1
|
Irekeola AA, Shueb RH, Engku Abd Rahman ENS, Afolabi HA, Wada Y, Elmi AH, Hakami MA, Alghzwani SM, Elnoubi OAE, Alshehri AA. High prevalence of carbapenem-resistant Enterobacterales (CRE) in human samples from Nigeria: A systematic review and meta-analysis. Heliyon 2024; 10:e34926. [PMID: 39144932 PMCID: PMC11320313 DOI: 10.1016/j.heliyon.2024.e34926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 08/16/2024] Open
Abstract
Objectives The rise in Carbapenem-resistant Enterobacterales (CRE) is perturbing. To curb the menace of CRE, a comprehensive understanding of its prevalence and epidemiology is crucial. As varying reports abound, the true prevalence of CRE in Nigeria remains unknown. Here, we conducted a systematic review and meta-analysis following standard guidelines to assess the situation of CRE in Nigeria. Methods We searched electronic databases including Pubmed, ScienceDirect, Scopus, Web of Science, and Google Scholar for articles providing information on CRE in Nigeria. The data gathered were analyzed using OpenMeta Analyst and Comprehensive Meta-Analysis software. The random-effect model was employed to calculate pooled resistance to carbapenem antibiotics. Results From 321 retrieved records, 57 were finally included. The studies were predominantly from the South-West region (n = 19). Escherichia coli and Klebsiella pneumoniae were the most frequently tested Enterobacterales among the included studies. The pooled prevalence estimate for imipenem resistance among CRE was 11.2 % (95 % CI: 7.9-15.7). Meropenem resistance had an estimate of 13.5 % (95 % CI: 9.1-19.6), whereas ertapenem and doripenem were estimated at 17.0 % (95 % CI: 9.9-27.7) and 37.9 % (95 % CI: 15.0-67.8), respectively. High heterogeneity (I 2 >85 %, p < 0.001) was observed for the estimates. The highest resistance rate to imipenem (28.4 %), meropenem (37.2 %) and ertapenem (46.5 %) were observed for the South-South region. Based on specific CRE genera, Morganella sp. was the most resistant (37.0 %) while Escherichia sp. was the least (9.4 %). Our analyses also revealed a progressive increase in resistance to carbapenem antibiotics over the years. Conclusion This study highlights carbapenem resistance as a concern in Africa's most populous nation, underscoring the need for proactive measures to address and mitigate the threat of CRE.
Collapse
Affiliation(s)
- Ahmad Adebayo Irekeola
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
- Microbiology Unit, Department of Biological Sciences, College of Natural and Applied Sciences, Summit University Offa, Offa, PMB 4412, Kwara State, Nigeria
| | - Rafidah Hanim Shueb
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
- Institute for Research in Molecular Medicine (INFORMM), Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Engku Nur Syafirah Engku Abd Rahman
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Hafeez Abiola Afolabi
- Department of General Surgery, School of Medical Sciences, Hospital Universiti Sains Malaysia, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
| | - Yusuf Wada
- Department of Zoology, Faculty of Life Sciences, Ahmadu Bello University, Zaria, 810107, Nigeria
| | - Abdirahman Hussein Elmi
- Department of Medical Microbiology and Parasitology, School of Medical Sciences, Health Campus, Universiti Sains Malaysia, Kubang Kerian, 16150, Kelantan, Malaysia
- Department of Medical Laboratory Sciences, Faculty of Medicine and Health Sciences, Jamhuriya University of Science and Technology, Mogadishu, Somalia
| | - Muath Abdu Hakami
- Microbiology Laboratory, Najran Armed Forces Hospital, Najran 108966, Saudi Arabia
| | | | - Osman AE. Elnoubi
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran, Saudi Arabia
| | - Ahmad A. Alshehri
- Department of Clinical Laboratory Sciences, Faculty of Applied Medical Sciences, Najran University, P.O. Box 1988, Najran, Saudi Arabia
| |
Collapse
|
2
|
Park JH, Bae KS, Kang J, Yoon JK, Lee SH. Comprehensive Assessment of Multidrug-Resistant and Extraintestinal Pathogenic Escherichia coli in Wastewater Treatment Plant Effluents. Microorganisms 2024; 12:1119. [PMID: 38930502 PMCID: PMC11205404 DOI: 10.3390/microorganisms12061119] [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: 05/08/2024] [Revised: 05/29/2024] [Accepted: 05/29/2024] [Indexed: 06/28/2024] Open
Abstract
Multidrug-resistant (MDR) Escherichia coli poses a significant threat to public health, contributing to elevated rates of morbidity, mortality, and economic burden. This study focused on investigating the antibiotic resistance profiles, resistance and virulence gene distributions, biofilm formation capabilities, and sequence types of E. coli strains resistant to six or more antibiotic classes. Among 918 strains isolated from 33 wastewater treatment plants (WWTPs), 53.6% (492/918) demonstrated resistance, 32.5% (298/918) were MDR, and over 8% (74/918) were resistant to six or more antibiotic classes, exhibiting complete resistance to ampicillin and over 90% to sulfisoxazole, nalidixic acid, and tetracycline. Key resistance genes identified included sul2, blaTEM, tetA, strA, strB, and fimH as the predominant virulence genes linked to cell adhesion but limited biofilm formation; 69% showed no biofilm formation, and approximately 3% were strong producers. Antibiotic residue analysis detected ciprofloxacin, sulfamethoxazole, and trimethoprim in all 33 WWTPs. Multilocus sequence typing analysis identified 29 genotypes, predominantly ST131, ST1193, ST38, and ST69, as high-risk clones of extraintestinal pathogenic E. coli. This study provided a comprehensive analysis of antibiotic resistance in MDR E. coli isolated from WWTPs, emphasizing the need for ongoing surveillance and research to effectively manage antibiotic resistance.
