19:2348235. [PMID: 38718270 PMCID: PMC11080667 DOI: 10.1080/19932820.2024.2348235] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 04/23/2024] [Indexed: 05/12/2024] Open
Abstract
Among hospitalized patients worldwide, infections caused by multidrug-resistant (MDR) bacteria are a major cause of morbidity and mortality. This study aimed to isolate MDR bacteria from five intensive care units (ICUs) at Tripoli University Hospital (TUH). A prospective cross-sectional study was conducted over a seven-month period (September 2022 to March 2023) across five ICUs at TUH. A total of 197 swabs were collected from Patients', healthcare workers' and ICUs equipment. Samples collected from patients were nasal swabs, oral cavity swabs, hand swabs, sputum specimens, skin swabs, umbilical venous catheter swabs, and around cannula. Swabs collected from health care workers were nasal swabs, whereas ICUs equipment's samples were from endotracheal tubes, oxygen masks, and neonatal incubators. Identification and antimicrobial susceptibility test was confirmed by using MicroScan auto SCAN 4 (Beckman Coulter). The most frequent strains were Gram negative bacilli 113 (57.4%) with the predominance of Acinetobacter baumannii 50/113 (44%) followed by Klebsiella pneumoniae 44/113 (40%) and Pseudomonas aeruginosa 6/113 (5.3%). The total Gram positive bacterial strains isolated were 84 (42.6%), coagulase negative Staphylococci 55 (66%) with MDRs (89%) were the most common isolates followed by Staphylococcus aureus 15 (17.8%). Different antibiotics were used against these isolates; Gram- negative isolates showed high resistance rates to ceftazidime, gentamicin, amikacin and ertapenem. A. baumannii were the most frequent MDROs (94%), and the highest resistance rates in Gram-positive strains were observed toward ampicillin, oxacillin, ampicillin/sulbactam and Cefoxitin, representing 90% of total MDR Gram-positive isolates. ESBL and MRS were identified in most of strains. The prevalence of antibiotic resistance was high for both Gram negative and Gram positive isolates. This prevalence requires strict infection prevention and control intervention, continuous monitoring, implementation of effective antibiotic stewardship, immediate, concerted and collaborative action to monitor its prevalence and spread in the hospital.
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Affiliation(s)
- Khaled Ibrahim
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Dalal Thwood
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Hajer ELgheriani
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Mohamed Salem
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Zaynab Elgadiym
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Ahmed Zaghdani
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Inas Alhudiri
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Abdulraouf Habibi
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Abdurrezagh Elfahem
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Saadeddin Belaid
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Otman Ermithi
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Mahmoud Almaghrabi
- Pediatric Intensive Care Unit, Tripoli University Hospital, Tripoli, Libya
| | - Abubaker ELmaryul
- Medical Intensive Care Unit, Tripoli University Hospital, Tripoli, Libya
| | - Suad Almadah
- Neonatal Intensive Care Unit, Tripoli University Hospital, Tripoli, Libya
| | - Abdunnabi Rayes
- Infection Control Office, Tripoli University Hospital, Tripoli, Libya
| | - Salah Edin El Meshri
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
| | - Allaaeddin El Salabi
- Department of Environmental Health, Faculty of Public Health, University of Benghazi, Benghazi, Libya
| | - Adam Elzagheid
- Department of Microbiology, Libyan Biotechnology Research Center, Tripoli, Libya
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Lo CKF, Ritchie G, Bilawka J, Gowland L, Chorlton SD, Jang W, Matic N, Romney MG, Stefanovic A, Lowe CF. Evaluating the accuracy of the MBT Lipid Xtract Kit for assessing colistin resistance in comparison to broth microdilution. J Med Microbiol 2024; 73:001881. [PMID: 39222340 PMCID: PMC11368154 DOI: 10.1099/jmm.0.001881] [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: 03/18/2024] [Accepted: 08/04/2024] [Indexed: 09/04/2024] Open
Abstract
Colistin resistance testing methods such as broth microdilution (BMD) are time-consuming and labour intensive for clinical laboratories. MBT Lipid Xtract Kit on MALDI Biotyper Sirius System (Bruker, Billerica, MA, USA) utilizes lipidomic analysis to identify specific cell wall modifications associated with colistin resistance. We compared MBT to BMD (ComASP Colistin, Liofilchem) across 36 Gram-negative isolates (non-resistant MIC ≤2 µg ml-1, resistant MIC ≥4 µg ml-1). All samples were tested twice on MBT with discrepant results repeated before assessing categorical agreement between MBT and BMD. 44.4% (16/36) of isolates were colistin resistant via BMD. MBT Lipid Xtract had 80.6% agreement (29/36) with BMD, with 5/7 discrepancies corrected to match upon repeat testing. There was 100% agreement for Escherichia coli isolates (n=16). The whole-genome sequencing was completed on the two discrepant Klebsiella pneumoniae isolates, with variants within colistin resistance-associated loci identified (MIC 0.5 µg ml-1: arnC S30T, pmrB T246A, lapB N212T, lpxM S253G, crrB Q287K and MIC >16 µg ml-1: arnC S30T, pmrB R90insRN, pmrB T246A, pmrA E57G, lpxM S253G). Further evaluation, particularly for non-E. coli, of MBT is required prior to implementation in clinical laboratories.
