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Chelaru EC, Muntean AA, Hogea MO, Muntean MM, Popa MI, Popa GL. The Importance of Carbapenemase-Producing Enterobacterales in African Countries: Evolution and Current Burden. Antibiotics (Basel) 2024; 13:295. [PMID: 38666971 PMCID: PMC11047529 DOI: 10.3390/antibiotics13040295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/29/2024] Open
Abstract
Antimicrobial resistance (AMR) is a worldwide healthcare problem. Multidrug-resistant organisms (MDROs) can spread quickly owing to their resistance mechanisms. Although colonized individuals are crucial for MDRO dissemination, colonizing microbes can lead to symptomatic infections in carriers. Carbapenemase-producing Enterobacterales (CPE) are among the most important MDROs involved in colonizations and infections with severe outcomes. This review aimed to track down the first reports of CPE in Africa, describe their dissemination throughout African countries and summarize the current status of CRE and CPE data, highlighting current knowledge and limitations of reported data. Two database queries were undertaken using Medical Subject Headings (MeSH), employing relevant keywords to identify articles that had as their topics beta-lactamases, carbapenemases and carbapenem resistance pertaining to Africa or African regions and countries. The first information on CPE could be traced back to the mid-2000s, but data for many African countries were established after 2015-2018. Information is presented chronologically for each country. Although no clear conclusions could be drawn for some countries, it was observed that CPE infections and colonizations are present in most African countries and that carbapenem-resistance levels are rising. The most common CPE involved are Klebsiella pneumoniae and Escherichia coli, and the most prevalent carbapenemases are NDM-type and OXA-48-type enzymes. Prophylactic measures, such as screening, are required to combat this phenomenon.
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Affiliation(s)
- Edgar-Costin Chelaru
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Andrei-Alexandru Muntean
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
- Department of Microbiology, Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania
| | - Mihai-Octav Hogea
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Mădălina-Maria Muntean
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
| | - Mircea-Ioan Popa
- Department of Microbiology II, Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania; (E.-C.C.); (A.-A.M.); (M.-O.H.); (M.-M.M.)
- Department of Microbiology, Cantacuzino National Military Medical Institute for Research and Development, 050096 Bucharest, Romania
| | - Gabriela-Loredana Popa
- Department of Microbiology, Faculty of Dentistry, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania;
- Parasitic Disease Department, Colentina Clinical Hospital, 020125 Bucharest, Romania
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Hu Y, Yang Y, Feng Y, Fang Q, Wang C, Zhao F, McNally A, Zong Z. Prevalence and clonal diversity of carbapenem-resistant Klebsiella pneumoniae causing neonatal infections: A systematic review of 128 articles across 30 countries. PLoS Med 2023; 20:e1004233. [PMID: 37339120 DOI: 10.1371/journal.pmed.1004233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 04/04/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is the most common pathogen causing neonatal infections, leading to high mortality worldwide. Along with increasing antimicrobial use in neonates, carbapenem-resistant K. pneumoniae (CRKP) has emerged as a severe challenge for infection control and treatment. However, no comprehensive systematic review is available to describe the global epidemiology of neonatal CRKP infections. We therefore performed a systematic review of available data worldwide and combined a genome-based analysis to address the prevalence, clonal diversity, and carbapenem resistance genes of CRKP causing neonatal infections. METHODS AND FINDINGS We performed a systematic review of studies reporting population-based neonatal infections caused by CRKP in combination with a genome-based analysis of all publicly available CRKP genomes with neonatal origins. We searched multiple databases (PubMed, Web of Science, Embase, Ovid MEDLINE, Cochrane, bioRxiv, and medRxiv) to identify studies that have reported data of neonatal CRKP infections up to June 30, 2022. We included studies addressing the prevalence of CRKP infections and colonization in neonates but excluded studies lacking the numbers of neonates, the geographical location, or independent data on Klebsiella or CRKP isolates. We used narrative synthesis for pooling data with JMP statistical software. We identified 8,558 articles and excluding those that did not meet inclusion criteria. We included 128 studies, none of which were preprints, comprising 127,583 neonates in 30 countries including 21 low- and middle-income countries (LMICs) for analysis. We found that bloodstream infection is the most common infection type in reported data. We estimated that the pooled global prevalence of CRKP infections in hospitalized neonates was 0.3% (95% confidence interval [CI], 0.2% to 0.3%). Based on 21 studies reporting patient outcomes, we found that the pooled mortality of neonatal CRKP infections was 22.9% (95% CI, 13.0% to 32.9%). A total of 535 neonatal CRKP genomes were identified from GenBank including Sequence Read Archive, of which 204 were not linked to any publications. We incorporated the 204 genomes with a literature review for understanding the species distribution, clonal diversity, and carbapenemase types. We identified 146 sequence types (STs) for neonatal CRKP strains and found that ST17, ST11, and ST15 were the 3 most common lineages. In particular, ST17 CRKP has been seen in neonates in 8 countries across 4 continents. The vast majority (75.3%) of the 1,592 neonatal CRKP strains available for analyzing carbapenemase have genes encoding metallo-β-lactamases and NDM (New Delhi metallo-β-lactamase) appeared to be the most common carbapenemase (64.3%). The main limitation of this study is the absence or scarcity of data from North America, South America, and Oceania. CONCLUSIONS CRKP contributes to a considerable number of neonatal infections and leads to significant neonatal mortality. Neonatal CRKP strains are highly diverse, while ST17 is globally prevalent and merits early detection for treatment and prevention. The dominance of blaNDM carbapenemase genes imposes challenges on therapeutic options in neonates and supports the continued inhibitor-related drug discovery.
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Affiliation(s)
- Ya Hu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yongqiang Yang
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Qingqing Fang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Chengcheng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Feifei Zhao
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
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Alshahrani AM, Ibrahim ME, Aldossary AK, Alghamdi MA, Ahmed OB, Bin Abdulhak AA. Molecular Epidemiology of Carbapenem-Resistant K. pneumoniae Clinical Isolates from the Adult Patients with Comorbidities in a Tertiary Hospital, Southern Saudi Arabia. Antibiotics (Basel) 2022; 11:antibiotics11121697. [PMID: 36551354 PMCID: PMC9774885 DOI: 10.3390/antibiotics11121697] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/27/2022] Open
Abstract
Hospitalized patients are likely to have chronic illnesses and are at an increased risk of mortality due to infection caused by MDR bacteria. We aimed to identify carbapenem-resistant genes carrying Klebsiella pneumoniae (K. pneumoniae) isolates and their risk factors recovered from adult patients with comorbidities. A cross-sectional study was carried out between April 2021 and December 2021 at King Abdullah Hospital (KAH) in Bisha province, Saudi Arabia. Seventy-one multi-drug resistant K. pneumoniae recovered from clinical samples and screened for carbapenemase genes of blaOXA-48-like, blaNDM-1, blaKPC, blaVIM, and blaIMP. Of 71 MDR K. pneumoniae examined, 47 (66.2%) isolates harbored various carbapenemase genes. The most prevalent single resistance gene was blaOXA-48-like (62.5%; n = 25), and 33.3% of them were recovered from sputum isolates. The blaNDM-1 gene was detected in 12 (30.0%) isolates, and eight of them were recovered from urine (n = 4) and blood (n = 4). Two (5.0%) single blaKPC genes were recovered from the sputum (n = 1) and blood (n = 1) isolates. In contrast, no blaIMP- and blaVIM-carrying isolates were detected. The co-existence of two resistance genes between blaOXA-48-like and blaNDM-1 was found in six strains, whereas only one strain was found to be produced in the three genes of blaNDM-1, blaKPC, and blaOXA-48-like. There were statistically significant associations between the presence of carbapenem-gene-carrying K. pneumoniae and patients' gender (χ2(1) = 5.94, p = 0.015), intensive care unit admission (χ2(1) = 7.649, p = 0.002), and chronic obstructive pulmonary disease (χ2(1) = 4.851, p = 0.028). The study highlighted the existence of carbapenemase-producing K. pneumoniae, particularly blaOXA-48-like and blaNDM-1, in patients with comorbidities. Our findings emphasize the importance of the molecular characterization of resistance-determinant-carrying bacterial pathogens as a part of infection control and prevention in hospital settings.
