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Gomaa Elsayed A, M Fahmy E, Abdellatif Alsayed M, Ahmed ME, El Sayed Zaki M, Mofreh Mohamed M. Study of plasmid mediated quinolone resistance genes among Escherichia coli and Klebsiella pneumoniae isolated from pediatric patients with sepsis. Sci Rep 2024; 14:11849. [PMID: 38783019 PMCID: PMC11116374 DOI: 10.1038/s41598-024-61357-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 05/06/2024] [Indexed: 05/25/2024] Open
Abstract
The resistance to antibiotics in Gram-negative bacilli causing sepsis is a warning sign of failure of therapy. Klebsiella pneumoniae (K. pneumoniae) and Escherichia coli (E. coli) represent major Gram-negative bacilli associated with sepsis. Quinolone resistance is an emerging resistance among E. coli and K. pneumoniae. Therefore, the present study aimed to study the presence of plasmid-mediated quinolone resistance (PMQR) genes qnrA, qnrB, and qnrS by polymerase chain reaction (PCR) in E. coli and K. pneumoniae isolated from pediatric patients with sepsis. This was a retrospective cross-sectional study that included pediatric patients with healthcare-associated sepsis. The E. coli and K. pneumoniae isolates were identified by microbiological methods. PMQR genes namely qnrA, qnrB, and qnrS were detected in E. coli and K. pneumoniae isolates by PCR. The results were analyzed by SPPS24, and the qualitative data was analyzed as numbers and percentages and comparison was performed by Chi-square test, P was significant if < 0.05. The most prevalent gene detected by PCR was qnrA (75%), followed by qnrB (28.1%), and qnrS (25%). The most frequently detected qnr gene in E coli and K. pneumoniae was qnrA (28.8%, and 16.3% respectively). The present study highlights the high prevalence of ciprofloxacin resistance among E. coli and K. pneumoniae isolated from pediatric patients with healthcare-associated sepsis. There was a high frequency of PMQR genes in E. coli and K. pneumoniae isolated from pediatric patients. Therefore, it is important to monitor the spread of PMQR genes in clinical isolates to ensure efficient antibiotic use in those children. The finding denotes the importance of an antibiotics surveillance program.
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Affiliation(s)
- Ahmed Gomaa Elsayed
- Medical Microbiology and Immunology, Mansoura Faculty of Medicine, Mansoura, Egypt
| | - Ehab M Fahmy
- Medical Microbiology and Immunology, Helwan Faculty of Medicine, Helwan, Egypt
| | | | - Mai Essam Ahmed
- Clinical Pathology, Beni suef Faculty of Medicine, Beni Suef, Egypt
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Rwigi D, Nyerere AK, Diakhate MM, Kariuki K, Tickell KD, Mutuma T, Tornberg SN, Soge OO, Walson JL, Singa B, Kariuki S, Pavlinac PB, Mogeni P. Phenotypic and molecular characterization of β-lactamase-producing Klebsiella species among children discharged from hospital in Western Kenya. BMC Microbiol 2024; 24:135. [PMID: 38654237 PMCID: PMC11040804 DOI: 10.1186/s12866-024-03284-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/31/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND The emergence and spread of β-lactamase-producing Klebsiella spp. has been associated with a substantial healthcare burden resulting in therapeutic failures. We sought to describe the proportion of phenotypic resistance to commonly used antibiotics, characterize β-lactamase genes among isolates with antimicrobial resistance (AMR), and assess the correlates of phenotypic AMR in Klebsiella spp. isolated from stool or rectal swab samples collected from children being discharged from hospital. METHODS We conducted a cross-sectional study involving 245 children aged 1-59 months who were being discharged from hospitals in western Kenya between June 2016 and November 2019. Whole stool or rectal swab samples were collected and Klebsiella spp. isolated by standard microbiological culture. β-lactamase genes were detected by PCR whilst phenotypic antimicrobial susceptibility was determined using the disc diffusion technique following standard microbiology protocols. Descriptive analyses were used to characterize phenotypic AMR and carriage of β-lactamase-producing genes. The modified Poisson regression models were used to assess correlates of phenotypic beta-lactam resistance. RESULTS The prevalence of β-lactamase carriage among Klebsiella spp. isolates at hospital discharge was 62.9% (154/245). Antibiotic use during hospitalization (adjusted prevalence ratio [aPR] = 4.51; 95%CI: 1.79-11.4, p < 0.001), longer duration of hospitalization (aPR = 1.42; 95%CI: 1.14-1.77, p < 0.002), and access to treated water (aPR = 1.38; 95%CI: 1.12-1.71, p < 0.003), were significant predictors of phenotypically determined β-lactamase. All the 154 β-lactamase-producing Klebsiella spp. isolates had at least one genetic marker of β-lactam/third-generation cephalosporin resistance. The most prevalent genes were blaCTX-M 142/154 (92.2%,) and blaSHV 142/154 (92.2%,) followed by blaTEM 88/154 (57.1%,) and blaOXA 48/154 (31.2%,) respectively. CONCLUSION Carriage of β-lactamase producing Klebsiella spp. in stool is common among children discharged from hospital in western Kenya and is associated with longer duration of hospitalization, antibiotic use, and access to treated water. The findings emphasize the need for continued monitoring of antimicrobial susceptibility patterns to inform the development and implementation of appropriate treatment guidelines. In addition, we recommend measures beyond antimicrobial stewardship and infection control within hospitals, improved sanitation, and access to safe drinking water to mitigate the spread of β-lactamase-producing Klebsiella pathogens in these and similar settings.