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Affiliation(s)
- Calvin Ka-Fung Lo
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Gordon Ritchie
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Jennifer Bilawka
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Leah Gowland
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | | | - Willson Jang
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Nancy Matic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Marc G. Romney
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Aleksandra Stefanovic
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
| | - Christopher F. Lowe
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Division of Medical Microbiology and Virology, Providence Health Care, St. Paul’s Hospital, Vancouver, British Columbia, Canada
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Khoshbayan A, Narimisa N, Elahi Z, Bostanghadiri N, Razavi S, Shariati A. Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Front Microbiol 2024; 15:1386478. [PMID: 38912352 PMCID: PMC11190090 DOI: 10.3389/fmicb.2024.1386478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae. Methods Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed. Results Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%. Conclusion Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.
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Affiliation(s)
- Amin Khoshbayan
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Narimisa
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vice Chancellery of Education and Research, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Narjess Bostanghadiri
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine research center, Khomein University of Medical Sciences, Khomein, Iran
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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García-Romero I, Srivastava M, Monjarás-Feria J, Korankye SO, MacDonald L, Scott NE, Valvano MA. Drug efflux and lipid A modification by 4-L-aminoarabinose are key mechanisms of polymyxin B resistance in the sepsis pathogen Enterobacter bugandensis. J Glob Antimicrob Resist 2024; 37:108-121. [PMID: 38552872 DOI: 10.1016/j.jgar.2024.03.012] [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: 12/16/2023] [Revised: 02/27/2024] [Accepted: 03/14/2024] [Indexed: 04/26/2024] Open
Abstract
OBJECTIVES A concern with the ESKAPE pathogen, Enterobacter bugandensis, and other species of the Enterobacter cloacae complex, is the frequent appearance of multidrug resistance against last-resort antibiotics, such as polymyxins. METHODS Here, we investigated the responses to polymyxin B (PMB) in two PMB-resistant E. bugandensis clinical isolates by global transcriptomics and deletion mutagenesis. RESULTS In both isolates, the genes of the CrrAB-regulated operon, including crrC and kexD, displayed the highest levels of upregulation in response to PMB. ∆crrC and ∆kexD mutants became highly susceptible to PMB and lost the heteroresistant phenotype. Conversely, heterologous expression of CrrC and KexD proteins increased PMB resistance in a sensitive Enterobacter ludwigii clinical isolate and in the Escherichia coli K12 strain, W3110. The efflux pump, AcrABTolC, and the two component regulators, PhoPQ and CrrAB, also contributed to PMB resistance and heteroresistance. Additionally, the lipid A modification with 4-L-aminoarabinose (L-Ara4N), mediated by the arnBCADTEF operon, was critical to determine PMB resistance. Biochemical experiments, supported by mass spectrometry and structural modelling, indicated that CrrC is an inner membrane protein that interacts with the membrane domain of the KexD pump. Similar interactions were modeled for AcrB and AcrD efflux pumps. CONCLUSION Our results support a model where drug efflux potentiated by CrrC interaction with membrane domains of major efflux pumps combined with resistance to PMB entry by the L-Ara4N lipid A modification, under the control of PhoPQ and CrrAB, confers the bacterium high-level resistance and heteroresistance to PMB.