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Affiliation(s)
- Abdullah M. Alshahrani
- Department of Family Medicine, College of Medicine, University of Bisha, Bisha 67614, Saudi Arabia
| | - Mutasim E. Ibrahim
- Department of Basic Medical Sciences (Microbiology Unit), College of Medicine, University of Bisha, Bisha 67614, Saudi Arabia
- Correspondence: or ; Tel.: +966-502656995
| | - Ahmed K. Aldossary
- Department of Family Medicine, College of Medicine, University of Bisha, Bisha 67614, Saudi Arabia
| | - Mushabab A. Alghamdi
- Department of Internal Medicine, College of Medicine, University of Bisha, Bisha 67614, Saudi Arabia
| | - Omar B. Ahmed
- Department of Environmental and Health Research, The Custodian of the Two Holy Mosques Institute for Hajj and Umrah Research, Umm Al-Qura University, Makkah 24382, Saudi Arabia
| | - Aref A. Bin Abdulhak
- Division of Cardiovascular Medicine, Department of Internal Medicine, University of Iowa Carver College of Medicine, Iowa City, IA 52240, USA
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Mmatli M, Leshaba TMS, Skosana LB, Mbelle NM, Osei Sekyere J. Molecular Screening of Clinical Multidrug-Resistant Gram-Negative Bacteria Shows Endemicity of Carbapenemases, Coexistence of Multiple Carbapenemases, and Rarity of mcr in South Africa. Microb Drug Resist 2022; 28:1028-1036. [PMID: 36251876 DOI: 10.1089/mdr.2022.0112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background: Extensive use of carbapenems to treat multidrug-resistant (MDR) Gram-negative bacteria (GNB) facilitates the wide dissemination of carbapenemase-producing carbapenem-resistant GNB. Colistin was reintroduced into clinical settings to manage these GNB infections. However, there is currently an increase in the dissemination of mobile colistin resistance (mcr)-producing colistin-resistant GNB isolates in clinical settings. The epidemiology of carbapenemases and mcr in Pretoria was evaluated. Methods: Clinical MDR GNB were collected and screened for carbapenemases and mcr using polymerase chain reaction (PCR); their antibiotic susceptibility profiles were elucidated using the Vitek® 2 automated system (Biomerieux, France) and microbroth dilution (for colistin). Results and Discussion: A total of 306 isolates were collected; a majority of these were Klebsiella pneumoniae (n = 208) and were collected from males (n = 158). The isolates were retrieved from a variety of infection sites, including urine, blood cultures, and rectal swabs. The Vitek 2 system found that these isolates were largely resistant to β-lactams, where 217 (70.9%) had reduced susceptibility to at least one carbapenem (ertapenem, meropenem, or imipenem), and 81 isolates (26.5%) were resistant to colistin. PCR screening identified 201 (65.7%) isolates harboring carbapenemase genes consisting of blaOXA-48 (170, 84.2%), blaNDM (31, 15.4%), blaIMP (5, 2%), blaKPC (4, 1%), and blaVIM (5, 2%). Furthermore, 14 blaOXA-48-producing isolates were coharboring blaVIM (2), blaNDM (9), blaKPC (1), and blaIMP (2) genes. Only one isolate harbored the mobile colistin resistance (mcr)-1 gene, and this is the first report of an mcr-1-producing Acinetobacter baumannii isolate in South Africa. Conclusion: There is high endemicity of carbapenemase genes and a low prevalence of mcr genes in GNB, particularly in K. pneumoniae, in health care facilities in Pretoria and surrounding regions of South Africa. Significance: Health care facilities in Pretoria are becoming breeding grounds for MDR infections that threaten public health. Careful use of carbapenems and other antibiotics is necessary to prevent further escalation and outbreak of these MDR strains that can claim several lives.
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Affiliation(s)
- Masego Mmatli
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | | | - Lebogang B Skosana
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Tshwane Academic Division, Department of Medical Microbiology, National Health Laboratory Service, Pretoria, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, University of Pretoria, Pretoria, South Africa.,Department of Dermatology, School of Medicine, University of Pretoria, Pretoria, South Africa
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Balushi MA, Kumar R, Al-Rashdi A, Ratna A, Al-Jabri A, Al-Shekaili N, Rani R, Sumri SA, Al-Ghabshi L, Al-Abri S, Al-Jardani A. Genomic analysis of the emerging carbapenem-resistant Klebsiella pneumoniae sequence type 11 harbouring Klebsiella pneumoniae carbapenemase (KPC) in Oman. J Infect Public Health 2022; 15:1089-1096. [PMID: 36116408 DOI: 10.1016/j.jiph.2022.08.014] [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: 07/20/2022] [Revised: 08/14/2022] [Accepted: 08/23/2022] [Indexed: 10/15/2022] Open
Abstract
BACKGROUND AND OBJECTIVE The presence of carbapenemase enzymes among Enterobacterales is the main mechanism to reduce susceptibility to a wide range of antibiotics. Carbapenemase enzymes such as the Klebsiella pneumoniae carbapenemase (KPC) hydrolyse beta-lactam antibiotics group, which includes carbapenem, leads to fewer treatment options. We aim to describe the first report of carbapenem-resistant K. pneumoniae (CRKP) sequence type (ST) 11 harbouring KPC in Oman. MATERIAL AND METHODS Five confirmed CRKP isolates were isolated from clinical samples during the period of January 2019 till December 2019. Strains were genotyped by pulse field gel electrophoresis (PFGE) for genetic relatedness. Whole genome sequencing (WGS) was performed to observe relationships with global strains using multilocus sequence typing (MLST). Antimicrobial genes, capsular loci-K-types, plasmids types and virulence genes were also identified using whole genome sequence data. RESULTS All five CRKP were determined to have blaKPC-2 with or without blaOX-A48 and blaNDM-2. The molecular genotyping by PFGE showed 100% similarity among the five isolates. The MLST allelic profile analysis clonally clustered our strains with SL-258, CG-11 and ST11 mainly reported from South Asia. Further molecular characterization of the capsular K-locus and O-locus genes, revealed the strains to belong to KL-47 type and OL101 type respectively. The core genome typing suggests that our strains were clonally related to Chinese strains with less than five chromosomal nucleotides differences. CONCLUSION Epidemiological and molecular analyses confirmed that these KPC-producing K. pneumoniae strains are from a single clone that caused multiple nosocomial infections in one health institution. This finding highlights the importance to sustain the surveillance and infection prevention efforts and to step up active screening to prevent the spread of nosocomial infection.
