Opening Pandora’s box: high level resistance to antibiotics of last resort in Gram negative bacteria from Nigeria

Ogbolu, David Olusoga; Webber, Mark A.; Piddock, Laura J. V.

doi:10.1101/344093

Cited by 4 publications

(4 citation statements)

References 47 publications

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“…Two ST90 isolates are identical, differ from a third by only 11 SNPs, and likely represent an outbreak. Our findings add to information that is chronicling ExPEC lineages of importance within Nigeria [14–16, 52, 53], other parts of Africa [16, 54], and other low-middle-income countries [16, 55].…”

Section: Discussionsupporting

confidence: 66%

“…Although studies conducted in Africa and other low-and middle-income countries (LMICs) have shown the abundance of invasive E. coli [9,10], these studies are too few and far between so that ExPEC and AMR epidemiology are poorly understood [7,11]. In Nigeria, there is sparse molecular information on ExPEC, but a few studies point to likely clonal expansion of resistant lineages and local presence of pandemic clones of concern [12][13][14][15][16]. These studies provide valuable information but represent an insufficient picture of ExPEC clones in Nigeria with few data available from South.…”

Section: Introductionmentioning

confidence: 99%

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An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

Afolayan

Aboderin

Oaikhena

et al. 2021

Preprint

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Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasion and, in recent years, are increasingly multiply antimicrobial resistant. In Nigeria, E. coli is a common cause of bloodstream infections but the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified, susceptibility-tested and whole genome-sequenced 68 bloodstream E. coli isolates recovered between 2016 and 2018 at three sentinel sites in southwestern Nigeria. Resistance to antimicrobials commonly used in Nigeria was high, reaching 100 % (n = 67) for trimethoprim, 92.5 % (n = 62) for ampicillin, 79.1 % (n = 53) for ciprofloxacin, and 55.2 % (n = 37) for aminoglycosides. All the isolates were susceptible to carbapenems and colistin. The strain set included isolates from globally disseminated high risk clones including those belonging to ST12 (n=2), ST131 (n=12) and ST648 (n = 4). Twenty-three (33.82%) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprised of O16:H5 and O25:H4 sub-lineages. The second was an ST10-ST167 complex clade comprised of strains carrying capsular genes that may have originated in Klebsiella. We additionally determined that four ST90 strains from one sentinel represented a retrospectively detected outbreak. Our data demonstrate that a broad repertoire of invasive E. coli isolates cause bloodstream infections in southwest Nigeria. In addition to pandemic lineages, particularly ST131, these include a previously undescribed lineage. Genomic surveillance is valuable for tracking these and other clones and for outbreak identification.Data SummaryPhylogenetic tree, clinical data, and epidemiological data were visualized using Microreact (https://microreact.org/project/NigeriaEcoliInvasive/d0dc3660) and Phandango (for visualization of pangenome, tree, and metadata). All the sequence data have been deposited in the ENA under the project ID PRJEB29739 (https://www.ebi.ac.uk/ena/browser/view/PRJEB29739). Accessions can be found in Table S6.

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Section: Discussionsupporting

confidence: 66%

Section: Introductionmentioning

confidence: 99%

An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

Afolayan

Aboderin

Oaikhena

et al. 2021

Preprint

View full text Add to dashboard Cite

show abstract

“…Although studies conducted in Africa and other low-and middle-income countries (LMICs) have shown the abundance of E. coli in infections from normally sterile sites [9,10], these studies are few and far between, so that ExPEC and their AMR epidemiology are poorly understood [7,11]. In Nigeria, there is sparse molecular information on ExPEC, but a few studies point to likely clonal expansion of resistant lineages and local presence of pandemic clones of concern [12][13][14][15][16]. These studies provide valuable information but represent an insufficient picture of ExPEC clones in Nigeria, with little data available from the South.…”