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Affiliation(s)
- Inmaculada García-Romero
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom; Centro Andaluz de Biología del Desarrollo, CSIC-Universidad Pablo de Olavide, Sevilla, Spain
| | - Mugdha Srivastava
- Functional Genomics & Systems Biology Group, Department of Bioinformatics, Biocenter, Am Hubland, University of Wuerzburg, Wuerzburg, Germany; Core Unit Systems Medicine, University of Wuerzburg, Wuerzburg, Germany
| | - Julia Monjarás-Feria
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Samuel O Korankye
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Lewis MacDonald
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom
| | - Nichollas E Scott
- Department of Microbiology and Immunology, University of Melbourne, Melbourne, Australia
| | - Miguel A Valvano
- Wellcome-Wolfson Institute for Experimental Medicine, Queen's University Belfast, United Kingdom.
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Talat A, Khan F, Khan AU. Genome analyses of colistin-resistant high-risk bla NDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings. BMC Microbiol 2024; 24:174. [PMID: 38769479 PMCID: PMC11103832 DOI: 10.1186/s12866-024-03306-4] [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: 12/19/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT). RESULTS This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357). CONCLUSION The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.
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Affiliation(s)
- Absar Talat
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Fatima Khan
- Microbiology Department, JNMC and Hospital, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Bhatia M, Shamanna V, Nagaraj G, Gupta P, Omar BJ, Diksha, Rohilla R, Ravikumar KL. Assessment of in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates using four commercially available systems & Whole-genome sequencing: A diagnostic accuracy study. Diagn Microbiol Infect Dis 2024; 108:116155. [PMID: 38219381 DOI: 10.1016/j.diagmicrobio.2023.116155] [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: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
AIM To analyze the diagnostic utility of commercially available platforms and Whole-genome sequencing (WGS) for accurate determination of colistin susceptibility test results. MATERIAL & METHODS An exploratory diagnostic accuracy study was conducted in which sixty carbapenem-resistant Gram-negative bacteria were subjected to identification and AST using MALDI-TOF MS & MicroScan walkaway 96 Plus. Additional AST was performed using the BD Phoenix system and Mikrolatest colistin kit. The test isolates were subjected to Vitek-2 and WGS at CRL, Bengaluru. RESULTS There was no statistically significant agreement between the colistin susceptibility results obtained by WGS, with those of commercial phenotypic platforms. The MicroScan 96 Plus had the highest sensitivity (31 %) & NPV (77 %), and the BD Phoenix system had the highest specificity (97 %) and PPV (50 %), respectively, for determining colistin resistance. CONCLUSION The utility of WGS as a tool in AMR surveillance and validation of phenotypic AST methods should be explored further.
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Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi, 110029, India.
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India; Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, Karnataka 574110, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Deoghar, Jharkhand 814152, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Diksha
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Ranjana Rohilla
- Department of Microbiology, Sri Guru Ram Rai Institute of Medical & Health Science, Dehradun, Uttarakhand 248001, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
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Tunç MN, Guéneau V, Loux V, Del Campo R, Carballido Lopez R, Briandet R. Genome sequences of four colistin-resistant ESKAPE bacterial strains isolated from patients within the same hospital. Microbiol Resour Announc 2024; 13:e0087423. [PMID: 38112476 DOI: 10.1128/mra.00874-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 11/18/2023] [Indexed: 12/21/2023] Open
Abstract
The genomes of four clinical Gram-negative ESKAPE bacterial strains highly resistant to the last-resort antibiotic colistin were sequenced and analyzed. The strains were found to carry multidrug-resistant genes besides colistin-resistant genes.