Collapse
Affiliation(s)
- Ji-Hyun Park
- Han River Environment Research Center, National Institute of Environment Research, Yangpyeong-gun, Incheon 12585, Gyeonggi-do, Republic of Korea
| | - Kyung-Seon Bae
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Jihyun Kang
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Jeong-Ki Yoon
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| | - Soo-Hyung Lee
- Division of Water Supply and Sewerage Research, National Institute of Environment Research, Yangpyeong-gun, Incheon 22689, Gyeonggi-do, Republic of Korea; (K.-S.B.); (J.K.); (J.-K.Y.); (S.-H.L.)
| |
Collapse
|
3
|
Ganjo AR, Balaky STJ, Mawlood AH, Smail SB, Shabila NP. Characterization of genes related to the efflux pump and porin in multidrug-resistant Escherichia coli strains isolated from patients with COVID-19 after secondary infection. BMC Microbiol 2024; 24:122. [PMID: 38600509 PMCID: PMC11005145 DOI: 10.1186/s12866-024-03283-8] [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: 07/28/2023] [Accepted: 03/28/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Escherichia coli (E. coli) is a multidrug resistant opportunistic pathogen that can cause secondary bacterial infections in patients with COVID-19. This study aimed to determine the antimicrobial resistance profile of E. coli as a secondary bacterial infection in patients with COVID-19 and to assess the prevalence and characterization of genes related to efflux pumps and porin. METHODS A total of 50 nonduplicate E. coli isolates were collected as secondary bacterial infections in COVID-19 patients. The isolates were cultured from sputum samples. Confirmation and antibiotic susceptibility testing were conducted by Vitek 2. PCR was used to assess the prevalence of the efflux pump and porin-related genes in the isolates. The phenotypic and genotypic evolution of antibiotic resistance genes related to the efflux pump was evaluated. RESULTS The E. coli isolates demonstrated high resistance to ampicillin (100%), cefixime (62%), cefepime (62%), amoxicillin-clavulanic acid (60%), cefuroxime (60%), and ceftriaxone (58%). The susceptibility of E. coli to ertapenem was greatest (92%), followed by imipenem (88%), meropenem (86%), tigecycline (80%), and levofloxacin (76%). Regarding efflux pump gene combinations, there was a significant association between the acrA gene and increased resistance to levofloxacin, between the acrB gene and decreased resistance to meropenem and increased resistance to levofloxacin, and between the ompF and ompC genes and increased resistance to gentamicin. CONCLUSIONS The antibiotics ertapenem, imipenem, meropenem, tigecycline, and levofloxacin were effective against E. coli in patients with COVID-19. Genes encoding efflux pumps and porins, such as acrA, acrB, and outer membrane porins, were highly distributed among all the isolates. Efflux pump inhibitors could be alternative antibiotics for restoring tetracycline activity in E. coli isolates.
Collapse
Affiliation(s)
- Aryan R Ganjo
- Department of Clinical Analysis, College of Pharmacy, Hawler Medical University, Erbil, Kurdistan Region, Iraq
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq
| | - Salah Tofik Jalal Balaky
- Department of Medical Analysis, Faculty of Applied Science, Tishk International University, Erbil, Iraq.
