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Kakaraskoska Boceska B, Vilken T, Xavier BB, Kostyanev T, Lin Q, Lammens C, Ellis S, O'Brien S, da Costa RMA, Cook A, Russell N, Bielicki J, Riddell A, Stohr W, Walker AS, Berezin EN, Roilides E, De Luca M, Romani L, Ballot D, Dramowski A, Wadula J, Lochindarat S, Boonkasidecha S, Namiiro F, Ngoc HTB, Tran MD, Cressey TR, Preedisripipat K, Berkley JA, Musyimi R, Zarras C, Nana T, Whitelaw A, da Silva CB, Jaglal P, Ssengooba W, Saha SK, Islam MS, Mussi-Pinhata MM, Carvalheiro CG, Piddock LJV, Heath PT, Malhotra-Kumar S, Sharland M, Glupczynski Y, Goossens H. Assessment of three antibiotic combination regimens against Gram-negative bacteria causing neonatal sepsis in low- and middle-income countries. Nat Commun 2024; 15:3947. [PMID: 38729951 PMCID: PMC11087563 DOI: 10.1038/s41467-024-48296-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/26/2024] [Indexed: 05/12/2024] Open
Abstract
Gram-negative bacteria (GNB) are a major cause of neonatal sepsis in low- and middle-income countries (LMICs). Although the World Health Organization (WHO) reports that over 80% of these sepsis deaths could be prevented through improved treatment, the efficacy of the currently recommended first- and second-line treatment regimens for this condition is increasingly affected by high rates of drug resistance. Here we assess three well known antibiotics, fosfomycin, flomoxef and amikacin, in combination as potential antibiotic treatment regimens by investigating the drug resistance and genetic profiles of commonly isolated GNB causing neonatal sepsis in LMICs. The five most prevalent bacterial isolates in the NeoOBS study (NCT03721302) are Klebsiella pneumoniae, Acinetobacter baumannii, E. coli, Serratia marcescens and Enterobacter cloacae complex. Among these isolates, high levels of ESBL and carbapenemase encoding genes are detected along with resistance to ampicillin, gentamicin and cefotaxime, the current WHO recommended empiric regimens. The three new combinations show excellent in vitro activity against ESBL-producing K. pneumoniae and E. coli isolates. Our data should further inform and support the clinical evaluation of these three antibiotic combinations for the treatment of neonatal sepsis in areas with high rates of multidrug-resistant Gram-negative bacteria.
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Affiliation(s)
- Biljana Kakaraskoska Boceska
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Tuba Vilken
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Department of Medical Microbiology and Infection Control, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Tomislav Kostyanev
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
- Research Group for Global Capacity Building, National Food Institute, Technical University of Denmark, Kgs, Lyngby, Denmark
| | - Qiang Lin
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Christine Lammens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Sally Ellis
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Seamus O'Brien
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | | | - Aislinn Cook
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Neal Russell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Julia Bielicki
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
- Paediatric Research Centre, University of Basel Children's Hospital, Basel, Switzerland
| | - Amy Riddell
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Wolfgang Stohr
- MRC Clinical Trials Unit, University College London, London, UK
| | | | | | - Emmanuel Roilides
- Infectious Diseases Unit, 3rd Dept Paediatrics, School of Medicine, Faculty of Health Sciences, Aristotle University and Hippokration General Hospital, Thessaloniki, Greece
| | - Maia De Luca
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Lorenza Romani
- Infectious Disease Unit, Bambino Gesu Children's Hospital, Rome, Italy
| | - Daynia Ballot
- Department of Pediatrics and Child Health, School of Clinical Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Angela Dramowski
- Department of Paediatrics and Child Health, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Jeannette Wadula
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | | | | | - Flavia Namiiro
- Mulago Specialized Women's and Neonatal Hospital, Kampala, Uganda
| | | | | | - Tim R Cressey
- AMS-PHPT Research Collaboration, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, Thailand
| | | | - James A Berkley
- Clinical Research Department, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
- Centre for Tropical Medicine & Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- The Childhood Acute Illness & Nutrition (CHAIN) Network, Nairobi, Kenya
| | - Robert Musyimi
- Department of Microbiology, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Charalampos Zarras
- Microbiology Department, Hippokration General Hospital, Thessaloniki, Greece
| | - Trusha Nana
- Department of Clinical Microbiology and Infectious Diseases, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- Microbiology Laboratory, National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Cely Barreto da Silva
- Infection Control and Prevention Service, Santa Casa de Sao Paulo, Sao Paulo, Brazil
| | - Prenika Jaglal
- Department of Clinical Microbiology & Infectious Diseases, National Health Laboratory Services, CH Baragwanath Academic Hospital, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Willy Ssengooba
- Makerere University, Department of Medical Microbiology, Kampala, Uganda
| | - Samir K Saha
- Child Health Research Foundation (CHRF), Dhaka, Bangladesh
| | | | | | | | - Laura J V Piddock
- Global Antibiotic Research and Development Partnership (GARDP), Geneva, Switzerland
| | - Paul T Heath
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Surbhi Malhotra-Kumar
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Michael Sharland
- Centre for Neonatal and Pediatric Infection, Institute for Infection & Immunity, St. George's University of London, London, UK
| | - Youri Glupczynski
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | - Herman Goossens
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
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Rahmat Ullah S, Irum S, Mahnoor I, Ismatullah H, Mumtaz M, Andleeb S, Rahman A, Jamal M. Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance. BMC Genomics 2024; 25:408. [PMID: 38664636 PMCID: PMC11044325 DOI: 10.1186/s12864-024-10139-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 02/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected Klebsiella pneumoniae isolates from a local tertiary care hospital from February 2019-February 2021. To gain molecular insight into the resistome, virulome, and genetic environment of significant genes of multidrug-resistant K. pneumoniae isolates, we performed the short-read whole-genome sequencing of 10 K. pneumoniae isolates recovered from adult patients, neonates, and hospital tap water samples. RESULTS The draft genomes of the isolates varied in size, ranging from 5.48 to 5.96 Mbp suggesting the genome plasticity of this pathogen. Various genes conferring resistance to different classes of antibiotics e.g., aminoglycosides, quinolones, sulfonamides, tetracycline, and trimethoprim were identified in all sequenced isolates. The highest resistance was observed towards carbapenems, which has been putatively linked to the presence of both class B and class D carbapenemases, blaNDM, and blaOXA, respectively. Moreover, the biocide resistance gene qacEdelta1 was found in 6/10 of the sequenced strains. The sequenced isolates exhibited a broad range of sequence types and capsular types. The significant antibiotic resistance genes (ARGs) were bracketed by a variety of mobile genetic elements (MGEs). Various spontaneous mutations in genes other than the acquired antibiotic-resistance genes were observed, which play an indirect role in making these bugs resistant to antibiotics. Loss or deficiency of outer membrane porins, combined with ESBL production, played a significant role in carbapenem resistance in our sequenced isolates. Phylogenetic analysis revealed that the study isolates exhibited evolutionary relationships with strains from China, India, and the USA suggesting a shared evolutionary history and potential dissemination of similar genes amongst the isolates of different origins. CONCLUSIONS This study provides valuable insight into the presence of multiple mechanisms of carbapenem resistance in K. pneumoniae strains including the acquisition of multiple antibiotic-resistance genes through mobile genetic elements. Identification of rich mobilome yielded insightful information regarding the crucial role of insertion sequences, transposons, and integrons in shaping the genome of bacteria for the transmission of various resistance-associated genes. Multi-drug resistant isolates that had the fewest resistance genes exhibited a significant number of mutations. K. pneumoniae isolate from water source displayed comparable antibiotic resistance determinants to clinical isolates and the highest number of virulence-associated genes suggesting the possible interplay of ARGs amongst bacteria from different sources.
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Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Sidra Irum
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Iqra Mahnoor
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Humaira Ismatullah
- Research Centre for Modelling & Simulation (RCMS), National University of Sciences and Technology, Islamabad, Pakistan
| | - Mariam Mumtaz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan.