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Affiliation(s)
- Doreen Rwigi
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya.
| | - Andrew K Nyerere
- Jomo Kenyatta University of Agriculture and Technology, Nairobi, Kenya
| | - Mame M Diakhate
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Kevin Kariuki
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Kirkby D Tickell
- Department of Global Health, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Timothy Mutuma
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | | | - Olusegun O Soge
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Judd L Walson
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Medicine, Division of Allergy and Infectious Diseases, University of Washington, Seattle, Washington, USA
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
- Department of International Health, Johns Hopkins University, Baltimore, MD, USA
| | - Benson Singa
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Samuel Kariuki
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
- Center for Microbiology Research (CMR), Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Patricia B Pavlinac
- Department of Global Health, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Polycarp Mogeni
- Kenya Medical Research Institute (KEMRI), Nairobi, Kenya.
- Department of Global Health, University of Washington, Seattle, Washington, USA.
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Afsharian M, Asadi S, Danesh C, Sedighi R, Karimi K, Miladi N, Miladi R, Azizi M, Madadi-Goli N, Ahmadi K, Zamanian MH. The Abundance of Plasmid-Mediated Quinolone Resistance Genes in Enterobacter cloacae Strains Isolated from Clinical Specimens in Kermanshah, Iran. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2024; 2024:8849097. [PMID: 38623587 PMCID: PMC11018368 DOI: 10.1155/2024/8849097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 03/07/2024] [Accepted: 03/23/2024] [Indexed: 04/17/2024]
Abstract
Background Enterobacter cloacae (E. cloacae) is one of the most common Enterobacteriaceae causing nosocomial infections. Plasmid-mediated quinolone resistance (PMQR) determinants have been considered recently. This study evaluated the abundance of PMQR genes in strains of E. cloacae obtained from clinical samples in Kermanshah, Iran. Methods In this descriptive cross-sectional study, after collecting 113 isolates of E. cloacae, their identity was confirmed using specific biochemical tests. After determining their drug resistance patterns using disc diffusion, the phenotypic frequency of extended-spectrum beta-lactamase (ESBL)-producing isolates was measured by the double-disk synergy test (DDST) method. The isolates were examined for the presence of qnrA, qnrB, qnrS, and aac(6')-Ib-cr genes by the polymerase chain reaction (PCR) assay. Results The antibiotic resistance rate of E. cloacae isolates varied from 9.7% to 60.2%; among them, 78% were multidrug-resistant (MDR). The highest quinolone resistance was observed in ESBL-producing strains of E. cloacae. The frequency of positive isolates for PMQR and ESBL was 79.6% and 57.5%, respectively. The genes aac(6')-ib-cr (70.8%) and qnrB (38.1%) had the highest frequency among other genes. The number of isolates simultaneously carrying 2 and 3 genes was 64 and 5 isolates, respectively. Conclusion The obtained results indicate a high degree of quinolone resistance among ESBL-producing E. cloacae strains. Nevertheless, there was a significant relationship between the PMQR gene and ESBL-positive isolates. Therefore, special attention should be paid to molecular epidemiological studies on antibiotic resistance to quinolones and beta-lactamases in these strains.
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Affiliation(s)
- Mandana Afsharian
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Somayeh Asadi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Camellia Danesh
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Reza Sedighi
- Student Research Committee, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Kohsar Karimi
- Student Research Committee, Kurdistan University of Medical Sciences, Sanandaj, Iran
| | - Nooshin Miladi
- Department of Pediatrics, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ronak Miladi
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mohsen Azizi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Nahid Madadi-Goli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Kamal Ahmadi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Hossein Zamanian
- Department of Infectious Disease, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
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Zhu DM, Ding Q, Li PH, Wang YL, Li YZ, Yu Li X, Li GM, Ma HX, Kong LC. Antimicrobial resistance in E. Coli of animal origin and discovery of a novel ICE mobile element in Northeast China. BMC Vet Res 2023; 19:255. [PMID: 38053138 DOI: 10.1186/s12917-023-03828-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 11/28/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Multidrug resistance in Enterobacteriaceae including resistance to quinolones is rising worldwide. The development of resistance may lead to the emergence of new transmission mechanisms. In this study, the collection of different E. coli was performed from animals and subjected to subsequent procedures including pulsed-field gel electrophoresis, micro-broth dilution method, polymerase chain reaction. Whole genome sequencing of E. coli C3 was performed to detect the affinity, antimicrobial resistance and major carriers of the isolates. RESULTS A total of 66 E. coli were isolated and their antibiotic resistance genes, frequency of horizontal transfer and genetic environment of E. coli C3 were determined. The results showed there were both different and same types in PFGE typing, indicating clonal transmission of E. coli among different animals. The detection of antimicrobial resistance and major antibiotic resistance genes and the plasmid transfer results showed that strains from different sources had high levels of resistance to commonly used clinical antibiotics and could be spread horizontally. Whole-genome sequencing discovered a novel ICE mobile element. CONCLUSION In summary, the antimicrobial resistance of E. coli in northeast China is a serious issue and there is a risk of antimicrobial resistance transmission. Meanwhile, a novel ICE mobile element appeared in the process of antimicrobial resistance formation.