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Affiliation(s)
- Mohammed Al Balushi
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Rajesh Kumar
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Azza Al-Rashdi
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Amin Ratna
- Infection Prevention and Control, Sultan Qaboos Hospital,Ministry of Health, Oman
| | - Ahood Al-Jabri
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Neima Al-Shekaili
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Ramasandhya Rani
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Sara Al Sumri
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Laila Al-Ghabshi
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman
| | - Seif Al-Abri
- Directorate General for Disease Surveillance and Control, Ministry of Health, Oman
| | - Amina Al-Jardani
- Central Public Health Laboratories, Ministry of Health, Al Mujamma Street, Bait Al Falaj, Darsait, P.O Box 393, Postal Code 100, Muscat, Oman.
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Parra-Flores J, Holý O, Acuña S, Lepuschitz S, Pietzka A, Contreras-Fernández A, Chavarría-Sepulveda P, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Castillo A, Ruppitsch W, Forsythe S. Genomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile. Front Microbiol 2022; 13:884721. [PMID: 35722296 PMCID: PMC9201451 DOI: 10.3389/fmicb.2022.884721] [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: 02/26/2022] [Accepted: 05/04/2022] [Indexed: 11/14/2022] Open
Abstract
This study characterized five Cronobacter spp. and six Salmonella spp. strains that had been isolated from 155 samples of powdered infant formula (PIF) sold in Chile and manufactured in Chile and Mexico in 2018–2020. Two strains of Cronobacter sakazakii sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of Cronobacter malonaticus ST60 (O:1) were identified. All Salmonella strains were identified as Salmonella Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The C. sakazakii and C. malonaticus isolates were resistant to cephalothin, whereas the Salmonella isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the C. sakazakii and C. malonaticus isolates; the most prevalent were mcr-9.1, blaCSA, and blaCMA. In Salmonella, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including aac(6′)-Iaa, β-lactamases ampH, ampC1, and marA. In the Cronobacter isolates, 32 virulence-associated genes were detected by WGS and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, invasion, plasminogen activator, colonization, transcriptional regulator, survival in macrophages, use of sialic acid, and toxin-antitoxin genes. In the Salmonella strains, 120 virulence associated genes were detected, adherence, magnesium uptake, resistance to antimicrobial peptides, secretion system, stress protein, toxin, resistance to complement killing, and eight pathogenicity islands. The C. sakazakii and C. malonaticus strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The Salmonella strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of C. sakazakii and Salmonella in PIF is a health risk for infants aged less than 6 months. For this reason, sanitary practices should be reinforced for its production and retail surveillance.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondřej Holý
- Science and Research Centre, Faculty of Health Sciences, Palacký University Olomouc, Olomouc, Czechia
| | - Sergio Acuña
- Department of Food Engineering, Universidad del Bío-Bío, Chillán, Chile
| | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | - Ariane Pietzka
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico.,Faculty of Medicine, Biological Sciences Graduate Program, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Castillo
- Department of Nutrition and Food Science, Texas A&M University, College Station, TX, United States
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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Comparison of Two Distinct Subpopulations of Klebsiella pneumoniae ST16 Co-Occurring in a Single Patient. Microbiol Spectr 2022; 10:e0262421. [PMID: 35467408 PMCID: PMC9241866 DOI: 10.1128/spectrum.02624-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The higher resistance rate to ceftazidime-avibactam (CZA) is mainly related to carbapenem resistance, especially New Delhi metallo-β-lactamase (NDM). The CZA-susceptible Klebsiella pneumoniae (K191663) and the later CZA-resistant isolates (K191724, K191725, K191773) co-producing NDM-4 and OXA-181 were obtained from the same hospitalized patient returning from Vietnam. Our study aims to elucidate the diversity of K. pneumoniae ST16 through comparative analysis of whole-genome sequencing (WGS) data and identify the potential evolution of plasmids by sequencing longitudinal clinical isolates during antibiotic treatment. Firstly, multilocus sequence typing analysis and phylogenic analysis suggested that these strains belong to the two lineages of K. pneumoniae ST16. Surprisingly, the CZA-resistant strains were closely related to K. pneumoniae ST16 described in South Korea, instead of the blaNDM-4- or blaOXA-181-carrying ST16 reported in Vietnam. Secondly, blaNDM-4, blaTEM-1B, and rmtB co-existed on a self-conjugative IncFII(Yp)-like plasmid, which played a significant role in CZA resistance. It could transfer into the recipient Escherichia coli J53 at high frequency, indicating the risk of mobile carbapenemases. In addition, the loss of 12-kbp fragment occurred in blaNDM-4-positive isolate (K191773), which was likely caused by insertion sequence-mediated homologous recombination. Last but not least, as a repressor of acrAB operon system, acrR was truncated by a frameshift mutation in K191663. Thus, our study provided baseline information for monitoring the occurrence and development of bacterial resistance. IMPORTANCE As a leading health care-acquired infection pathogen, Klebsiella pneumoniae is threatening a large number of inpatients due to its diverse antibiotic resistance and virulence factors. Heretofore, with a growing number of reports about the coexistence of several carbapenemases in carbapenem-resistant K. pneumoniae (CRKP), epidemiologic surveillance has been strengthened. Nevertheless, the nosocomial outbreaks by CRKP ST16 are gradually increasing worldwide. Our study provides a deeper insight into the diversification of clinical isolates of CRKP ST16 in China. In addition, the comparison analysis of resistant plasmids may reveal the transmission of carbapenemase-encoding genes. Furthermore, our study also highlights the importance of longitudinal specimen collection and continuous monitoring during the treatment, which play a crucial role in understanding the development of antibiotic resistance and the evolution of resistance plasmids.
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Wareth G, Linde J, Hammer P, Pletz MW, Neubauer H, Sprague LD. WGS-Based Phenotyping and Molecular Characterization of the Resistome, Virulome and Plasmid Replicons in Klebsiella pneumoniae Isolates from Powdered Milk Produced in Germany. Microorganisms 2022; 10:microorganisms10030564. [PMID: 35336140 PMCID: PMC8956024 DOI: 10.3390/microorganisms10030564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/03/2022] [Accepted: 03/03/2022] [Indexed: 02/04/2023] Open
Abstract
The emergence of Klebsiella pneumoniae (K. pneumoniae) in German healthcare is worrying. It is not well-investigated in the veterinary world and food chains. In the current study, antibiotic susceptibility profiles of 24 K. pneumoniae strains isolated from powdered milk samples produced in Germany were investigated by a microdilution test. Next-generation sequencing (NGS) was applied to identify genomic determinants for antimicrobial resistance (AMR), virulence-associated genes and plasmids replicons. All isolates were susceptible to the majority (14/18) of tested antibiotics. Resistance to colistin, fosfomycin, chloramphenicol and piperacillin was found. The ambler class A ß-lactamase, blaSHV variants were identified in all isolates, of which blaSHV-187 was most prevalent and found in 50% of isolates. Single-nucleotide-variants of oqxA and oqxB conferring resistance to phenicol/quinolone were found in all isolates, and the oqxB17 was the most prevalent found in 46% of isolates. 67% of isolates harbored fosA genes; however, only one was fosfomycin-resistant. Two isolates harbored genes conferring resistance to colistin, despite being susceptible. The majority of identified virulome genes were iron uptake siderophores. Two enterobactins (entB, fepC), six adherence-related genes belonging to E. coli common pilus (ECP) and one secretion system (ompA gene) were found in all isolates. In contrast, yersiniabactin was found in two isolates. One ST23 strain was susceptible to all tested antibiotics, and harbored determinants discriminatory for hypervirulent strains, e.g., aerobactin, salmochelin, yersiniabactin, enterobactin and regulator of mucoid phenotype A genes that are highly associated with hypervirulent K. pneumoniae. The IncF plasmid family was found in all strains, while almost half of the isolates harbored Col440I-type plasmids and nine isolates harbored various Inc-type plasmids. The presence of K. pneumoniae carrying different resistomes and major virulent specific virulomes in powdered milk samples is alarming. This could threaten public health, particularly of neonates and infants consuming dried milk.