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
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Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LE, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024; 12:751. [PMID: 38674695 PMCID: PMC11051875 DOI: 10.3390/microorganisms12040751] [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: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is one of the predominant pathogens in healthcare settings. However, the prevalence and resistome of this organism within residential aged care facilities (RACFs), which are potential hotspots for antimicrobial resistance, remain unexplored. Here, we provide a phenotypic and molecular characterization of antimicrobial-resistant K. pneumoniae isolated from RACFs. K. pneumoniae was isolated from urine, faecal and wastewater samples and facility swabs. The antimicrobial susceptibility profiles of all the isolates were determined and the genomic basis for resistance was explored with whole-genome sequencing on a subset of isolates. A total of 147 K. pneumoniae were isolated, displaying resistance against multiple antimicrobials. Genotypic analysis revealed the presence of beta-lactamases and the ciprofloxacin-resistance determinant QnrB4 but failed to confirm the basis for the observed cephalosporin resistance. Clonal spread of the multidrug-resistant, widely disseminated sequence types 323 and 661 was observed. This study was the first to examine the resistome of K. pneumoniae isolates from RACFs and demonstrated a complexity between genotypic and phenotypic antimicrobial resistance. The intra-facility dissemination and persistence of multidrug-resistant clones is concerning, given that residents are particularly vulnerable to antimicrobial resistant infections, and it highlights the need for continued surveillance and interventions to reduce the risk of outbreaks.
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Affiliation(s)
- Jack M. Blaikie
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Sylvia A. Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Naomi L. Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Bradley J. Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Anteneh Amsalu
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Department of Medical Microbiology, University of Gondar, Gondar 196, Ethiopia
| | - Lex E.X. Leong
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
| | - Morgyn S. Warner
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
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Sumbana JJ, Santona A, Abdelmalek N, Fiamma M, Deligios M, Manjate A, Sacarlal J, Rubino S, Paglietti B. Polyclonal Multidrug ESBL-Producing Klebsiella pneumoniae and Emergence of Susceptible Hypervirulent Klebsiella pneumoniae ST23 Isolates in Mozambique. Antibiotics (Basel) 2023; 12:1439. [PMID: 37760735 PMCID: PMC10525843 DOI: 10.3390/antibiotics12091439] [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: 08/04/2023] [Revised: 08/30/2023] [Accepted: 09/09/2023] [Indexed: 09/29/2023] Open
Abstract
Globally, antibiotic-resistant Klebsiella spp. cause healthcare-associated infections with high mortality rates, and the rise of hypervirulent Klebsiella pneumoniae (hvKp) poses a significant threat to human health linked to community-acquired infections and increasing non-susceptibility. We investigated the phenotypic and genetic features of 36 Klebsiella isolates recovered from invasive infections at Hospital Central of Maputo in Mozambique during one year. The majority of the isolates displayed multidrug resistance (MDR) (29/36) to cephalosporins, gentamicin, ciprofloxacin, and trimethoprim-sulfamethoxazole but retained susceptibility to amikacin, carbapenems, and colistin. Most isolates were ESBLs-producing (28/36), predominantly carrying the blaCTX-M-15 and other beta-lactamase genes (blaSHV, blaTEM-1, and blaOXA-1). Among the 16 genomes sequenced, multiple resistance genes from different antibiotic classes were identified, with blaCTX-M-15, mostly in the ISEcp1-blaCTX-M-15-orf477 genetic environment, co-existing with blaTEM-1 and aac(3)-IIa in five isolates. Our results highlight the presence of polyclonal MDR ESBL-producing K. pneumoniae from eight sequence types (ST), mostly harbouring distinct yersiniabactin within the conjugative integrative element (ICE). Further, we identified susceptible hvKp ST23, O1-K1-type isolates carrying yersiniabactin (ybt1/ICEKp10), colibactin, salmochelin, aerobactin, and hypermucoid locus (rmpADC), associated with severe infections in humans. These findings are worrying and underline the importance of implementing surveillance strategies to avoid the risk of the emergence of the most threatening MDR hvKp.
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Affiliation(s)
- José João Sumbana
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Antonella Santona
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Nader Abdelmalek
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Maura Fiamma
- Clinical-Chemical Analysis and Microbiology Laboratory, San Francesco Hospital, 08100 Nuoro, Italy
| | - Massimo Deligios
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Alice Manjate
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Jahit Sacarlal
- Department of Microbiology, Faculty of Medicine, Eduardo Mondlane University, Maputo P.O. Box 257, Mozambique
| | - Salvatore Rubino
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
| | - Bianca Paglietti
- Department of Biomedical Sciences, University of Sassari, 07100 Sassari, Italy; (J.J.S.); (A.S.)
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Aruhomukama D, Nakabuye H. Investigating the evolution and predicting the future outlook of antimicrobial resistance in sub-saharan Africa using phenotypic data for Klebsiella pneumoniae: a 12-year analysis. BMC Microbiol 2023; 23:214. [PMID: 37553587 PMCID: PMC10408162 DOI: 10.1186/s12866-023-02966-y] [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: 05/25/2023] [Accepted: 08/01/2023] [Indexed: 08/10/2023] Open
Abstract
BACKGROUND Antimicrobial resistance (AMR) is a major public health challenge, particularly in sub-Saharan Africa (SSA). This study aimed to investigate the evolution and predict the future outlook of AMR in SSA over a 12-year period. By analysing the trends and patterns of AMR, the study sought to enhance our understanding of this pressing issue in the region and provide valuable insights for effective interventions and control measures to mitigate the impact of AMR on public health in SSA. RESULTS The study found that general medicine patients had the highest proportion of samples with AMR. Different types of samples showed varying levels of AMR. Across the studied locations, the highest resistance was consistently observed against ceftaroline (ranging from 68 to 84%), while the lowest resistance was consistently observed against ceftazidime avibactam, imipenem, meropenem, and meropenem vaborbactam (ranging from 92 to 93%). Notably, the predictive analysis showed a significant increasing trend in resistance to amoxicillin-clavulanate, cefepime, ceftazidime, ceftaroline, imipenem, meropenem, piperacillin-tazobactam, and aztreonam over time. CONCLUSIONS These findings suggest the need for coordinated efforts and interventions to control and prevent the spread of AMR in SSA. Targeted surveillance based on local resistance patterns, sample types, and patient populations is crucial for effective monitoring and control of AMR. The study also highlights the urgent need for action, including judicious use of antibiotics and the development of alternative treatment options to combat the growing problem of AMR in SSA.
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Affiliation(s)
- Dickson Aruhomukama
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda.
| | - Hellen Nakabuye
- Department of Medical Microbiology, College of Health Sciences, Makerere University, Kampala, Uganda
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Licona G, Ballot D, Moon TD, Banerjee R, Amorim G, Agthe AG, Weitkamp JH. Multidrug-Resistant Bacterial Infections Among Very Low Birthweight Infants With Late-Onset Sepsis in Johannesburg, South Africa. Open Forum Infect Dis 2023; 10:ofad362. [PMID: 37564739 PMCID: PMC10411040 DOI: 10.1093/ofid/ofad362] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/11/2023] [Indexed: 08/12/2023] Open
Abstract
Background An estimated 2.4 million babies died within the first 28 days of life in 2020. The third leading cause of neonatal death continues to be neonatal sepsis. Sepsis-causing bacterial pathogens vary temporally and geographically and, with a rise in multidrug-resistant organisms (MDROs), pose a threat to the neonatal population. Methods This was a single-center, retrospective study of very low birth weight (VLBW) infants with late-onset sepsis (LOS) admitted to a neonatal unit in South Africa. We aimed to calculate the prevalence of multidrug-resistant (MDR) infections in this population. The data collected included demographic and clinical characteristics, length of hospital stay, risk factors for MDRO and mortality, and microbiology results. Logistic regression was used to assess the association between prespecified risk factors with MDR infections and mortality. Results Of 2570 VLBW infants admitted, 34% had LOS, of which 33% was caused by MDROs. Infection with Acinetobacter spp., Pseudomonas spp., extended-spectrum beta-lactamase Klebsiella spp., or Escherichia coli was associated with the highest mortality in the LOS cohort. Infants with congenital infections (adjusted odds ratio [aOR], 5.13; 95% CI, 1.19-22.02; P = .028) or a history of necrotizing enterocolitis (aOR, 2.17; 95% CI, 1.05-4.49; P = .037) were at significantly higher risk for MDR infections. Conclusions More than one-third of LOS cases in VLBW infants were caused by MDROs in this study. MDR infections cause substantial neonatal mortality. Antimicrobial stewardship programs, infection control protocols, and ongoing surveillance are needed to prevent further emergence and spread of MDR infections worldwide.