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Affiliation(s)
- Merve Nur Tunç
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute , Jouy-en-Josas, France
| | - Virgile Guéneau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute , Jouy-en-Josas, France
- Lallemand SAS , Blagnac, France
| | - Valentin Loux
- Université Paris-Saclay, INRAE, MaIAGE , Jouy-en-Josas, France
- INRAE, BioinfOmics, MIGALE bioinformatics facility, Université Paris-Saclay , Jouy-en-Josas, France
| | - Rosa Del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria , Madrid, Spain
| | - Rut Carballido Lopez
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute , Jouy-en-Josas, France
| | - Romain Briandet
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute , Jouy-en-Josas, France
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Ficik J, Andrezál M, Drahovská H, Böhmer M, Szemes T, Liptáková A, Slobodníková L. Carbapenem-Resistant Klebsiella pneumoniae in COVID-19 Era-Challenges and Solutions. Antibiotics (Basel) 2023; 12:1285. [PMID: 37627705 PMCID: PMC10451955 DOI: 10.3390/antibiotics12081285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 07/25/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
The COVID-19 era brought about new medical challenges, which, together with nosocomial bacterial infections, resulted in an enormous burden for the healthcare system. One of the most alarming nosocomial threats was carbapenem-resistant Klebsiella pneumoniae (CRKP). Monitoring CRKP incidence and antimicrobial resistance globally and locally is vitally important. In a retrospective study, the incidence of CRKP in the pre-COVID-19 period (2017-2019) and the COVID-19 pandemic (2020-2022) was investigated in the Central Military Hospital in Ružomberok, Slovak Republic. The relative incidence of CRKP significantly increased during the COVID-19 period-by 4.8 times, from 0.18 to 0.76%. At the same time, 47% of CRKP-positive patients also had COVID-19. Twenty-six KPC and sixty-nine NDM-producing isolates were identified. CRKPs isolated in the year 2022 were submitted to whole genome sequencing, and their susceptibility was tested to cefiderocol, ceftazidime-avibactam, imipenem-relebactam and meropenem-vaborbactam, with excellent results. KPC-producing isolates were also highly susceptible to colistin (92%). The NDM isolates revealed lower susceptibility rates, including only 57% colistin susceptibility. ST-307 prevailed in KPC and ST-11 in NDM isolates. Despite the excellent activity of new antimicrobials, rational antibiotic policy must be thoroughly followed, supported by complementary treatments and strict anti-epidemic precautions.
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Affiliation(s)
- Jozef Ficik
- Institute of Clinical Microbiology, Central Military Hospital, 034 26 Ružomberok, Slovakia;
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
| | - Michal Andrezál
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
| | - Hana Drahovská
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
| | - Miroslav Böhmer
- Comenius University Science Park, 841 02 Bratislava, Slovakia;
- Public Health Authority of the Slovak Republic, 826 45 Bratislava, Slovakia
| | - Tomáš Szemes
- Department of Molecular Biology, Faculty of Natural Sciences, Comenius University, 842 15 Bratislava, Slovakia; (M.A.); (H.D.); (T.S.)
- Comenius University Science Park, 841 02 Bratislava, Slovakia;
- Public Health Authority of the Slovak Republic, 826 45 Bratislava, Slovakia
| | - Adriána Liptáková
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
| | - Lívia Slobodníková
- Institute of Microbiology, Faculty of Medicine, Comenius University and the University Hospital in Bratislava, 811 08 Bratislava, Slovakia;
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Dortet L, Niccolai C, Pfennigwerth N, Frisch S, Gonzalez C, Antonelli A, Giani T, Hoenings R, Gatermann S, Rossolini GM, Naas T. Performance evaluation of the UMIC® Cefiderocol to determine MIC in Gram-negative bacteria. J Antimicrob Chemother 2023:7174883. [PMID: 37209112 DOI: 10.1093/jac/dkad149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/02/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Cefiderocol is a catechol-substituted cephalosporin with potent in vitro activity against carbapenem-resistant (CR) Gram-negative bacteria (GNB). Cefiderocol susceptibility testing is complex because iron concentrations need to be taken into consideration. Here, we assessed the clinical performance of Bruker's UMIC® Cefiderocol and corresponding iron-depleted CAMHB to determine MIC by broth microdilution (BMD) for clinically relevant GNB. METHODS MICs of cefiderocol for 283 GN clinical isolates were determined by BMD using iron-depleted CAMHB. Frozen panels were used as a reference. The concentration range of cefiderocol was 0.03-32 mg/L. The isolates, with different degrees of susceptibility to cefiderocol, included Enterobacterales (n = 180), Pseudomonas aeruginosa (n = 49), Acinetobacter baumannii (n = 44) and Stenotrophomonas maltophilia (n = 10). RESULTS The rates of categorical agreement (CA), essential agreement (EA) and bias were calculated to evaluate the performance of the UMIC® Cefiderocol, as compared with the reference method. Overall, the UMIC® Cefiderocol showed 90.8% EA (95% CI: 86.9%-93.7%) with a bias of -14.5% and a CA of 90.1% (95% CI: 86.1%-93.1%). For Enterobacterales, the UMIC® Cefiderocol showed 91.7% EA (95% CI: 86.7%-94.9%) with a bias of -25.0% and a CA of 87.8% (95% CI: 82.2%-91.8%). For non-fermenters, the UMIC® Cefiderocol showed 89.3% EA (95% CI: 81.9%-93.9%) (not significantly different from 90.0%, Student t-test) with a bias of -3.9% and a CA of 94.2% (95% CI: 87.7%-97.3%). CONCLUSIONS UMIC® Cefiderocol is a valid method for the determination of cefiderocol MICs even if higher than expected discrepancies were observed with NDM-producing Enterobacterales, which presented in most cases MIC values close to the breakpoint.
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Affiliation(s)
- Laurent Dortet
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Service de Bactériologie-Hygiène, Hôpital Bicêtre, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacterales, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Claudia Niccolai
- Department of Microbiology and Virology, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Niels Pfennigwerth
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Ruhr-Universität Bochum, Bochum, Germany
| | - Stefanie Frisch
- Microbiology and Diagnostics, Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Camille Gonzalez
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Service de Bactériologie-Hygiène, Hôpital Bicêtre, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
| | - Alberto Antonelli
- Department of Microbiology and Virology, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Tommaso Giani
- Department of Microbiology and Virology, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Robert Hoenings
- Microbiology and Diagnostics, Bruker Daltonics GmbH & Co. KG, Bremen, Germany
| | - Soeren Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Ruhr-Universität Bochum, Bochum, Germany
| | - Gian Maria Rossolini
- Department of Microbiology and Virology, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Thierry Naas
- Team "Resist", INSERM Unit 1184, Faculty of Medicine, Université Paris-Saclay, Service de Bactériologie-Hygiène, Hôpital Bicêtre, 78 rue du Général Leclerc, 94275, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Assistance Publique-Hôpitaux de Paris, AP-HP Paris-Saclay, Bicêtre Hospital, Le Kremlin-Bicêtre, France
- Associated French National Reference Center for Antibiotic Resistance, Carbapenemase-Producing Enterobacterales, Bicêtre Hospital, Le Kremlin-Bicêtre, France
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Behrens W, Kolte B, Junker V, Frentrup M, Dolsdorf C, Börger M, Jaleta M, Kabelitz T, Amon T, Werner D, Nübel U. Bacterial genome sequencing tracks the housefly-associated dispersal of fluoroquinolone- and cephalosporin-resistant Escherichia coli from a pig farm. Environ Microbiol 2023. [PMID: 36772962 DOI: 10.1111/1462-2920.16352] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 02/08/2023] [Indexed: 02/12/2023]
Abstract
The regular use of antimicrobials in livestock production selects for antimicrobial resistance. The potential impact of this practice on human health needs to be studied in more detail, including the role of the environment for the persistence and transmission of antimicrobial-resistant bacteria. During an investigation of a pig farm and its surroundings in Brandenburg, Germany, we detected abundant cephalosporin- and fluoroquinolone-resistant Escherichia coli in pig faeces, sedimented dust, and house flies (Musca domestica). Genome sequencing of E. coli isolates revealed large phylogenetic diversity and plasmid-borne extended-spectrum beta lactamase (ESBL) genes CTX-M-1 in multiple strains. [Correction added on 28 February 2023, after first online publication: In the preceding sentence, 'and TEM-1' was previously included but has been deleted in this version.] Close genomic relationships indicated frequent transmission of antimicrobial-resistant E. coli between pigs from different herds and across buildings of the farm and suggested dust and flies as vectors for dissemination of faecal pathogens. Strikingly, we repeatedly recovered E. coli from flies collected up to 2 km away from the source, whose genome sequences were identical or closely related to those from pig faeces isolates, indicating the fly-associated transport of diverse ESBL-producing E. coli from the pig farm into urban habitation areas. The observed proximity of contaminated flies to human households poses a risk of transmission of antimicrobial-resistant enteric pathogens from livestock to man.