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Affiliation(s)
- Gamal Wareth
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Department of Bacteriology, Immunology and Mycology, Faculty of Veterinary Medicine, Benha University, Toukh 13736, Egypt
- Correspondence:
| | - Jörg Linde
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Philipp Hammer
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Mathias W. Pletz
- Institute for Infectious Diseases and Infection Control, Jena University Hospital, Jena University, 07743 Jena, Germany;
- Research Campus Infectognostics, Philosophenweg 7, 07743 Jena, Germany
| | - Heinrich Neubauer
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
| | - Lisa D. Sprague
- Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses (IBIZ), Naumburger Str. 96a, 07743 Jena, Germany; (J.L.); (H.N.); (L.D.S.)
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9
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Ragheb SM, Govinden U, Osei Sekyere J. Genetic support of carbapenemases: a One Health systematic review and meta-analysis of current trends in Africa. Ann N Y Acad Sci 2021; 1509:50-73. [PMID: 34753206 DOI: 10.1111/nyas.14703] [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: 05/21/2020] [Revised: 09/06/2021] [Accepted: 09/26/2021] [Indexed: 11/28/2022]
Abstract
Antimicrobial resistance (AMR) is a public health threat globally. Carbapenems are β-lactam antibiotics used as last-resort agents for treating antibiotic-resistant infections. Mobile genetic elements (MGEs) play an important role in the dissemination and expression of antimicrobial resistance genes (ARGs), including the mobilization of ARGs within and between species. The presence of MGEs around carbapenem-hydrolyzing enzymes, called carbapenemases, in bacterial isolates in Africa is concerning. The association between MGEs and carbapenemases is described herein. Specific plasmid replicons, integrons, transposons, and insertion sequences were found flanking specific and different carbapenemases across the same and different clones and species isolated from humans, animals, and the environment. Notably, similar genetic contexts have been reported in non-African countries, supporting the importance of MGEs in driving the intra- and interclonal and species transmission of carbapenemases in Africa and globally. Technical and budgetary limitations remain challenges for epidemiological analysis of carbapenemases in Africa, as studies undertaken with whole-genome sequencing remained relatively few. Characterization of MGEs in antibiotic-resistant infections can deepen our understanding of carbapenemase epidemiology and facilitate the control of AMR in Africa. Investment in genomic epidemiology will facilitate faster clinical interventions and containment of outbreaks.
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Affiliation(s)
- Suzan Mohammed Ragheb
- Department of Microbiology and Immunology, Faculty of Pharmacy, Modern University for Technology and Information (MTI), Cairo, Egypt
| | - Usha Govinden
- Discipline of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, KwaZulu-Natal, South Africa
| | - John Osei Sekyere
- Department of Microbiology & Immunology, Indiana University School of Medicine-Northwest, Gary, Indiana.,Department of Dermatology, School of Medicine, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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10
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Flores-Valdez M, Ares MA, Rosales-Reyes R, Torres J, Girón JA, Weimer BC, Mendez-Tenorio A, De la Cruz MA. Whole Genome Sequencing of Pediatric Klebsiella pneumoniae Strains Reveals Important Insights Into Their Virulence-Associated Traits. Front Microbiol 2021; 12:711577. [PMID: 34489901 PMCID: PMC8418058 DOI: 10.3389/fmicb.2021.711577] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 07/27/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae is recognized as a common cause of nosocomial infections and outbreaks causing pneumonia, septicemia, and urinary tract infections. This opportunistic bacterium shows an increasing acquisition of antibiotic-resistance genes, which complicates treatment of infections. Hence, fast reliable strain typing methods are paramount for the study of this opportunistic pathogen’s multi-drug resistance genetic profiles. In this study, thirty-eight strains of K. pneumoniae isolated from the blood of pediatric patients were characterized by whole-genome sequencing and genomic clustering methods. Genes encoding β-lactamase were found in all the bacterial isolates, among which the blaSHV variant was the most prevalent (53%). Moreover, genes encoding virulence factors such as fimbriae, capsule, outer membrane proteins, T4SS and siderophores were investigated. Additionally, a multi-locus sequence typing (MLST) analysis revealed 24 distinct sequence types identified within the isolates, among which the most frequently represented were ST76 (16%) and ST70 (11%). Based on LPS structure, serotypes O1 and O3 were the most prevalent, accounting for approximately 63% of all infections. The virulence capsular types K10, K136, and K2 were present in 16, 13, and 8% of the isolates, respectively. Phylogenomic analysis based on virtual genome fingerprints correlated with the MLST data. The phylogenomic reconstruction also denoted association between strains with a higher abundance of virulence genes and virulent serotypes compared to strains that do not possess these traits. This study highlights the value of whole-genomic sequencing in the surveillance of virulence attributes among clinical K. pneumoniae strains.
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Affiliation(s)
- Mauricio Flores-Valdez
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional De Ciencias Biológicas (ENCB), Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico.,Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Roberto Rosales-Reyes
- Unidad de Medicina Experimental, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Jorge A Girón
- Centro de Detección Biomolecular, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Bart C Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
| | - Alfonso Mendez-Tenorio
- Laboratorio de Biotecnología y Bioinformática Genómica, Escuela Nacional De Ciencias Biológicas (ENCB), Instituto Politécnico Nacional, Mexico City, Mexico
| | - Miguel A De la Cruz
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
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11
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Parra-Flores J, Holý O, Riffo F, Lepuschitz S, Maury-Sintjago E, Rodríguez-Fernández A, Cruz-Córdova A, Xicohtencatl-Cortes J, Mancilla-Rojano J, Troncoso M, Figueroa G, Ruppitsch W, Forsythe S. Profiling the Virulence and Antibiotic Resistance Genes of Cronobacter sakazakii Strains Isolated From Powdered and Dairy Formulas by Whole-Genome Sequencing. Front Microbiol 2021; 12:694922. [PMID: 34276629 PMCID: PMC8278472 DOI: 10.3389/fmicb.2021.694922] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/03/2021] [Indexed: 11/13/2022] Open
Abstract
Cronobacter sakazakii is an enteropathogen that causes neonatal meningitis, septicemia, and necrotizing enterocolitis in preterm infants and newborns with a mortality rate of 15 to 80%. Powdered and dairy formulas (P-DF) have been implicated as major transmission vehicles and subsequently the presence of this pathogen in P-DF led to product recalls in Chile in 2017. The objective of this study was to use whole genome sequencing (WGS) and laboratory studies to characterize Cronobacter strains from the contaminated products. Seven strains were identified as C. sakazakii, and the remaining strain was Franconibacter helveticus. All C. sakazakii strains adhered to a neuroblastoma cell line, and 31 virulence genes were predicted by WGS. The antibiograms varied between strains. and included mcr-9.1 and bla CSA genes, conferring resistance to colistin and cephalothin, respectively. The C. sakazakii strains encoded I-E and I-F CRISPR-Cas systems, and carried IncFII(pECLA), Col440I, and Col(pHHAD28) plasmids. In summary, WGS enabled the identification of C. sakazakii strains and revealed multiple antibiotic resistance and virulence genes. These findings support the decision to recall the contaminated powdered and dairy formulas from the Chilean market in 2017.