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Affiliation(s)
- Genesis Licona
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Daynia Ballot
- Division of Neonatology, Department of Pediatrics, Charlotte Maxeke Academic Hospital, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Troy D Moon
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Ritu Banerjee
- Division of Infectious Diseases, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Gustavo Amorim
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Alexander G Agthe
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
| | - Jörn-Hendrik Weitkamp
- Division of Neonatology, Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee, USA
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7
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Okafor JU, Nwodo UU. Molecular Characterization of Antibiotic Resistance Determinants in Klebsiella pneumoniae Isolates Recovered from Hospital Effluents in the Eastern Cape Province, South Africa. Antibiotics (Basel) 2023; 12:1139. [PMID: 37508235 PMCID: PMC10376002 DOI: 10.3390/antibiotics12071139] [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: 05/30/2023] [Revised: 06/20/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic bacteria responsible for many nosocomial and community-acquired infections. The emergence and spread of antibiotic resistances have resulted in widespread epidemics and endemic dissemination of multidrug-resistant pathogens. A total of 145 K. pneumoniae isolates were recovered from hospital wastewater effluents and subjected to antibiogram profiling. Furthermore, the antibiotic resistance determinants were assessed among phenotypic resistant isolates using polymerase chain reaction (PCR). The isolates showed a wide range of antibiotic resistance against 21 selected antibiotics under 11 classes, with the most susceptible shown against imipenem (94.5%) and the most resistant shown against ampicillin (86.2%). The isolates also showed susceptibility to piperacillin/tazobactam (89.0%), ertapenem (87.6%), norfloxacin (86.2%), cefoxitin (86.2%), meropenem (76.6%), doripenem (76.6%), gentamicin (76.6%), chloramphenicol (73.1%), nitrofurantoin (71.7%), ciprofloxacin (79.3%), amikacin (60.7%), and amoxicillin/clavulanic acid (70.4%). Conversely, resistance was also recorded against tetracycline (69%), doxycycline (56.6%), cefuroxime (46.2%), cefotaxime (48.3%), ceftazidime (41.4%). Out of the 32 resistance genes tested, 28 were confirmed, with [tetA (58.8%), tetD (47.89%), tetM (25.2%), tetB (5.9%)], [sul1 (68.4%), sul1I (66.6%)], and [aadA (62.3%), strA (26%), aac(3)-IIa(aacC2)a (14.4%)] genes having the highest occurrence. Strong significant associations exist among the resistance determinants screened. About 82.7% of the K. pneumoniae isolates were multidrug-resistant (MDR) with a multiple antibiotics resistance index (MARI) range of 0.24 to 1.0. A dual presence of the resistant genes among K. pneumoniae was also observed to occur more frequently than multiple presences. This study reveals a worrisome presence of multidrug-resistant K. pneumoniae isolates and resistance genes in hospital waste effluent, resulting in higher public health risks using untreated surface water for human consumption. As a result, adequate water treatment and monitoring initiatives designed to monitor antimicrobial resistance patterns in the aquatic ecosystem are required.
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Affiliation(s)
- Joan U Okafor
- Patho-Biocatalysis Group (PBG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
| | - Uchechukwu U Nwodo
- Patho-Biocatalysis Group (PBG), Department of Biochemistry and Microbiology, University of Fort Hare, Private Bag X1314, Alice 5700, South Africa
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Venkateswaran P, Vasudevan S, David H, Shaktivel A, Shanmugam K, Neelakantan P, Solomon AP. Revisiting ESKAPE Pathogens: virulence, resistance, and combating strategies focusing on quorum sensing. Front Cell Infect Microbiol 2023; 13:1159798. [PMID: 37457962 PMCID: PMC10339816 DOI: 10.3389/fcimb.2023.1159798] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 06/08/2023] [Indexed: 07/18/2023] Open
Abstract
The human-bacterial association is long-known and well-established in terms of both augmentations of human health and attenuation. However, the growing incidents of nosocomial infections caused by the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter sp.) call for a much deeper understanding of these organisms. Adopting a holistic approach that includes the science of infection and the recent advancements in preventing and treating infections is imperative in designing novel intervention strategies against ESKAPE pathogens. In this regard, this review captures the ingenious strategies commissioned by these master players, which are teamed up against the defenses of the human team, that are equally, if not more, versatile and potent through an analogy. We have taken a basketball match as our analogy, dividing the human and bacterial species into two teams playing with the ball of health. Through this analogy, we make the concept of infectious biology more accessible.
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Affiliation(s)
- Parvathy Venkateswaran
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Sahana Vasudevan
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Helma David
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Adityan Shaktivel
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Karthik Shanmugam
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
| | - Prasanna Neelakantan
- Division of Restorative Dental Sciences, Faculty of Dentistry, The University of Hong Kong, Hong Kong, Hong Kong SAR, China
| | - Adline Princy Solomon
- Quorum Sensing Laboratory, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology, SASTRA Deemed to be University, Thanjavur, India
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9
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Dan B, Dai H, Zhou D, Tong H, Zhu M. Relationship Between Drug Resistance Characteristics and Biofilm Formation in Klebsiella Pneumoniae Strains. Infect Drug Resist 2023; 16:985-998. [PMID: 36824066 PMCID: PMC9942501 DOI: 10.2147/idr.s396609] [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: 11/16/2022] [Accepted: 02/04/2023] [Indexed: 02/19/2023] Open
Abstract
Objective To conduct epidemiological analysis of Klebsiella pneumoniae (K. pneumoniae) with hypervirulence, and to investigate its drug resistance phenotype, Extended-spectrum β-lactamase (ESBLs) gene, virulence factor, capsular serotype and biofilm formation, so as to provide theoretical basis for further understanding of the drug resistance mechanism of K. pneumoniae with hypervirulence. Methods K. Pneumoniae were isolated from clinical samples collected from inpatients. All strains were identified by VITEK2 Compact using fully automatic microbial analyzer, the minimal inhibitory concentration (MIC) of antibiotics was determined by microbroth dilution test. The double disk diffusion method was used to detect the production of ESBLs, modified carbapenem inactivation method (mCIM) was used to detect the production of carbapenemase, and hypermucoviscosity phenotype was detected by wire drawing test. PCR was used to detect ESBLs gene, virulence factor and capsular serotype. Crystal violet staining was used to detect the ability of biofilm formation. Results The ESBLs genes detected in this study included strains blaTEM 35 (36.5%), blaSHV 51 (53.1%), and blaCTX-M 49 (51.0%). Most strains carried multiple ESBLs genes, but not all of them produce ESBLs. K1 and K2 accounted for 14.6% and 11.5% respectively. Most (91.7%) strains carried the fimH gene, and the other virulence genes were ybtS (53.1%), entB (46.9%), rmpA (41.7%), aerobactin (32.3%), allS (15.6%), kfu (15.6%). Of all the Klebsiella pneumoniae strains, 33 (34.4%) exhibited ESBLs phenotype, 16 (16.7%) were carbapenemase-producing, and 20 (20.8%) with ESBLs phenotype tested were resistant to all four drugs. The correlation between ESBLs-producing strains and biofilm formation was significantly increased compared to strains without ESBLs phenotype (P=0.035). Conclusion Compared to hypervirulent Klebsiella pneumoniae (hvKP), classical Klebsiella pneumoniae (cKP) has a tendency to acquire antibiotic resistance. Our study showed that genes encoding rmpA, K1 or K2, and kfu were highly associated with hvKP.