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region, Iraq.
| | - Ahang Hasan Mawlood
- Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Erbil, Kurdistan Region, Iraq
- Department of Medical Laboratory Technique, College of Medical Technology, AL-Kitab University, Kirkuk, Iraq
| | | | - Nazar P Shabila
- College of Health Sciences, Catholic University in Erbil, Erbil, Kurdistan Region, Iraq
- Department of Community Medicine, College of Medicine, Hawler Medical University, Erbil, Iraq
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Kandi V, Shahapur PR, Suvvari TK, Bharadwaj VG, P CR, Shahapur R, Podaralla E, Godishala V. Molecular Characterization of Escherichia coli Causing Urinary Tract Infections Through Next-Generation Sequencing: A Comprehensive Analysis of Serotypes, Sequence Types, and Antimicrobial and Virulence Genes. Cureus 2024; 16:e55556. [PMID: 38576671 PMCID: PMC10993757 DOI: 10.7759/cureus.55556] [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] [Accepted: 03/05/2024] [Indexed: 04/06/2024] Open
Abstract
Introduction An enormous increase in antimicrobial resistance (AMR) among bacteria isolated from human clinical specimens contributed to treatment failures. Increased surveillance through next-generation sequencing (NGS) or whole genome sequencing (WGS) could facilitate the study of the epidemiology of drug-resistant bacterial strains, resistance genes, and other virulence determinants they are potentially carrying. Methods This study included 30 Escherichia coli (E. coli) isolates obtained from patients suffering from urinary tract infections (UTIs) attending Prathima Institute of Medical Sciences, Karimnagar, India. All bacterial isolates were identified, and antimicrobial susceptibility patterns were determined through conventional microbiological techniques and confirmed by automated systems. All the isolates were investigated using NGS to identify genes coding for resistance, such as extended-spectrum beta-lactamases (ESBLs), metallo-beta-lactamases, and virulence genes. Multilocus sequence typing (MLST) was used to understand the prevalent strain types, and serotyping was carried out to evaluate the type of O (cell wall antigen) and H (flagellar antigen) serotypes carried by the isolates. Results The conventional antimicrobial susceptibility testing revealed that 15 (50%) isolates were resistant to imipenem (IPM), 10 (33.33%) were resistant to amikacin (AK), 13 (43.33%) were resistant to piperacillin-tazobactam (PTZ), 17 (56.66%) were resistant to cephalosporins, and 14 (46.66%) were resistant to nitrofurantoin (NIT). Among the isolates, 26 (86.66%) had revealed the presence of multiple antibiotic-resistant genes with evidence of at least one gene coding for beta-lactamase resistance. There was a high prevalence of blaCTX-M (19/30, 63.33%) genes, followed by blaTEM and blaOXA-1. The blaNDM-5 gene was found in three isolates (3/30, 10%). The virulence genes identified in the present study were iutA, sat, iss, and papC, among others. The E. coli serotype found predominantly belonged to O25:H4 (5, 16.66%), followed by O102:H6 (4, 13.33%). A total of 16 MLST variants were identified among the examined samples. Of the MLST-based sequence types (STs) identified, ST-131 (7, 23.33%) was the predominant one, followed by ST-167 (3, 10%) and ST-12 (3, 10%). Conclusions The study results demonstrated that the E. coli strains isolated from patients suffering from UTIs potentially carried antimicrobial resistance and virulence genes and belonged to different strain types based on MLST. Careful evaluation of bacterial strains using molecular analyses such as NGS could facilitate an improved understanding of bacterial antibiotic resistance and its virulence potential. This could enable physicians to choose appropriate antimicrobial agents and contribute to better patient management, thereby preventing the emergence and spread of drug-resistant bacteria.