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Affiliation(s)
- Julio Parra-Flores
- Department of Nutrition and Public Health, Universidad del Bío-Bío, Chillán, Chile
| | - Ondrej Holý
- Department of Public Health, Palacký University Olomouc, Olomouc, Czechia
| | | | - Sarah Lepuschitz
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
| | | | | | - Ariadnna Cruz-Córdova
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Juan Xicohtencatl-Cortes
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
| | - Jetsi Mancilla-Rojano
- Intestinal Bacteriology Research Laboratory, Hospital Infantil de México Federico Gómez, Mexico City, Mexico
- Faculty of Medicine, Biological Sciences Graduate Program, Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Miriam Troncoso
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Guillermo Figueroa
- Microbiology and Probiotics Laboratory, Institute of Nutrition and Food Technology, Universidad de Chile, Santiago, Chile
| | - Werner Ruppitsch
- Austrian Agency for Health and Food Safety, Institute for Medical Microbiology and Hygiene, Vienna, Austria
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12
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Genomic Investigation of Carbapenem-Resistant Klebsiella pneumonia Colonization in an Intensive Care Unit in South Africa. Genes (Basel) 2021; 12:genes12070951. [PMID: 34206235 PMCID: PMC8308027 DOI: 10.3390/genes12070951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 02/07/2023] Open
Abstract
The study investigated carbapenemase-producing Klebsiella pneumoniae (CPKP) isolates of patients in an intensive care unit (ICU) in a public hospital in the KwaZulu-Natal province, South Africa using whole-genome sequencing (WGS). Ninety-seven rectal swabs, collected from all consenting adult patients (n = 31) on days 1, 3, and 7 and then weekly, were screened for carbapenemase-production using Chrome-ID selective media. Antibiotic susceptibility was determined for the fourteen positive CPKP isolates obtained using the VITEK 2 automated system. All isolates (100%) were resistant to ertapenem and meropenem, and 71.4% (n = 10) were resistant to imipenem. All CPKP isolates were subjected to ERIC/PCR, and a sub-sample of isolates was selected for WGS based on their antibiograms and clonality. All sequenced isolates harbored the blaOXA-181 carbapenemase (100%) and co-carried other β-lactamase genes such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and blaSHV-1. IncF, IncX3, and Col plasmid replicons groups and class I integrons (ln191 and ln27) were detected. All isolates belonged to the same sequence type ST307 and capsular serotypes (K102, O2v2). All the isolates carried the same virulence repertoire, reflecting the epidemiological relationship between isolates. blaOXA-181 was located on a multi-replicon plasmid similar to that of E. coli p010_B-OXA181, and isolates were aligned with several South African and international clades, demonstrating horizontal and vertical transboundary distribution. The findings suggest that blaOXA-181 producing K. pneumoniae is endemic in this ICU, colonizing the patients. CRE screening and enhanced infection prevention and control measures are urgently required.
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13
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Iskandar K, Molinier L, Hallit S, Sartelli M, Hardcastle TC, Haque M, Lugova H, Dhingra S, Sharma P, Islam S, Mohammed I, Naina Mohamed I, Hanna PA, Hajj SE, Jamaluddin NAH, Salameh P, Roques C. Surveillance of antimicrobial resistance in low- and middle-income countries: a scattered picture. Antimicrob Resist Infect Control 2021; 10:63. [PMID: 33789754 PMCID: PMC8011122 DOI: 10.1186/s13756-021-00931-w] [Citation(s) in RCA: 123] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 03/22/2021] [Indexed: 01/07/2023] Open
Abstract
Data on comprehensive population-based surveillance of antimicrobial resistance is lacking. In low- and middle-income countries, the challenges are high due to weak laboratory capacity, poor health systems governance, lack of health information systems, and limited resources. Developing countries struggle with political and social dilemma, and bear a high health and economic burden of communicable diseases. Available data are fragmented and lack representativeness which limits their use to advice health policy makers and orientate the efficient allocation of funding and financial resources on programs to mitigate resistance. Low-quality data means soaring rates of antimicrobial resistance and the inability to track and map the spread of resistance, detect early outbreaks, and set national health policy to tackle resistance. Here, we review the barriers and limitations of conducting effective antimicrobial resistance surveillance, and we highlight multiple incremental approaches that may offer opportunities to strengthen population-based surveillance if tailored to the context of each country.
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Affiliation(s)
- Katia Iskandar
- Department of Mathématiques Informatique et Télécommunications, Université Toulouse III, Paul Sabatier, INSERM, UMR 1027, 31000, Toulouse, France.
- INSPECT-LB, Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban, Beirut, 6573-14, Lebanon.
- Faculty of Pharmacy, Lebanese University, Mount Lebanon, Lebanon.
| | - Laurent Molinier
- Faculté de Médecine, Equipe constitutive du CERPOP, UMR1295, unité mixte INSERM, Université Paul Sabatier Toulouse III, 31000, Toulouse, France
| | - Souheil Hallit
- INSPECT-LB, Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban, Beirut, 6573-14, Lebanon
- Faculty of Medicine and Medical Sciences, Holy Spirit University of Kaslik (USEK), Jounieh, Lebanon
| | - Massimo Sartelli
- Department of Surgery, University of Macerata, 62100, Macerata, Italy
| | - Timothy Craig Hardcastle
- Department of Trauma Service, Inkosi Albert Luthuli Central Hospital, Durban, 4091, South Africa
- Department of Surgery, Nelson Mandela School of Clinical Medicine, University of KwaZulu-Natal, Congela, 4041, Durban, South Africa
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kem Perdana Sungai Besi, 57000, Malaysia
| | - Halyna Lugova
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, 57000, Kuala Lumpur, Malaysia
| | - Sameer Dhingra
- Department of Pharmacy Practice, National Institute of Pharmaceutical Education and Research (NIPER) Hajipur, Bihar, India
| | - Paras Sharma
- Department of Pharmacognosy, BVM College of Pharmacy, Gwalior, India
| | - Salequl Islam
- Department of Microbiology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Irfan Mohammed
- Department of Restorative Dentistry, Federal University of Pelotas School of Dentistry, Pelotas, RS, 96020-010, Brazil
| | - Isa Naina Mohamed
- Pharmacoepidemiology and Drug Safety Unit, Pharmacology Department, Medical Faculty, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Pierre Abi Hanna
- Faculty of Pharmacy, Lebanese University, Mount Lebanon, Lebanon
| | - Said El Hajj
- Department of Medicine, Lebanese University, Beirut, Lebanon
| | - Nurul Adilla Hayat Jamaluddin
- Pharmacoepidemiology and Drug Safety Unit, Pharmacology Department, Medical Faculty, Universiti Kebangsaan Malaysia, Jalan Yaacob Latif, Kuala Lumpur, Malaysia
| | - Pascale Salameh
- INSPECT-LB, Institut National de Santé Publique, d'Épidémiologie Clinique et de Toxicologie-Liban, Beirut, 6573-14, Lebanon
- Department of Medicine, Lebanese University, Beirut, Lebanon
- Faculty of Medicine, University of Nicosia, Nicosia, Cyprus
| | - Christine Roques
- Department of Bactériologie-Hygiène, Centre Hospitalier Universitaire, Hôpital Purpan, 31330, Toulouse, France
- Department of Bioprocédés et Systèmes Microbiens, Laboratoire de Génie Chimique, Université Paul Sabatier Toulouse III, UMR 5503, 31330, Toulouse, France
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14
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Touati A, Manseur L, Mehidi I, Mairi A. Epidemiological and Genetic Features of Plasmids Carrying blaNDM Genes: An In Silico Analysis with Emphasis on Replicon Types, and Resistome. Microb Drug Resist 2021; 27:1232-1242. [PMID: 33417812 DOI: 10.1089/mdr.2020.0427] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Background: New Delhi metallo-β-lactamase (NDM) is a metallo-β-lactamase that has been disseminated worldwide. Plasmids harboring the blaNDM gene belonged to many incompatibility groups, of which IncX3, IncF, and IncA/C were the most represented. This in silico study aimed at analyzing a set of 649 plasmids carrying NDM-type carbapenemase (pNDMs) previously assigned in GenBank. Materials and Methods: The selected plasmids were analyzed by ResFinder (antibiotic resistome identification), BacMet (metal/biocides resistome identification), PlasmidFinder/PLSDB (replicon typing), TAfinder (toxin-antitoxin system [TAS] identification), and OriTfinder (prediction of the transferability). Results: We found that Escherichia coli and Klebsiella pneumoniae amounted to about 68.6% of all reported species. The distribution of these plasmids by samples showed a diversity of origins. Many plasmids carried different genes encoding resistance to antibiotics, heavy metals, and biocides with different frequencies. The TAfinder allowed the identification of a TAS in 292 plasmids (45%). Twenty-four different incompatibility groups were predicted, of which IncX3 (34.2%; n = 222), IncC (10.9%, n = 71), and IncFII (9.9%, n = 64) were the most often described. Besides, 23.6% (n = 151) of pNDMs were recognized as multireplicon plasmids. Conclusion: This study has shown the importance of plasmids in the dissemination of the NDM carbapenemase and raises the importance of monitoring these elements to better understand the evolution of the antibiotic resistance threat.