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Affiliation(s)
- Binzhi Dan
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Chaohu, Anhui, People’s Republic of China
| | - Heping Dai
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Chaohu, Anhui, People’s Republic of China
| | - Dangui Zhou
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Chaohu, Anhui, People’s Republic of China
| | - Hongfang Tong
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Chaohu, Anhui, People’s Republic of China
| | - Mei Zhu
- Department of Clinical Laboratory, the Affiliated Chaohu Hospital of Anhui Medical University, Chaohu, Anhui, People’s Republic of China,Correspondence: Mei Zhu, Tel +86 551 8232 4254, Email
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10
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Brink AJ, Coetzee J, Richards GA, Feldman C, Lowman W, Tootla HD, Miller MGA, Niehaus AJ, Wasserman S, Perovic O, Govind CN, Schellack N, Mendelson M. Best practices: Appropriate use of the new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam in South Africa. S Afr J Infect Dis 2022; 37:453. [PMID: 36338193 PMCID: PMC9634826 DOI: 10.4102/sajid.v37i1.453] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 07/14/2022] [Indexed: 06/16/2023] Open
Abstract
Antibiotic stewardship of hospital-acquired infections because of difficult-to-treat resistant (DTR) Gram-negative bacteria is a global challenge. Their increasing prevalence in South Africa has required a shift in prescribing in recent years towards colistin, an antibiotic of last resort. High toxicity levels and developing resistance to colistin are narrowing treatment options further. Recently, two new β-lactam/β-lactamase inhibitor combinations, ceftazidime-avibactam and ceftolozane-tazobactam were registered in South Africa, bringing hope of new options for management of these life-threatening infections. However, with increased use in the private sector, increasing levels of resistance to ceftazidime-avibactam are already being witnessed, putting their long-term viability as treatment options of last resort, in jeopardy. This review focuses on how these two vital new antibiotics should be stewarded within a framework that recognises the resistance mechanisms currently predominant in South Africa's multi-drug and DTR Gram-negative bacteria. Moreover, the withholding of their use for resistant infections that can be treated with currently available antibiotics is a critical part of stewardship, if these antibiotics are to be conserved in the long term.
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Affiliation(s)
- Adrian J Brink
- Division of Medical Microbiology, Institute of Infectious Diseases and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Jennifer Coetzee
- Division of Microbiology, Ampath National Reference Laboratory, Centurion, South Africa
| | - Guy A Richards
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Charles Feldman
- Department of Internal Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Warren Lowman
- Department of Clinical Microbiology, Pathcare/Vermaak Pathologists, Gauteng, South Africa, South Africa
- Department Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
- Department of Clinical Microbiology and Infection Prevention and Control, Wits Donald Gordon Medical Centre, Johannesburg, South Africa
| | - Hafsah D Tootla
- Division of Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children's Hospital, Cape Town, South Africa
| | - Malcolm G A Miller
- Division of Critical Care, Department of Anaesthesia and Perioperative Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Abraham J Niehaus
- Department of Medical Microbiology, Ampath Laboratory Services, Cape Town, South Africa
| | - Sean Wasserman
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Olga Perovic
- National Institute for Communicable Disease, National Health Laboratory Services, Johannesburg, South Africa
- School of Pathology, Clinical Microbiology and Infectious Diseases, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Chetna N Govind
- Department of Medical Microbiology, Lancet Laboratories, KwaZulu-Natal, Durban, South Africa
- Antimicrobial Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Natalie Schellack
- Department of Pharmacology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
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11
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Hassen B, Hammami S, Hassen A, Abbassi MS. Molecular mechanisms and clonal lineages of colistin-resistant bacteria across the African continent: A scoping review. Lett Appl Microbiol 2022; 75:1390-1422. [PMID: 36000241 DOI: 10.1111/lam.13818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 07/11/2022] [Accepted: 08/16/2022] [Indexed: 11/28/2022]
Abstract
Colistin (also known as Polymyxin E), a polymyxin antibiotic discovered in the late 1940s, has recently reemerged as a last-line treatment option for multidrug-resistant infections. However, in recent years, colistin-resistant pathogenic bacteria have been increasingly reported worldwide. Accordingly, the presented review was undertaken to identify, integrate and synthesize current information regarding the detection and transmission of colistin-resistant bacteria across the African continent, in addition to elucidating their molecular mechanisms of resistance. PubMed, Google Scholar, and Science Direct were employed for study identification, screening and extraction. Overall, based on the developed literature review protocol and associated inclusion/exclusion criteria, 80 studies published between 2000 and 2021 were included comprising varying bacterial species and hosts. Numerous mechanisms of colistin resistance were reported, including chromosomal mutation(s) and transferable plasmid-mediated colistin resistance (encoded by mcr genes). Perhaps unexpectedly, mcr-variants have exhibited rapid emergence and spread across most African regions. The genetic variant mcr-1 is predominant in humans, animals, and the natural environment, and is primarily carried by IncHI2- type plasmid. The highest numbers of studies reporting the dissemination of colistin-resistant Gram-negative bacteria were conducted in the North African region.
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Affiliation(s)
- B Hassen
- University of Tunis El Manar, Laboratory of Bacteriological Research, Institute of Veterinary Research of Tunisia, 20 street Jebel Lakhdhar, Bab Saadoun, Tunis, 1006, Tunisia
| | - S Hammami
- University of Manouba, IRESA, School of Veterinary Medicine of Sidi-Thabet, Ariana, Tunis, Tunisia
| | - A Hassen
- Laboratoire de Traitement et de Valorisation des rejets hydriques, Centre des Recherches et des Technologies des Eaux (CERTE), Technopole Borj-Cédria, BP, 273, 8020, Soliman, Tunisia
| | - M S Abbassi
- University of Tunis El Manar, Laboratory of Bacteriological Research, Institute of Veterinary Research of Tunisia, 20 street Jebel Lakhdhar, Bab Saadoun, Tunis, 1006, Tunisia.,University of Tunis El Manar, Faculty de Medicine of Tunis, Laboratory of antibiotic resistance LR99ES09, Tunis, Tunisia
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12
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Conceição-Neto OC, da Costa BS, Pontes LDS, Silveira MC, Justo-da-Silva LH, de Oliveira Santos IC, Teixeira CBT, Tavares e Oliveira TR, Hermes FS, Galvão TC, Antunes LCM, Rocha-de-Souza CM, Carvalho-Assef APD. Polymyxin Resistance in Clinical Isolates of K. pneumoniae in Brazil: Update on Molecular Mechanisms, Clonal Dissemination and Relationship With KPC-Producing Strains. Front Cell Infect Microbiol 2022; 12:898125. [PMID: 35909953 PMCID: PMC9334684 DOI: 10.3389/fcimb.2022.898125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 06/24/2022] [Indexed: 11/14/2022] Open
Abstract
In Brazil, the production of KPC-type carbapenemases in Enterobacteriales is endemic, leading to widespread use of polymyxins. In the present study, 502 Klebsiella pneumoniae isolates were evaluated for resistance to polymyxins, their genetic determinants and clonality, in addition to the presence of carbapenem resistance genes and evaluation of antimicrobial resistance. Resistance to colistin (polymyxin E) was evaluated through initial selection on EMB agar containing 4% colistin sulfate, followed by Minimal Inhibitory Concentration (MIC) determination by broth microdilution. The susceptibility to 17 antimicrobials was assessed by disk diffusion. The presence of blaKPC, blaNDM and blaOXA-48-like carbapenemases was investigated by phenotypic methods and conventional PCR. Molecular typing was performed by PFGE and MLST. Allelic variants of the mcr gene were screened by PCR and chromosomal mutations in the pmrA, pmrB, phoP, phoQ and mgrB genes were investigated by sequencing. Our work showed a colistin resistance frequency of 29.5% (n = 148/502) in K. pneumoniae isolates. Colistin MICs from 4 to >128 µg/mL were identified (MIC50 = 64 µg/mL; MIC90 >128 µg/mL). All isolates were considered MDR, with the lowest resistance rates observed for amikacin (34.4%), and 19.6% of the isolates were resistant to all tested antimicrobials. The blaKPC gene was identified in 77% of the isolates, in consonance with the high rate of resistance to polymyxins related to its use as a therapeutic alternative. Through XbaI-PFGE, 51 pulsotypes were identified. MLST showed 21 STs, with ST437, ST258 and ST11 (CC11) being the most prevalent, and two new STs were determined: ST4868 and ST4869. The mcr-1 gene was identified in 3 K. pneumoniae isolates. Missense mutations in chromosomal genes were identified, as well as insertion sequences in mgrB. Furthermore, the identification of chromosomal mutations in K. pneumoniae isolates belonging from CC11 ensures its success as a high-risk epidemic clone in Brazil and worldwide.