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Affiliation(s)
- Dao Mi Zhu
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Qiang Ding
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Peng Hui Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Yong Liang Wang
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Ya Zhuo Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Xuan Yu Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China
| | - Gong Mei Li
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China
| | - Hong Xia Ma
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Engineering Research Center of Bioreactor and Drug Development, Ministry of Education, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China.
| | - Ling Cong Kong
- College of Animal Science and Technology, Jilin Agricultural University, Xincheng Street#2888, Changchun, 130118, P.R. China.
- The Key Laboratory of New Veterinary Drug Research and Development of Jilin Province, Jilin Agricultural University, Xincheng #Street, Changchun, 2888, 130118, P.R. China.
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Kawa DE, Tickler IA, Tenover FC, Shettima SA. Characterization of Beta-Lactamase and Fluoroquinolone Resistance Determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa Isolates from a Tertiary Hospital in Yola, Nigeria. Trop Med Infect Dis 2023; 8:500. [PMID: 37999619 PMCID: PMC10675496 DOI: 10.3390/tropicalmed8110500] [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: 10/03/2023] [Revised: 11/09/2023] [Accepted: 11/10/2023] [Indexed: 11/25/2023] Open
Abstract
Infections due to antimicrobial resistant gram-negative bacteria cause significant morbidity and mortality in sub-Saharan Africa. To elucidate the molecular epidemiology of antimicrobial resistance in gram-negative bacteria, we characterized beta-lactam and fluoroquinolone resistance determinants in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa isolates collected from November 2017 to February 2018 (Period 1) and October 2021 to January 2022 (Period 2) in a tertiary medical center in north-eastern Nigeria. Whole genome sequencing (WGS) was used to identify sequence types and resistance determinants in 52 non-duplicate, phenotypically resistant isolates. Antimicrobial susceptibility was determined using broth microdilution and modified Kirby-Bauer disk diffusion methods. Twenty sequence types (STs) were identified among isolates from both periods using WGS, with increased strain diversity observed in Period 2. Common ESBL genes identified included blaCTX-M, blaSHV, and blaTEM in both E. coli and K. pneumoniae. Notably, 50% of the E. coli in Period 2 harbored either blaCTX-M-15 or blaCTX-M-1 4 and phenotypically produced ESBLs. The blaNDM-7 and blaVIM-5 metallo-beta-lactamase genes were dominant in E. coli and P. aeruginosa in Period 1, but in Period 2, only K. pneumoniae contained blaNDM-7, while blaNDM-1 was predominant in P. aeruginosa. The overall rate of fluoroquinolone resistance was 77% in Period 1 but decreased to 47.8% in Period 2. Various plasmid-mediated quinolone resistance (PMQR) genes were identified in both periods, including aac(6')-Ib-cr, oqxA/oqxB, qnrA1, qnrB1, qnrB6, qnrB18, qnrVC1, as well as mutations in the chromosomal gyrA, parC and parE genes. One E. coli isolate in Period 2, which was phenotypically multidrug resistant, had ESBL blaCTX-M-15, the serine carbapenemase, blaOXA-181 and mutations in the gyrA gene. The co-existence of beta-lactam and fluoroquinolone resistance markers observed in this study is consistent with widespread use of these antimicrobial agents in Nigeria. The presence of multidrug resistant isolates is concerning and highlights the importance of continued surveillance to support antimicrobial stewardship programs and curb the spread of antimicrobial resistance.
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Affiliation(s)
- Diane E. Kawa
- Department of Medical and Scientific Affairs, Cepheid, Sunnyvale, CA 94089, USA
| | | | - Fred C. Tenover
- College of Arts and Sciences, University of Dayton, Dayton, OH 45469, USA;
| | - Shuwaram A. Shettima
- Department of Medical Microbiology, Parasitology and Immunology, Modibbo Adama University Teaching Hospital, Yola 640001, Adamawa State, Nigeria;
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