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Affiliation(s)
- Abdelaziz Touati
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Lyticia Manseur
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Imene Mehidi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
| | - Assia Mairi
- Laboratoire d'Ecologie Microbienne, FSNV, Université de Bejaia, Bejaia, Algérie
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15
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In Vitro and In Vivo Evaluations of β-Lactam/β-Lactamase Mono- and Combined Therapies against Carbapenem-Nonsusceptible Enterobacteriaceae in Taiwan. Microorganisms 2020; 8:microorganisms8121981. [PMID: 33322803 PMCID: PMC7764198 DOI: 10.3390/microorganisms8121981] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 12/10/2020] [Indexed: 12/28/2022] Open
Abstract
Increasing carbapenem resistance rates worldwide underscored the urgent need of novel antimicrobials. Ceftazidime–avibactam and aztreonam–avibactam combinations are developed to combat carbapenem resistance, but biological and geographic variations must be considered for antibiotic susceptibility patterns varied. Thus, we sought to assess the susceptibilities of ceftazidime–avibactam and aztreonam–avibactam against 660 carbapenem-nonsusceptible Enterobacteriaceae isolates (472 Klebsiella pneumoniae and 188 Escherichia coli) collected during an earlier Taiwan surveillance study. Agar dilution method was used to determine ceftazidime–avibactam and aztreonam–avibactam susceptibility. Metallo-carbapenemase’s contribution to resistance were investigated with EDTA addition. The in vivo efficacies were evaluated using a Caenorhabditis elegans model. High susceptibility rates were observed for ceftazidime–avibactam and aztreonam–avibactam against the 472 carbapenem-nonsusceptible K. pneumoniae (CnsKP) (85.2% and 95.3%, respectively) and 188 carbapenem-nonsusceptible E. coli (CnsEC) isolates (91.5% and 94.1%, respectively). For non-metallo-carbapenemase producers, the susceptibility rates for ceftazidime–avibactam were 93.6% for CnsKP and 97.7% for CnsEC, whereas only 7.1% CnsKP and 11.1% CnsEC in metallo-carbapenemase producers were susceptible to ceftazidime–avibactam. Of all isolates, 95.3% CnsKP and 94.1% CnsEC were susceptible to aztreonam–avibactam. In C. elegans model, ceftazidime–avibactam and aztreonam–avibactam revealed effective against a blaKPC-producing K. pneumoniae isolate in vivo. Our results propose a positive therapeutic approach for both combinations against carbapenem-nonsusceptible Enterobacteriaceae in Taiwan.
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16
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Tshitshi L, Manganyi MC, Montso PK, Mbewe M, Ateba CN. Extended Spectrum Beta-Lactamase-Resistant Determinants among Carbapenem-Resistant Enterobacteriaceae from Beef Cattle in the North West Province, South Africa: A Critical Assessment of Their Possible Public Health Implications. Antibiotics (Basel) 2020; 9:E820. [PMID: 33213050 PMCID: PMC7698526 DOI: 10.3390/antibiotics9110820] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/10/2020] [Accepted: 11/12/2020] [Indexed: 12/27/2022] Open
Abstract
Carbapenems are considered to be the last resort antibiotics for the treatment of infections caused by extended-spectrum beta-lactamase (ESBL)-producing strains. The purpose of this study was to assess antimicrobial resistance profile of Carbapenem-resistant Enterobacteriaceae (CRE) isolated from cattle faeces and determine the presence of carbapenemase and ESBL encoding genes. A total of 233 faecal samples were collected from cattle and analysed for the presence of CRE. The CRE isolates revealed resistance phenotypes against imipenem (42%), ertapenem (35%), doripenem (30%), meropenem (28%), cefotaxime, (59.6%) aztreonam (54.3%) and cefuroxime (47.7%). Multidrug resistance phenotypes ranged from 1.4 to 27% while multi antibiotic resistance (MAR) index value ranged from 0.23 to 0.69, with an average of 0.40. Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), Proteus mirabilis (P. mirabilis) and Salmonella (34.4, 43.7, 1.3 and 4.6%, respectively) were the most frequented detected species through genus specific PCR analysis. Detection of genes encoding carbapenemase ranged from 3.3% to 35% (blaKPC, blaNDM, blaGES, blaOXA-48, blaVIM and blaOXA-23). Furthermore, CRE isolates harboured ESBL genes (blaSHV (33.1%), blaTEM (22.5%), blaCTX-M (20.5%) and blaOXA (11.3%)). In conclusion, these findings indicate that cattle harbour CRE carrying ESBL determinants and thus, proper hygiene measures must be enforced to mitigate the spread of CRE strains to food products.