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Affiliation(s)
- Orlando C. Conceição-Neto
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- Faculdade de Medicina, Universidade Estácio de Sá (UNESA), Rio de Janeiro, Brazil
| | - Bianca Santos da Costa
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Leilane da Silva Pontes
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Melise Chaves Silveira
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | | | - Ivson Cassiano de Oliveira Santos
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Camila Bastos Tavares Teixeira
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Thamirys Rachel Tavares e Oliveira
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Fernanda Stephens Hermes
- Laboratório de Genômica Funcional e Bioinformática (LAGFB), Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - Teca Calcagno Galvão
- Laboratório de Genômica Funcional e Bioinformática (LAGFB), Instituto Oswaldo Cruz-FIOCRUZ, Rio de Janeiro, Brazil
| | - L. Caetano M. Antunes
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Cláudio Marcos Rocha-de-Souza
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
| | - Ana P. D. Carvalho-Assef
- Laboratório de Pesquisa em Infecção Hospitalar (LAPIH), Instituto Oswaldo Cruz - Fundação Oswaldo Cruz (FIOCRUZ), Rio de Janeiro, Brazil
- *Correspondence: Ana P. D. Carvalho-Assef,
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13
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Kariuki S, Kering K, Wairimu C, Onsare R, Mbae C. Antimicrobial Resistance Rates and Surveillance in Sub-Saharan Africa: Where Are We Now? Infect Drug Resist 2022; 15:3589-3609. [PMID: 35837538 PMCID: PMC9273632 DOI: 10.2147/idr.s342753] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/16/2022] [Indexed: 01/03/2023] Open
Abstract
Introduction Although antimicrobials have traditionally been used to treat infections and improve health outcomes, resistance to commonly used antimicrobials has posed a major challenge. An estimated 700,000 deaths occur globally every year as a result of infections caused by antimicrobial-resistant pathogens. Antimicrobial resistance (AMR) also contributes directly to the decline in the global economy. In 2019, sub-Saharan Africa (SSA) had the highest mortality rate (23.5 deaths per 100,000) attributable to AMR compared to other regions. Methods We searched PubMed for articles relevant to AMR in pathogens in the WHO-GLASS list and in other infections of local importance in SSA. In this review, we focused on AMR rates and surveillance of AMR for these priority pathogens and some of the most encountered pathogens of public health significance. In addition, we reviewed the implementation of national action plans to mitigate against AMR in countries in SSA. Results and Discussion The SSA region is disproportionately affected by AMR, in part owing to the prevailing high levels of poverty, which result in a high burden of infectious diseases, poor regulation of antimicrobial use, and a lack of alternatives to ineffective antimicrobials. The global action plan as a strategy for prevention and combating AMR has been adopted by most countries, but fewer countries are able to fully implement country-specific action plans, and several challenges exist in many settings. Conclusion A concerted One Health approach will be required to ramp up implementation of action plans in the region. In addition to AMR surveillance, effective implementation of infection prevention and control, water, sanitation, and hygiene, and antimicrobial stewardship programs will be key cost-effective strategies in helping to tackle AMR.
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Affiliation(s)
- Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya,Correspondence: Samuel Kariuki, Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya, Email
| | - Kelvin Kering
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Celestine Wairimu
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Robert Onsare
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Cecilia Mbae
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
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14
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Sharba ZA, Farazdaq Rafeeq H. The Incidence of Extended Spectrum β-Lactamase Enzymes and Their Connection to Virulence Genes in Community-Acquired Urinary Tract Infection. BIONATURA 2022. [DOI: 10.21931/rb/2022.07.02.27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
In community-acquired urinary tract infections, Klebsiella pneumoniae is considered one of the most common etiological agents. Multidrug resistance and virulence are common in Klebsiella pneumoniae populations. In this study, fifty Klebsiella pneumoniae isolates were isolated from urine samples and identified using a vitek 2 compact device. The Kirby–Bauer disk diffusion technique used the antibiotic susceptibility test. According to the findings, approximately [n = 46 (92%)] of Klebsiella pneumoniae isolates are multidrug-resistant (MDR). To detect the production of Extended Spectrum β-lactamase (ESBL) enzymes, the Modified Double Disc Synergy Test (MDDST) was used. The results show that approximately [n=45 (90%)] of the isolates produce ESBLs. The most common ESBL genes (TEM, SHV, and CTX-M) were investigated in isolates. The results show that the SHV gene had the highest prevalence among ESBL genes [n = 34 (68%)], followed by the CTX-M gene [n = 33 (66%)]. while none of the isolates possessed the TEM gene. The virulence factor type 3 fimbriae (MrKD) gene and biofilm (BssS) gene were revealed. The results found that the isolates contain the MrKD gene at [n = 41 (82%)]. At the same time, the results found that the isolates contained the BssS gene at [n =36 (72%)]. The prevalence of Virulence genes within ESBL-producing Klebsiella pneumoniae isolates shows that only [n = 3 (6%)] of isolates that are non-ESBL producers carry one or both virulence genes, while [n=41 (82%)] of ESBL-producing isolates contain one or both virulence genes. The prevalence of ESBL-producing Klebsiella pneumoniae in community patients was high in this research. There may also be a correlation between ESBL production and some virulence factors.
Keywords. Klebsiella pneumoniae; Antibiotic Resistance; Virulence Gene; ESBL; Urinary Tract Infection; CTX-M.
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15
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Leyton-Carcaman B, Abanto M. Beyond to the Stable: Role of the Insertion Sequences as Epidemiological Descriptors in Corynebacterium striatum. Front Microbiol 2022; 13:806576. [PMID: 35126341 PMCID: PMC8811144 DOI: 10.3389/fmicb.2022.806576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 01/04/2022] [Indexed: 11/20/2022] Open
Abstract
In recent years, epidemiological studies of infectious agents have focused mainly on the pathogen and stable components of its genome. The use of these stable components makes it possible to know the evolutionary or epidemiological relationships of the isolates of a particular pathogen. Under this approach, focused on the pathogen, the identification of resistance genes is a complementary stage of a bacterial characterization process or an appendix of its epidemiological characterization, neglecting its genetic components’ acquisition or dispersal mechanisms. Today we know that a large part of antibiotic resistance is associated with mobile elements. Corynebacterium striatum, a bacterium from the normal skin microbiota, is also an opportunistic pathogen. In recent years, reports of infections and nosocomial outbreaks caused by antimicrobial multidrug-resistant C. striatum strains have been increasing worldwide. Despite the different existing mobile genomic elements, there is evidence that acquired resistance genes are coupled to insertion sequences in C. striatum. This perspective article reviews the insertion sequences linked to resistance genes, their relationship to evolutionary lineages, epidemiological characteristics, and the niches the strains inhabit. Finally, we evaluate the potential of the insertion sequences for their application as a descriptor of epidemiological scenarios, allowing us to anticipate the emergence of multidrug-resistant lineages.
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16
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Genome analysis of
Klebsiella oxytoca
complex for antimicrobial resistance and virulence genes. Antimicrob Agents Chemother 2022; 66:e0218321. [PMID: 35007133 DOI: 10.1128/aac.02183-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Klebsiella oxytoca
complex comprises nine closely-related species causing human infections. We curated genomes labeled
Klebsiella
(n=14,256) in GenBank and identified 588 belonging to the complex, which were examined for precise species, sequence types, K- and O-antigen types, virulence and antimicrobial resistance genes. The complex and
Klebsiella pneumoniae
share many K- and O-antigen types. Of the complex,
K. oxytoca
and
Klebsiella michiganensis
appear to carry more virulence genes and be more commonly associated with human infections.