Collapse
Affiliation(s)
- Venkataramana Kandi
- Clinical Microbiology, Prathima Institute of Medical Sciences, Karimnagar, IND
| | - Praveen R Shahapur
- Microbiology, Bijapur Lingayat District Educational (BLDE) (Deemed to be) University, Shri B. M. Patil Medical College, Vijayapura, IND
| | - Tarun Kumar Suvvari
- General Medicine, Rangaraya Medical College, Kakinada, IND
- Research, Squad Medicine and Research (SMR), Visakhapatnam, IND
| | - Vallab Ganesh Bharadwaj
- Microbiology, Trichy Sri Ramaswamy Memorial (SRM) Medical College Hospital and Research Centre, Tiruchirappalli, IND
| | - Chitra Rajalakshmi P
- Microbiology, Trichy Sri Ramaswamy Memorial (SRM) Medical College Hospital and Research Centre, Tiruchirappalli, IND
| | - Roopa Shahapur
- Dentistry, Bijapur Lingayat District Educational (BLDE) (Deemed to be) University, Shri B. M. Patil Medical College, Vijayapura, IND
| | | | - Vikram Godishala
- Biotechnology/Food and Nutrition, Vaagdevi Degree and PG College, Hanamkonda, IND
| |
Collapse
|
6
|
Pitout JDD, Peirano G, Matsumura Y, DeVinney R, Chen L. Escherichia coli sequence type 410 with carbapenemases: a paradigm shift within E. coli toward multidrug resistance. Antimicrob Agents Chemother 2024; 68:e0133923. [PMID: 38193668 PMCID: PMC10869336 DOI: 10.1128/aac.01339-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024] Open
Abstract
Escherichia coli sequence type ST410 is an emerging carbapenemase-producing multidrug-resistant (MDR) high-risk One-Health clone with the potential to significantly increase carbapenem resistance among E. coli. ST410 belongs to two clades (ST410-A and ST410-B) and three subclades (ST410-B1, ST410-B2, and ST410-B3). After a fimH switch between clades ST410-A and ST410-B1, ST410-B2 and ST410-B3 subclades showed a stepwise progression toward developing MDR. (i) ST410-B2 initially acquired fluoroquinolone resistance (via homologous recombination) in the 1980s. (ii) ST410-B2 then obtained CMY-2, CTX-M-15, and OXA-181 genes on different plasmid platforms during the 1990s. (iii) This was followed by the chromosomal integration of blaCMY-2, fstl YRIN insertion, and ompC/ompF mutations during the 2000s to create the ST410-B3 subclade. (iv) An IncF plasmid "replacement" scenario happened when ST410-B2 transformed into ST410-B3: F36:31:A4:B1 plasmids were replaced by F1:A1:B49 plasmids (both containing blaCTX-M-15) followed by blaNDM-5 incorporation during the 2010s. User-friendly cost-effective methods for the rapid identification of ST410 isolates and clades are needed because limited data are available about the frequencies and global distribution of ST410 clades. Basic mechanistic, evolutionary, surveillance, and clinical studies are urgently required to investigate the success of ST410 (including the ability to acquire successive MDR determinants). Such information will aid with management and prevention strategies to curb the spread of carbapenem-resistant E. coli. The medical community can ill afford to ignore the spread of a global E. coli clone with the potential to end the carbapenem era.
Collapse
Affiliation(s)
- Johann D. D. Pitout
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, Gauteng, South Africa
| | - Gisele Peirano
- Cummings School of Medicine, Calcary, Alberta, Canada
- University of Calgary, Alberta Precision Laboratories, Calgary, Alberta, Canada
| | - Yasufumi Matsumura
- Kyoto University Graduate School of Medicine, Pretoria, Gauteng, South Africa
| | | | - Liang Chen
- Meridian Health Center for Discovery and Innovation, Kyoto, Japan
- Hackensack Meridian School of Medicine at Seton Hall University, Nutley, New Jersey, USA
| |
Collapse
|
7
|
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.
Collapse
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;
| |
Collapse
|
8
|
Medugu N, Tickler IA, Duru C, Egah R, James AO, Odili V, Hanga F, Olateju EK, Jibir B, Ebruke BE, Olanipekun G, Tenover FC, Obaro SK. Phenotypic and molecular characterization of beta-lactam resistant Multidrug-resistant Enterobacterales isolated from patients attending six hospitals in Northern Nigeria. Sci Rep 2023; 13:10306. [PMID: 37365355 DOI: 10.1038/s41598-023-37621-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 06/24/2023] [Indexed: 06/28/2023] Open
Abstract
Infections caused by multi-drug resistant Enterobacterales (MDR-E) are difficult to treat and cause significant mortality, especially in developing countries. This study characterized the phenotypic and genotypic profiles of 49 randomly selected beta-lactam resistant MDR-E previously isolated from patients being managed in hospitals in Nigeria using whole genome sequencing. The study isolates exhibited 85.5% resistance to 3rd generation cephalosporins and 65.3% resistance to carbapenems. The blaTEM-1B (29, 59.2%), blaCTX-M-15 (38, 77.6%), and blaNDM-1 (17, 51.5%) were the most common penicillinase, ESBL, and carbapenem resistant genes across isolates, respectively. Seventeen (45%) of blaCTX-M-15 was carried on the insertion sequence ISEc9 while blaNDM-1 (11, 64.7%) were associated with ISEc33. None of the 21 plasmids detected were associated with β-lactamase genes. Higher resistance rates were found in E. coli ST-88 (n = 2) and the high-risk ST-692 (n = 2). For Klebsiella species, the high-risk clones ST-476 (n = 8) and ST-147 (n = 3) predominated and had higher phenotypic resistance rates and higher number of AMR genes. The mechanisms and pattern of antibiotic resistance differ from patterns previously described with isolates harbouring a wide range of AMRGs. The detection of several chromosomally mediated carbapenemases in our study also represents a significant finding that warrants further investigation to better understand its' implications for clinical practice and public health. The selected MDR-Es were found to be pan-susceptible to tigecycline and had very low resistance to fosfomycin, suggesting a potential for these as empiric treatments. A surveillance approach incorporating both conventional laboratory techniques and modern molecular techniques is essential for the comprehensive characterization of the emergence and dissemination of antimicrobial resistance in Enterobacterales infections within Nigeria.