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Affiliation(s)
- Lungisile Tshitshi
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
- Faculty of Agriculture and Natural Sciences, University of Mpumalanga, Private Bag X11283, Mbombela 1200, South Africa;
| | - Madira Coutlyne Manganyi
- Unit for Environmental Sciences and Management, North-West University, Potchefstroom 2520, South Africa;
| | - Peter Kotsoana Montso
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
| | - Moses Mbewe
- Faculty of Agriculture and Natural Sciences, University of Mpumalanga, Private Bag X11283, Mbombela 1200, South Africa;
| | - Collins Njie Ateba
- Antimicrobial Resistance and Phage Biocontrol Research Group, Department of Microbiology, School of Biological Sciences, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North West University, Private Bag X2046, Mmabatho 2735, South Africa;
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17
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Tsotetsi N, Amoako DG, Somboro AM, Khumalo HM, Khan RB. Molecular mechanisms underlying the renoprotective effects of 1,4,7-triazacyclononane: a βeta-lactamase inhibitor. Cytotechnology 2020; 72:785-796. [PMID: 32920746 DOI: 10.1007/s10616-020-00422-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/07/2020] [Indexed: 12/11/2022] Open
Abstract
Broad-spectrum β-lactam antibiotics such as penicillin are routinely used against both Gram-negative and Gram-positive bacteria. However, bacteria that produce β-lactamase have developed resistance against these antibiotics by cleaving the β-lactam ring and rendering the antibiotic inactive. To combat this effect, 1,4,7- Triazacyclononane (TACN), a cyclic organic compound derived from cyclononanes has been shown to preserve the activity of β-lactam antibiotics by inhibiting β-lactamase. However, its cytotoxic effects require elucidation. Given that the cytotoxic target for many therapeutics is the kidney, this study investigated the effects of TACN on human embryonic kidney cells (Hek293) cells. Hek293 cells were treated with TACN (0-500 µM) for 24 h and the cytotoxicity was assessed (MTT and LDH assay). Apoptosis was luminometrically detected by measuring phosphatidylserine externalisation and caspase activity and fluorescently detecting necrosis. DNA fragmentation was visualised using fluorescent microscopy. Expression of the apoptosis-related protein were determined by western blot. The results generated indicate that TACN does not initiate necrosis as LDH was decreased. Likewise, decreased apoptosis was supported by the decreased phosphatidylserine, caspases, Bax, cleaved PARP, IAP and NF-kB. However, increased DNA fragmentation was associated with increased p53. Therefore, effects of TACN at the nucleus, produced a p53 response to initiate DNA repair and did not culminate in cell death. The findings show that TACN is not cytotoxic to Hek293 cells via the apoptotic route. Since TACN did not induce cell death, its potential as a metallo-β-lactamase inhibitor (MBLI) may be exploited to counteract the effect of MBL-producing bacteria. Restoring β-lactam activity will curb the global menace of antibiotic resistance.
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Affiliation(s)
- Nrateng Tsotetsi
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.
| | - Anou M Somboro
- Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Khumalo
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rene B Khan
- Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.
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18
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Mcoyi S, Amoako DG, Somboro AM, Khumalo HM, Khan RB. The molecular effect of 1,4,7-triazacyclononane on oxidative stress parameters in human hepatocellular carcinoma (HepG2) cells. J Biochem Mol Toxicol 2020; 34:e22607. [PMID: 32869927 DOI: 10.1002/jbt.22607] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/04/2020] [Accepted: 08/15/2020] [Indexed: 12/23/2022]
Abstract
Antibiotic resistance poses a great threat to human, animal and environmental health. β-Lactam antibiotics have been successful in combating bacterial infections. However, the overuse, inappropriate prescribing, unavailability of new antibiotics and regulation barriers have exacerbated bacterial resistance to these antibiotics. 1,4,7-Triazacyclononane (TACN) is a cyclic organic tridentate inhibitor with strong metal-chelating abilities that has been shown to inhibit β-lactamase enzymes and may represent an important breakthrough in the treatment of drug-resistant bacterial strains. However, its cytotoxicity in the liver is unknown. This study aimed to determine the effect of TACN on oxidative stress in HepG2 cells. The HepG2 cells were treated with 0 to 500 µM TACN for 24 hours to obtain an IC50 for use in subsequent assays. Free radicals were measured using the thiobarbituric acid reactive substance and nitric oxide synthase assays, respectively, while antioxidant levels were assessed using luminometry (glutathione [GSH] and adenosine triphosphate [ATP]) and Western blot analysis (SOD, catalase, GPx-1, HSP70 and Nrf2). Percentage survival fluctuated as TACN concentration increased with a calculated IC50 of 545 µM. A slight increase in HSP70 and Nrf2 expression indicated the presence of stress and a response against it, respectively. However, free radical production was not increased as indicated by decreased malondialdehyde levels and reactive nitrogen species. Glutathione levels increased slightly, while ATP levels were marginally altered. The results suggest that TACN does not induce oxidative stress in HepG2 cells and can be exploited as a potential inhibitor.
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Affiliation(s)
- Simphiwe Mcoyi
- Drug and Innovation Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Daniel G Amoako
- Drug and Innovation Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Anou M Somboro
- Drug and Innovation Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa.,Biomedical Resource Unit, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hezekiel M Khumalo
- Drug and Innovation Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
| | - Rene B Khan
- Drug and Innovation Research Unit, Discipline of Medical Biochemistry, School of Laboratory Medicine and Medical Science, University of KwaZulu-Natal, Durban, South Africa
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19
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Sartelli M, C. Hardcastle T, Catena F, Chichom-Mefire A, Coccolini F, Dhingra S, Haque M, Hodonou A, Iskandar K, Labricciosa FM, Marmorale C, Sall I, Pagani L. Antibiotic Use in Low and Middle-Income Countries and the Challenges of Antimicrobial Resistance in Surgery. Antibiotics (Basel) 2020; 9:E497. [PMID: 32784880 PMCID: PMC7459633 DOI: 10.3390/antibiotics9080497] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial resistance (AMR) is a phenomenon resulting from the natural evolution of microbes. Nonetheless, human activities accelerate the pace at which microorganisms develop and spread resistance. AMR is a complex and multidimensional problem, threatening not only human and animal health, but also regional, national, and global security, and the economy. Inappropriate use of antibiotics, and poor infection prevention and control strategies are contributing to the emergence and dissemination of AMR. All healthcare providers play an important role in preventing the occurrence and spread of AMR. The organization of healthcare systems, availability of diagnostic testing and appropriate antibiotics, infection prevention and control practices, along with prescribing practices (such as over-the-counter availability of antibiotics) differs markedly between high-income countries and low and middle-income countries (LMICs). These differences may affect the implementation of antibiotic prescribing practices in these settings. The strategy to reduce the global burden of AMR includes, among other aspects, an in-depth modification of the use of existing and future antibiotics in all aspects of medical practice. The Global Alliance for Infections in Surgery has instituted an interdisciplinary working group including healthcare professionals from different countries with different backgrounds to assess the need for implementing education and increasing awareness about correct antibiotic prescribing practices across the surgical pathways. This article discusses aspects specific to LMICs, where pre-existing factors make surgeons' compliance with best practices even more important.