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17
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Huang C, Tao S, Yuan J, Li X. Effect of sodium hypochlorite on biofilm of Klebsiella pneumoniae with different drug resistance. Am J Infect Control 2022; 50:922-928. [PMID: 34986390 DOI: 10.1016/j.ajic.2021.12.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 12/18/2021] [Accepted: 12/20/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND Biofilm formation is a major factor in the resistance mechanism of Klebsiella pneumoniae. This study aimed to evaluate the effects of sodium hypochlorite on the biofilm of K. pneumoniae with different drug resistance. METHODS We collected 3 different types of K. pneumoniae respectively. The growth trend of biofilms of different drug-resistant K. pneumoniae was quantified by measuring the OD590 for 7 consecutive days using crystal violet staining. Scanning confocal fluorescence microscopy was used to observe biofilm morphology. RESULTS After adding sodium hypochlorite, there were significant differences between the OD590 value of the 200, 500, and 1,000 µg/mL groups and the positive control group (all P < .05) on the fifth day. Concentrations of 2,000 and 5,000 µg/mL sodium hypochlorite were added after the biofilm had matured. In the 5,000 µg/mL sodium hypochlorite group, the OD590 of K. pneumoniae biofilm in the 3 groups decreased significantly compared with the blank control group (all P < .05). CONCLUSIONS Sodium hypochlorite inhibited and cleared the biofilm of K. pneumoniae with different drug resistance, and the effect was enhanced with the increase of concentration in the range of bacteriostatic and bactericidal concentration.
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Affiliation(s)
- Chenlei Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Shaoneng Tao
- Department of Nuclear Medicine, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Jinlong Yuan
- Department of Neurosurgery, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China
| | - Xiaoning Li
- Department of Clinical Laboratory, The First Affiliated Hospital of Wannan Medical College (Yijishan Hospital of Wannan Medical College), Wuhu, China.
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Afolayan AO, Oaikhena AO, Aboderin AO, Olabisi OF, Amupitan AA, Abiri OV, Ogunleye VO, Odih EE, Adeyemo AT, Adeyemo AT, Obadare TO, Abrudan M, Argimón S, David S, Kekre M, Underwood A, Egwuenu A, Ihekweazu C, Aanensen DM, Okeke IN. Clones and Clusters of Antimicrobial-Resistant Klebsiella From Southwestern Nigeria. Clin Infect Dis 2021; 73:S308-S315. [PMID: 34850837 PMCID: PMC8634535 DOI: 10.1093/cid/ciab769] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a World Health Organization high-priority antibiotic-resistant pathogen. However, little is known about Klebsiella lineages circulating in Nigeria. METHODS We performed whole-genome sequencing (WGS) of 141 Klebsiella isolated between 2016 and 2018 from clinical specimens at 3 antimicrobial-resistance (AMR) sentinel surveillance tertiary hospitals in southwestern Nigeria. We conducted in silico multilocus sequence typing; AMR gene, virulence gene, plasmid, and K and O loci profiling; as well as phylogenetic analyses, using publicly available tools and Nextflow pipelines. RESULTS Phylogenetic analysis revealed that the majority of the 134 K. pneumoniae and 5 K. quasipneumoniae isolates from Nigeria characterized are closely related to globally disseminated multidrug-resistant clones. Of the 39 K. pneumoniae sequence types (STs) identified, the most common were ST307 (15%), ST5241 (12%), ST15 (~9%), and ST25 (~6%). ST5241, 1 of 10 novel STs detected, is a single locus variant of ST636 carrying dfrA14, tetD, qnrS, and oqxAB resistance genes. The extended-spectrum β-lactamase (ESBL) gene blaCTX_M-15 was seen in 72% of K. pneumoniae genomes, while 8% encoded a carbapenemase. No isolate carried a combination of carbapenemase-producing genes. Four likely outbreak clusters from 1 facility, within STs 17, 25, 307, and 5241, were ESBL but not carbapenemase-bearing clones. CONCLUSIONS This study uncovered known and novel K. pneumoniae lineages circulating in 3 hospitals in Southwest Nigeria that include multidrug-resistant ESBL producers. Carbapenemase-producing isolates remain uncommon. WGS retrospectively identified outbreak clusters, pointing to the value of genomic approaches in AMR surveillance for improving infection prevention and control in Nigerian hospitals.
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Affiliation(s)
- Ayorinde O Afolayan
- Global Health Research
Unit on Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Anderson O Oaikhena
- Global Health Research
Unit on Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Aaron O Aboderin
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Olatunde F Olabisi
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Adewale A Amupitan
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Oyekola V Abiri
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Veronica O Ogunleye
- Department of Medical Microbiology and Parasitology, University College Hospital, Ibadan, Nigeria
| | - Erkison Ewomazino Odih
- Global Health Research
Unit on Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
| | - Abolaji T Adeyemo
- Department of Medical Microbiology and Parasitology, Osun State University Teaching Hospital,
Teaching Hospital, Osogbo, Nigeria
| | - Adeyemi T Adeyemo
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Temitope O Obadare
- Department of Medical Microbiology and Parasitology, Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
- Wellcome Genome Campus, Hinxton, United Kingdom
| | | | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Big Data Institute, University of Oxford, Oxford, United Kingdom
| | - Iruka N Okeke
- Global Health Research
Unit on Genomic Surveillance of Antimicrobial Resistance, Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Ibadan, Nigeria
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19
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Richter L, du Plessis EM, Duvenage S, Allam M, Ismail A, Korsten L. Whole Genome Sequencing of Extended-Spectrum- and AmpC- β-Lactamase-Positive Enterobacterales Isolated From Spinach Production in Gauteng Province, South Africa. Front Microbiol 2021; 12:734649. [PMID: 34659162 PMCID: PMC8517129 DOI: 10.3389/fmicb.2021.734649] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/01/2021] [Indexed: 02/06/2023] Open
Abstract
The increasing occurrence of multidrug-resistant (MDR) extended-spectrum β-lactamase- (ESBL) and/or AmpC β-lactamase- (AmpC) producing Enterobacterales in irrigation water and associated irrigated fresh produce represents risks related to the environment, food safety, and public health. In South Africa, information about the presence of ESBL/AmpC-producing Enterobacterales from non-clinical sources is limited, particularly in the water-plant-food interface. This study aimed to characterize 19 selected MDR ESBL/AmpC-producing Escherichia coli (n=3), Klebsiella pneumoniae (n=5), Serratia fonticola (n=10), and Salmonella enterica (n=1) isolates from spinach and associated irrigation water samples from two commercial spinach production systems within South Africa, using whole genome sequencing (WGS). Antibiotic resistance genes potentially encoding resistance to eight different classes were present, with bla CTX-M-15 being the dominant ESBL encoding gene and bla ACT-types being the dominant AmpC encoding gene detected. A greater number of resistance genes across more antibiotic classes were seen in all the K. pneumoniae strains, compared to the other genera tested. From one farm, bla CTX-M-15-positive K. pneumoniae strains of the same sequence type 985 (ST 985) were present in spinach at harvest and retail samples after processing, suggesting successful persistence of these MDR strains. In addition, ESBL-producing K. pneumoniae ST15, an emerging high-risk clone causing nosocomical outbreaks worldwide, was isolated from irrigation water. Known resistance plasmid replicon types of Enterobacterales including IncFIB, IncFIA, IncFII, IncB/O, and IncHI1B were observed in all strains following analysis with PlasmidFinder. However, bla CTX-M-15 was the only β-lactamase resistance gene associated with plasmids (IncFII and IncFIB) in K. pneumoniae (n=4) strains. In one E. coli and five K. pneumoniae strains, integron In191 was observed. Relevant similarities to human pathogens were predicted with PathogenFinder for all 19 strains, with a confidence of 0.635-0.721 in S. fonticola, 0.852-0.931 in E. coli, 0.796-0.899 in K. pneumoniae, and 0.939 in the S. enterica strain. The presence of MDR ESBL/AmpC-producing E. coli, K. pneumoniae, S. fonticola, and S. enterica with similarities to human pathogens in the agricultural production systems reflects environmental and food contamination mediated by anthropogenic activities, contributing to the spread of antibiotic resistance genes.