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Affiliation(s)
- Wiebke Behrens
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Baban Kolte
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vera Junker
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Martinique Frentrup
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Claudia Dolsdorf
- Teaching and Research Station for Animal Breeding and Husbandry (LVAT), Ruhlsdorf, Germany
| | - Maria Börger
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Megarsa Jaleta
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Tina Kabelitz
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Thomas Amon
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany.,Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Doreen Werner
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
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11
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Chen X, Sun Z, Xu X, Jiang J, Su J. Genomic characterization of colistin resistance in Klebsiella spp. under the pressure of colistin. J Med Microbiol 2023; 72. [PMID: 36748641 DOI: 10.1099/jmm.0.001647] [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: 01/12/2023] Open
Abstract
Introduction. Carbapenem-resistant Klebsiella pneumoniae (CRKP) has become a serious threat to global public health. Colistin is regarded as the last-resort antibiotic for CRKP infections, but colistin resistance among CRKP is increasingly being reported, making clinical treatment for CRKP infections more difficult.Hypothesis/Gap Statement. The molecular mechanisms of colistin resistance in Klebsiella spp. under the pressure of colistin have not been fully investigated.Aim. We aimed to investigate the phenotypic and genetic variation in two colistin-susceptible Klebsiella spp. strains under selective pressure of colistin.Methodology. One hundred microlitres of overnight cultures of the CRKP clinical strain CRKP12-130 and of ATCC 700603 was spread on five Mueller-Hinton Agar (MHA) plates with colistin concentrations of 2, 4, 8, 16 and 32 µg ml-1, and growth of colonies was observed for five consecutive days. Colonies collected from plates were passaged daily for 10 days on MHA plates without colistin and susceptibility testing of colistin was performed by broth microdilution. Thirty-four colistin-resistant strains randomly selected were submitted to whole genome sequencing (WGS). Transcriptional levels of genes involved in colistin resistance (mgrB, phoP, phoQ, pmrA, pmrB, pmrD, pmrE and pmrK) were measured by quantitative real-time PCR.Results. A total of 114 and 119 colistin-resistant colonies were obtained from CRKP12-130 and ATCC 700603 in this study, among which 16 and 18 colonies were submitted to WGS, respectively. Among these 34 sequenced isolates, mutation in phoQ (13/16, 81.25 %) was the main genetic factor mediating colistin resistance in strains from CRKP12-130, while for strains from ATCC 700603, mutation associated with mgrB (8/18, 44.44 %) was found to be the commonest. Mutation of mgrB led to a significant increase in the MIC for colistin (from 64 to >128 µg ml-1), and a novel mutation C28R in mgrB was first reported in this study.Conclusion. Colistin-resistant Klebsiella spp. could be easily selected under pressure of different concentrations of colistin. Mutations of mgrB, phoP, phoQ and pmrB genes were the main mechanisms leading to chromosomally mediated colistin resistance in Klebsiella spp.
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Affiliation(s)
- Xin Chen
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Zhewei Sun
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Xiaogang Xu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China.,National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, PR China
| | - Jianping Jiang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
| | - Jiachun Su
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, PR China.,Key Laboratory of Clinical Pharmacology of Antibiotics, National Health and Family Planning Commission, Shanghai, PR China
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12
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Performance evaluation of colistin rapid NP test for detection of colistin resistance in colistin resistant Enterobacterales. Med J Armed Forces India 2022. [DOI: 10.1016/j.mjafi.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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