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Affiliation(s)
| | - Timothy C. Hardcastle
- Trauma Service, Inkosi Albert Luthuli Central Hospital and Department of Surgery, Nelson R. Mandela School of Clinical Medicine, Durban 4058, South Africa;
| | - Fausto Catena
- Department of Emergency Surgery, Parma Maggiore Hospital, 43126 Parma, Italy;
| | - Alain Chichom-Mefire
- Department of Surgery and Obs/Gyn, Faculty of Health Sciences University of Buea, Buea P.O. Box 63, South West Province, Cameroon;
| | - Federico Coccolini
- General, Emergency and Trauma Surgery Department, Cisanello University Hospital, 56100 Pisa, Italy;
| | - Sameer Dhingra
- School of Pharmacy, Faculty of Medical Sciences, The University of the West Indies, St. Augustine, Eric Williams Medical Sciences Complex, Uriah Butler Highway, Champ Fleurs 33178, Trinidad and Tobago;
| | - Mainul Haque
- Unit of Pharmacology, Faculty of Medicine and Defence Health, Universiti Pertahanan Nasional Malaysia (National Defence University of Malaysia), Kuala Lumpur 57000, Malaysia;
| | - Adrien Hodonou
- Department of General Surgery, Regional Hospital Borgou, Faculty of Medicine, University of Parakou, Parakou P.O. Box 123, Benin;
| | - Katia Iskandar
- Department of Pharmacy, Lebanese, International University, Beirut 1106, Lebanon;
| | | | - Cristina Marmorale
- Department of Surgery, Università Politecnica delle Marche, 60126 Ancona, Italy;
| | - Ibrahima Sall
- General Surgery Department, Military Teaching Hospital, Dakar 3006, Senegal;
| | - Leonardo Pagani
- Infectious Diseases Unit, Bolzano Central Hospital, 39100 Bolzano, Italy;
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20
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Iskandar K, Molinier L, Hallit S, Sartelli M, Catena F, Coccolini F, Craig Hardcastle T, Roques C, Salameh P. Drivers of Antibiotic Resistance Transmissionin Low- and Middle-Income Countriesfrom a "One Health" Perspective-A Review. Antibiotics (Basel) 2020; 9:E372. [PMID: 32630353 PMCID: PMC7400606 DOI: 10.3390/antibiotics9070372] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is an ecosystem problem threatening the interrelated human-animalenvironmenthealth under the "One Health" framework. Resistant bacteria arising in onegeographical area can spread via cross-reservoir transmission to other areas worldwide either bydirect exposure or through the food chain and the environment. Drivers of antibiotic resistance arecomplex and multi-sectoral particularly in Lower- and Middle-income countries. These includeinappropriate socio-ecological behaviors; poverty; overcrowding; lack of surveillance systems; foodsupply chain safety issues; highly contaminated waste effluents; and loose rules and regulations. Inorder to examine the drivers of antibiotic resistance from a "one health" perspective, a literaturereview was conducted on three databases including PubMed, Medline and Google Scholar. A totalof 485 studies of potential relevance were selected, out of which 182 were included in this review.Results have shown that the aforementioned market failures are the leading cause for the negativeexternality of antibiotic resistance that extends in scope from the individual to the global ecosystem.Incremental and sustainable global actions can make the change, however, the problem willcontinue to prevail if governments do not prioritize the "One health" approach and if individual'saccountability is still denied in a world struggling with profound socio-economic problems.
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Affiliation(s)
- Katia Iskandar
- Department of Mathématiques Informatique et Télécommunications, Université Toulouse III, Paul Sabatier, INSERM, UMR 1027, F-31000 Toulouse, France
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573-14, Lebanon; (S.H.); (P.S.)
- Faculty of Pharmacy, Lebanese University, Beirut 1106, Lebanon
| | - Laurent Molinier
- Department of Medical Information, Centre Hospitalier Universitaire, INSERM, UMR 1027, Université Paul Sabatier Toulouse III, F-31000 Toulouse, France;
| | - Souheil Hallit
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573-14, Lebanon; (S.H.); (P.S.)
- Faculty of Medicine and Medical Sciences, Holy Spirit University of Kaslik (USEK), Jounieh P.O. Box 446, Lebanon
| | - Massimo Sartelli
- Department of surgery, University of Macerata, 62100 Macerata, Italy;
| | - Fausto Catena
- Department of Emergency Surgery, Parma Maggiore Hospital, 43126 Parma, Italy;
| | - Federico Coccolini
- Department of General, Emergency and Trauma Surgery, Cisanello University Hospital, 56100 Pisa, Italy;
| | - Timothy Craig Hardcastle
- Department of Trauma service, Inkosi Albert Luthuli Central Hospital, Durban 4091, South Africa;
- Department of Surgery, Nelson Mandela School of Clinical Medicine, University of KwaZulu-Natal, Congela, Durban 4041, South Africa
| | - Christine Roques
- Departement of Bioprocédés et Systèmes Microbiens, Laboratoire de Génie Chimique, Université Paul Sabatier Toulouse III, UMR 5503, 31330 Toulouse, France;
- Department of Bactériologie-Hygiène, Centre Hospitalier Universitaire, Hôpital Purpan, 31330 Toulouse, France
| | - Pascale Salameh
- INSPECT-LB: Institut National de Santé Publique, d’Épidémiologie Clinique et de Toxicologie-Liban, Beirut 6573-14, Lebanon; (S.H.); (P.S.)
- Faculty of Pharmacy, Lebanese University, Beirut 1106, Lebanon
- Faculty of Public Health, Lebanese University, Beirut 1103, Lebanon
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21
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Ramsamy Y, Mlisana KP, Amoako DG, Allam M, Ismail A, Singh R, Abia ALK, Essack SY. Pathogenomic Analysis of a Novel Extensively Drug-Resistant Citrobacter freundii Isolate Carrying a bla NDM-1 Carbapenemase in South Africa. Pathogens 2020; 9:pathogens9020089. [PMID: 32024012 PMCID: PMC7168644 DOI: 10.3390/pathogens9020089] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 01/24/2020] [Accepted: 01/30/2020] [Indexed: 02/06/2023] Open
Abstract
Pathogenomic analysis was performed on a novel carbapenem-resistant Citrobacter freundii isolate (H2730R) from a rectal swab of an adult male patient admitted to a tertiary hospital, Durban, South Africa. H2730R was identified using selective media and API 20e kit. Confirmatory identification and antibiotic susceptibility testing were performed using the VITEK II. H2730R was whole-genome sequenced on the Illumina MiSeq platform. H2730R was resistant to all tested antibiotics except tigecycline and was defined as ST498 by the C. freundii multilocus sequence typing (MLST) database. The estimated pathogenic potential predicted a higher probability (Pscore ≈ 0.875), supporting H2730R as a human pathogen. H2730R harbored 25 putative acquired resistance genes, 4 plasmid replicons, 4 intact prophages, a class 1 integron (IntI1), 2 predominant insertion sequences (IS3 and IS5), numerous efflux genes, and virulome. BLASTn analysis of the blaNDM-1 encoding contig (00022) and its flanking sequences revealed the blaNDM-1 was located on a plasmid similar to the multireplicon p18-43_01 plasmid reported for the spread of carbapenem resistance in South Africa. Phylogenomic analysis showed clustering of H2730R with CF003/CF004 strains in the same clade, suggesting a possible association between C. freundii strains/clones. Acquiring the p18-43_01 plasmid containing blaNDM-1, the diversity, and complex resistome, virulome, and mobilome of this pathogen makes its incidence very worrying regarding mobilized resistance. This study presents the background genomic information for future surveillance and tracking of the spread of carbapenem-resistant Enterobacteriaceae in South Africa.
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Affiliation(s)
- Yogandree Ramsamy
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- National Health Laboratory Services, Durban 4000, South Africa;
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
- Correspondence:
| | | | - Daniel G. Amoako
- Infection Genomics and Applied Bioinformatics Division, Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg 2131, South Africa; (M.A.); (A.I.)
| | - Ravesh Singh
- Medical Microbiology, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa;
- National Health Laboratory Services, Durban 4000, South Africa;
| | - Akebe Luther King Abia
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
| | - Sabiha Y. Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban 4000, South Africa; (A.L.K.A.); (S.Y.E.)
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