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Affiliation(s)
- Loandi Richter
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Erika M. du Plessis
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Stacey Duvenage
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
| | - Mushal Allam
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, South Africa
- Department of Science and Innovation, National Research Foundation Centre of Excellence in Food Security, Pretoria, South Africa
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20
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Yang Y, Zhang AN, Che Y, Liu L, Deng Y, Zhang T. Underrepresented high diversity of class 1 integrons in the environment uncovered by PacBio sequencing using a new primer. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 787:147611. [PMID: 34000537 DOI: 10.1016/j.scitotenv.2021.147611] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/01/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
Class 1 integrons (CL1s) are one of the major contributors to the horizontal transfer of antibiotic resistance genes (ARGs). However, our knowledge of CL1 in the environment is still very limited due to the limitations of the current PCR primers and the sequencing methods adopted. This study developed a new primer coupled with PacBio sequencing to investigate the underrepresented diversity of CL1s in a mixed environmental sample (i.e. activated sludge from wastewater treatment plant and pig feces from animal farm). The new primer successfully uncovered 20 extra ARGs subtypes and 57% (422/739) more unique integron array structures than the previous primers. Compared to the whole genome database, CL1s revealed in the environment in this study were of much greater diversity, having 93% (900/967) novel array structures. Antibiotic resistance is the predominant function (78.3% genes) carried by CL1, and a vast majority (98.6% genes) of them confer resistance to aminoglycoside, beta-lactam, trimethoprim, or chloramphenicol. Additionally, 78.5% unique CL1 arrays carried more than one ARGs, and 25.9% of them carried ARGs of clinical relevance with high transferability potential posing threat to the general public. Our results indicated the importance of CL1s in the spread of ARGs. Overall, combining PacBio sequencing with the new primer designed in this study largely broadened our knowledge of CL1s in the environment and their significance in the environmental proliferation of ARGs.
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Affiliation(s)
- Yu Yang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - An-Ni Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - You Che
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Lei Liu
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Yu Deng
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong
| | - Tong Zhang
- Environmental Microbiome Engineering and Biotechnology Laboratory, Centre for Environmental Engineering Research, Department of Civil Engineering, The University of Hong Kong, Hong Kong.
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21
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Bobbadi S, Chinnam BK, Reddy PN, Kandhan S. Analysis of antibiotic resistance and virulence patterns in Klebsiella pneumoniae isolated from human urinary tract infections in India. Lett Appl Microbiol 2021; 73:590-598. [PMID: 34331358 DOI: 10.1111/lam.13544] [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: 04/10/2021] [Revised: 07/23/2021] [Accepted: 07/23/2021] [Indexed: 11/27/2022]
Abstract
In this study, 504 urine samples collected from patients suffering from urinary tract infection (UTIs) were screened for the presence of Klebsiella pneumoniae. The overall occurrence of Klebsiella spp. and K. pneumoniae was found to be 23·2% (117/504) and 16·8% (85/504) respectively. Antibiotic susceptibility testing of 85 K. pneumoniae isolates was carried out by disc diffusion which revealed alarming levels of antibiotic resistance (ABR). Antimicrobial resistance was prominently observed against cefpodoxime (76·47%) followed by ampicillin (70·59%), ceftriaxone (52·94%), cefoxitin (50·59%), amoxyclav (48·24%), ofloxacin (45·88%), cefotaxime (44·71%), cefepime (43·53%) and doxycycline hydrochloride (40%). A small percentage of strains also exhibited resistance to other antimicrobials in the range of 7-35%. Around 77·6% of the isolates were found to be resistant to three or more antibiotic classes and 66·7% of the isolates had multiple antibiotic resistance index values >0·2. Screening of virulence genes in 85 K. pneumoniae isolates revealed that uge gene was the most predominant (11/85, 12·9%), followed by rmpA (9/85, 10·5%), kfu (4/85, 4·7%) and aerobactin genes (2/85, 2·35%). Further, the overall percentage of biofilm producers were found to be 17·65% (15/85). This study warrants hospitals and health care centres to reduce misuse of antibiotics and manage UTI with appropriate treatment after performing antibiotic susceptibility testing.
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Affiliation(s)
- S Bobbadi
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur district, Andhra Pradesh, India
| | - B K Chinnam
- Department of Veterinary Public Health and Epidemiology, NTR College of Veterinary Science, Gannavaram, Andhra Pradesh, India
| | - P N Reddy
- Department of Biotechnology, Vignan's Foundation for Science, Technology and Research (Deemed to be University), Vadlamudi, Guntur district, Andhra Pradesh, India
| | - S Kandhan
- Division of Veterinary Public Health, ICAR - Indian Veterinary Research Institute, Izatnagar, Uttar Pradesh, India
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22
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A Molecular Perspective on Colistin and Klebsiella pneumoniae: Mode of Action, Resistance Genetics, and Phenotypic Susceptibility. Diagnostics (Basel) 2021; 11:diagnostics11071165. [PMID: 34202395 PMCID: PMC8305994 DOI: 10.3390/diagnostics11071165] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/11/2021] [Accepted: 06/16/2021] [Indexed: 12/26/2022] Open
Abstract
Klebsiella pneumoniae is a rod-shaped, encapsulated, Gram-negative bacteria associated with multiple nosocomial infections. Multidrug-resistant (MDR) K. pneumoniae strains have been increasing and the therapeutic options are increasingly limited. Colistin is a long-used, polycationic, heptapeptide that has regained attention due to its activity against Gram-negative bacteria, including the MDR K. pneumoniae strains. However, this antibiotic has a complex mode of action that is still under research along with numerous side-effects. The acquisition of colistin resistance is mainly associated with alteration of lipid A net charge through the addition of cationic groups synthesized by the gene products of a multi-genic regulatory network. Besides mutations in these chromosomal genes, colistin resistance can also be achieved through the acquisition of plasmid-encoded genes. Nevertheless, the diversity of molecular markers for colistin resistance along with some adverse colistin properties compromises the reliability of colistin-resistance monitorization methods. The present review is focused on the colistin action and molecular resistance mechanisms, along with specific limitations on drug susceptibility testing for K. pneumoniae.
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23
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The COVID-19 pandemic: a threat to antimicrobial resistance containment. Future Sci OA 2021; 7:FSO736. [PMID: 34290883 PMCID: PMC8204817 DOI: 10.2144/fsoa-2021-0012] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 05/26/2021] [Indexed: 12/23/2022] Open
Abstract
As of 23 April 2021, the outbreak of COVID-19 claimed around 150 million confirmed cases with over 3 million deaths worldwide. Yet, an even more serious but silent pandemic, that of antimicrobial resistance (AMR), is likely complicating the outcome of COVID-19 patients. This study discusses the current knowledge on the emergence of the SARS-CoV-2 and highlights the likely contribution of the COVID-19 pandemic on the escalation of AMR. COVID-19 engenders extensive antibiotic overuse and misuse, and will undoubtedly and substantially increase AMR rates worldwide. Amid the expanding COVID-19 pandemic, policymakers should consider the hidden threat of AMR much more, which may well be enhanced through improper use of antibiotics to treat patients with severe COVID-19 infection. Antimicrobial resistance (AMR) is a natural phenomenon that allows microorganisms to resist to the action of antimicrobial medicines that were previously active against them and cured the infection. AMR is caused by the appropriate and inappropriate use of antimicrobial medicines. The occurrence of the COVID-19 pandemic engenders extensive antimicrobial use that is likely to aggravated the AMR pandemic. This paper discusses the current knowledge on the SARS-CoV-2, and underscores the contribution of the COVID-19 pandemic on the escalation of AMR. Beyond the expanding COVID-19 pandemic, the hidden threat of AMR should also be considered by the decision-makers.