Collapse
Affiliation(s)
- Nubwa Medugu
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria.
- International Foundation Against Infectious Disease in Nigeria, Dutse Street, Gwarinpa, Abuja, Nigeria.
| | | | - Carissa Duru
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | - Ruth Egah
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | - Abu Ocheiku James
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | - Vivian Odili
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | | | | | - Binta Jibir
- Hasiya Bayero Children's Hospital, Kano, Nigeria
| | - Bernard E Ebruke
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | - Grace Olanipekun
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
| | - Fred C Tenover
- College of Arts and Sciences, University of Dayton, Dayton, OH, 45469, USA
| | - Stephen K Obaro
- Nile University of Nigeria, Cadastral Zone, Research and Institutions Area, Abuja, Nigeria
- University of Nebraska Medical Center, Omaha, NE, 68198, USA
| |
Collapse
|
9
|
Pankok F, Fuchs F, Loderstädt U, Kaase M, Balczun C, Scheithauer S, Frickmann H, Hagen RM. Molecular Epidemiology of Escherichia coli with Resistance against Third-Generation Cephalosporines Isolated from Deployed German Soldiers-A Retrospective Assessment after Deployments to the African Sahel Region and Other Sites between 2007 and 2016. Microorganisms 2022; 10:microorganisms10122448. [PMID: 36557701 PMCID: PMC9788009 DOI: 10.3390/microorganisms10122448] [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: 11/12/2022] [Revised: 12/06/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
Colonization and infection with bacteria with acquired antibiotic resistance are among the risks for soldiers on international deployments. Enterobacterales with resistance against third-generation cephalosporines are amongst the most frequently imported microorganisms. To contribute to the scarcely available epidemiological knowledge on deployment-associated resistance migration, we assessed the molecular epidemiology of third-generation cephalosporine-resistant Escherichia coli isolated between 2007 and 2016 from German soldiers after deployments, with a particular focus on the African Sahel region. A total of 51 third-generation cephalosporine-resistant E. coli isolated from 51 military returnees from deployment collected during the assessment period between 2007 and 2016 were subjected to short-read next-generation sequencing analysis. Returnees from the Sahel region (Djibouti, Mali, South Sudan, Sudan, Sudan, and Uganda) comprised a proportion of 52.9% (27/51). Repeatedly isolated sequence types according to the Warwick University scheme from returnees from the Sahel region were ST38, ST131, and ST648, confirming previous epidemiological assessments from various sub-Saharan African regions. Locally prevalent resistance genes in isolates from returnees from the Sahel region associated with third-generation resistance were blaCTX-M-15, blaCTX-M-27, blaCTX-M-1, blaTEM-169, blaCTX-M-14, blaCTX-M-99-like, blaCTX-M-125, blaSHV-12, and blaDHA-1, while virulence genes were east1, sat, and tsh in declining order of frequency of occurrence each. In line with phenotypically observed high resistance rates for aminoglycosides and trimethoprim/sulfamethoxazole, multiple associated resistance genes were observed. A similar, slightly more diverse situation was recorded for the other deployment sites. In summary, this assessment provides first next-generation sequencing-based epidemiological data on third-generation cephalosporine-resistant E. coli imported by deployed German soldiers with a particular focus on deployments to the Sahel region, thus serving as a small sentinel. The detected sequence types are well in line with the results from previous epidemiological assessments in sub-Saharan Africa.
Collapse
Affiliation(s)
- Frederik Pankok
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Frieder Fuchs
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
- Institute for Medical Microbiology, Immunology and Hygiene, University of Cologne, Medical Faculty and University Hospital of Cologne, 50931 Cologne, Germany
| | - Ulrike Loderstädt
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
- Correspondence: (F.P.); (U.L.)
| | - Martin Kaase
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Carsten Balczun
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| | - Simone Scheithauer
- Institute for Infection Control and Infectious Diseases, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hospital Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Ralf Matthias Hagen
- Department of Microbiology and Hospital Hygiene, Bundeswehr Central Hospital Koblenz, 56070 Koblenz, Germany
| |
Collapse
|