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24
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Osei Sekyere J, Reta MA. Global evolutionary epidemiology and resistome dynamics of Citrobacter species, Enterobacter hormaechei, Klebsiella variicola, and Proteeae clones. Environ Microbiol 2021; 23:7412-7431. [PMID: 33415808 DOI: 10.1111/1462-2920.15387] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/03/2021] [Indexed: 12/15/2022]
Abstract
Citrobacter spp., Enterobacter hormaechei subsp., Klebsiella variicola and Proteae tribe members are rarely isolated Enterobacterales increasingly implicated in nosocomial infections. Herein, we show that these species contain multiple genes encoding resistance to important antibiotics and are widely and globally distributed, being isolated from human, animal, plant, and environmental sources in 67 countries. Certain clones and clades of these species were internationally disseminated, serving as reservoirs and mediums for the global dissemination of antibiotic resistance genes. As they can easily transmit these genes to more pathogenic species, additional molecular surveillance studies should be undertaken to identify and contain these antibiotic-resistant species.
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Affiliation(s)
- John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
| | - Melese Abate Reta
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Prinshof, Pretoria, Gauteng, South Africa
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25
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Fadare FT, Adefisoye MA, Okoh AI. Occurrence, identification, and antibiogram signatures of selected Enterobacteriaceae from Tsomo and Tyhume rivers in the Eastern Cape Province, Republic of South Africa. PLoS One 2020; 15:e0238084. [PMID: 33284819 PMCID: PMC7721149 DOI: 10.1371/journal.pone.0238084] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 11/23/2020] [Indexed: 12/19/2022] Open
Abstract
The increasing occurrence of multidrug-resistant Enterobacteriaceae in clinical and environmental settings has been seen globally as a complex public health challenge, mostly in the developing nations where they significantly impact freshwater used for a variety of domestic purposes and irrigation. This paper detail the occurrence and antibiogram signatures of the Enterobacteriaceae community in Tsomo and Tyhume rivers within the Eastern Cape Province, the Republic of South Africa, using standard methods. The average distribution of the presumptive Enterobacteriaceae in the rivers ranged from 1 × 102 CFU/100ml to 1.95 × 104 CFU/100ml. We confirmed 56 (70.8%) out of 79 presumptive Enterobacteriaceae isolated being species within the family Enterobacteriaceae through the Matrix-Assisted Laser Desorption Ionization Time of Flight technique. Citrobacter-, Enterobacter-, Klebsiella species, and Escherichia coli were selected (n = 40) due to their pathogenic potentials for antibiogram profiling. The results of the antibiotic susceptibility testing gave a revelation that all the isolates were phenotypically multidrug-resistant. The resistance against ampicillin (95%), tetracycline and doxycycline (88%), and trimethoprim-sulfamethoxazole (85%) antibiotics were most prevalent. The Multiple Antibiotic Resistance indices stretched from 0.22 to 0.94, with the highest index observed in a C. freundii isolate. Molecular characterisation using the PCR technique revealed the dominance of blaTEM (30%; 12/40) among the eight groups of β-lactams resistance determinants assayed. The prevalence of others was blaCTX-M genes including group 1, 2 and 9 (27.5%), blaSHV (20%), blaOXA-1-like (10%), blaPER (2.5%), and blaVEB (0%). The frequencies of the resistance determinants for the carbapenems were blaKPC (17.6%), blaGES (11.8%), blaIMP (11.8%), blaVIM (11.8%), and blaOXA-48-like (5.9%). Out of the six plasmid-mediated AmpC (pAmpC) genes investigated blaACC, blaEBC, blaFOX, blaCIT, blaDHA, and blaMOX, only the first four were detected. In this category, the most dominant was blaEBC, with 18.4% (7/38). The prevalence of the non-β-lactamases include tetA (33.3%), tetB (30.5%), tetC (2.8%), tetD (11.1%), tetK (0%), tetM (13.9%), catI (12%), catII (68%), sulI (14.3%), sulII (22.9%) and aadA (8.3%). Notably, a C. koseri harboured 42.8% (12/28) of the genes assayed for which includes five of the ESBL genes (including the only blaPER detected in this study), two of the pAmpC resistance genes (blaACC and blaCIT), and five of the non-β-lactamase genes. This study gives the first report on C. koseri exhibiting the co-occurrence of ESBL/AmpC β-lactamase genes from the environment to the best of our knowledge. The detection of a blaPER producing Citrobacter spp. in this study is remarkable. These findings provide evidence that freshwater serves as reservoirs of antimicrobial resistance determinants, which can then be easily transferred to human beings via the food chain and water.
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Affiliation(s)
- Folake Temitope Fadare
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
- * E-mail:
| | - Martins Ajibade Adefisoye
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
| | - Anthony Ifeanyi Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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26
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Kopotsa K, Mbelle NM, Osei Sekyere J. Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains. Microb Genom 2020; 6:mgen000474. [PMID: 33170117 PMCID: PMC8116673 DOI: 10.1099/mgen.0.000474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio's SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - Nontombi M. Mbelle
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
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27
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Genomic and Resistance Epidemiology of Gram-Negative Bacteria in Africa: a Systematic Review and Phylogenomic Analyses from a One Health Perspective. mSystems 2020; 5:5/6/e00897-20. [PMID: 33234606 PMCID: PMC7687029 DOI: 10.1128/msystems.00897-20] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni, etc., were common pathogens shuttling AR genes in Africa. Transmission of the same clones/strains across countries and between animals, humans, plants, and the environment was observed. We recommend Enterobacter spp. or K. pneumoniae as better sentinel species for AR surveillance. Antibiotic resistance (AR) remains a major threat to public and animal health globally. However, AR ramifications in developing countries are worsened by limited molecular diagnostics, expensive therapeutics, inadequate numbers of skilled clinicians and scientists, and unsanitary environments. The epidemiology of Gram-negative bacteria, their AR genes, and geographical distribution in Africa are described here. Data were extracted and analyzed from English-language articles published between 2015 and December 2019. The genomes and AR genes of the various species, obtained from the Pathosystems Resource Integration Center (PATRIC) and NCBI were analyzed phylogenetically using Randomized Axelerated Maximum Likelihood (RAxML) and annotated with Figtree. The geographic location of resistant clones/clades was mapped manually. Thirty species from 31 countries and 24 genera from 41 countries were analyzed from 146 articles and 3,028 genomes, respectively. Genes mediating resistance to β-lactams (including blaTEM-1, blaCTX-M, blaNDM, blaIMP, blaVIM, and blaOXA-48/181), fluoroquinolones (oqxAB, qnrA/B/D/S, gyrA/B, and parCE mutations, etc.), aminoglycosides (including armA and rmtC/F), sulfonamides (sul1/2/3), trimethoprim (dfrA), tetracycline [tet(A/B/C/D/G/O/M/39)], colistin (mcr-1), phenicols (catA/B, cmlA), and fosfomycin (fosA) were mostly found in Enterobacter spp. and Klebsiella pneumoniae, and also in Serratia marcescens, Escherichia coli, Salmonella enterica, Pseudomonas, Acinetobacter baumannii, etc., on mostly IncF-type, IncX3/4, ColRNAI, and IncR plasmids, within IntI1 gene cassettes, insertion sequences, and transposons. Clonal and multiclonal outbreaks and dissemination of resistance genes across species and countries and between humans, animals, plants, and the environment were observed; Escherichia coli ST103, K. pneumoniae ST101, S. enterica ST1/2, and Vibrio cholerae ST69/515 were common strains. Most pathogens were of human origin, and zoonotic transmissions were relatively limited. IMPORTANCE Antibiotic resistance (AR) is one of the major public health threats and challenges to effective containment and treatment of infectious bacterial diseases worldwide. Here, we used different methods to map out the geographical hot spots, sources, and evolutionary epidemiology of AR. Escherichia coli, Klebsiella pneumoniae, Salmonella enterica, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter spp., Neisseria meningitis/gonorrhoeae, Vibrio cholerae, Campylobacter jejuni, etc., were common pathogens shuttling AR genes in Africa. Transmission of the same clones/strains across countries and between animals, humans, plants, and the environment was observed. We recommend Enterobacter spp. or K. pneumoniae as better sentinel species for AR surveillance.
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