Section: Introductionmentioning

confidence: 99%

An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals

et al. 2022

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Escherichia coli bloodstream infections are typically attributed to a limited number of lineages that carry virulence factors associated with invasiveness. In Nigeria, the identity of circulating clones is largely unknown and surveillance of their antimicrobial resistance has been limited. We verified and whole-genome sequenced 68 2016–2018 bloodstream E. coli isolates from three sentinel sites in South-Western Nigeria and susceptibility tested 67 of them. Resistance to antimicrobials commonly used in Nigeria was high, with 67 (100 %), 62 (92.5 %), 53 (79.1 %) and 37 (55.2 %) showing resistance to trimethoprim, ampicillin, ciprofloxacin and aminoglycosides, respectively. Thirty-five (51 %) isolates carried extended-spectrum β-lactamase genes and 32 (91 %) of these were multidrug resistant. All the isolates were susceptible to carbapenems and colistin. The strain set included globally disseminated high-risk clones from sequence type (ST)12 (2), ST131 (12) and ST648 (4). Twenty-three (33.8 %) of the isolates clustered within two clades. The first of these consisted of ST131 strains, comprising O16:H5 and O25:H4 sub-lineages. The second was an ST10–ST167 complex clade comprising strains carrying O-antigen and capsular genes of likely Klebsiella origin, identical to those of avian pathogenic E. coli Sanji, and serotyped in silico as O89, O101 or ONovel32, depending on the tool used. Four temporally associated ST90 strains from one sentinel were closely related enough to suggest that at least some of them represented a retrospectively detected outbreak cluster. Our data implicate a broad repertoire of E. coli isolates associated with bloodstream infections in South-West Nigeria. Continued genomic surveillance is valuable for tracking clones of importance and for outbreak identification.

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“…In the USA, carbapenem-resistance rates are revealed as 0.1% and 5.3% for E. coli and Klebsiella pneumoniae (K. pneumoniae), correspondingly, whereas in Europe, most nations report resistance rates below 1% for both pathogens. 19 Even though studies from Africa stated a carbapenem resistance of (3.8-52.6%), [20][21][22][23] still there are a few data on CR-GNB in Africa. 21 While there are a few studies in Ethiopia conveyed on CR with a range of 2-27.1%, [24][25][26][27] however, there is limited data in the study area.…”

Section: Introductionmentioning

confidence: 99%

Phenotypic Detection of Carbapenem-Resistant Gram-Negative Bacilli from a Clinical Specimen in Sidama, Ethiopia: A Cross-Sectional Study

Alemayehu

Asnake

Tadesse

et al. 2021

IDR

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Background Carbapenem-resistant gram-negative bacteria are an emergent source of both community-acquired and healthcare-associated infection that poses a substantial hazard to public health. This study aimed to conclude the magnitude of carbapenem resistance gram-negative bacteria from a clinical specimen at Hawassa University Comprehensive Specialized Hospital. Methods A hospital-based cross-sectional study was accompanied from February 13 to June 7, 2020, in which consecutive patients with 103 gram-negative bacteria were encompassed. The isolates included were 54 urine, 17 blood, 17 pusses, 4 cerebrospinal fluid (CSF), 3 aspirates, 3 effusions, 2 stools, 2 ear discharges, and 1 nasal swab. A semi-structured questionnaire was used to gather socio-demographic data from the attendant and clinical data from the patient’s chart. Patients admitted in any wards and visited outpatients department were included for the study if gram-negative bacteria was identified for those who accepted the consent. A routine manual culture, Gram’s staining and biochemical tests used to identify the bacteria. Antibiotic susceptibility was determined for twelve antibiotics including cotrimoxazole, ceftazidime, meropenem, gentamycin, chloramphenicol, ampicillin, ciprofloxacin, cefotaxime, cefuroxime, nitrofurantoin, piperacillin-tazobactam, and amikacin using the Kirby-Bauer disc diffusion method. Modified carbapenem inactivation (mCIM) method was used to determine carbapenem resistance using meropenem disk as per the recommendation of Clinical and Laboratory Standards Institute guideline. Statistical package for social science software version 21 was used for data entry and analysis. The odds ratio at 95% confidence interval (CI) and p-value <0.05 were taken as a statistically significant association. Results Generally, 111 gram-negative bacteria were identified from 103 patients. Of 111 isolates, thirteen isolates (nine resistance and four intermediates) were identified in disk diffusion testing for meropenem. Of this, 10 isolates were carbapenemases producer with the overall rates of 9% in the Modified carbapenem inactivation method (mCIM). Pseudomonas spp. 3 (30.0%), E. coli, K. pneumonia, Acinetobacter spp. each two (20.0%), and K. oxytoca 1 (10.0%) were identified as carbapenemases positive. The rates of the multidrug, extensive, pan drug were 86.5, 43.3, and 1.8, respectively. Ampicillin 94 (97.9%), followed by cefuroxime 52 (91.2%), cefotaxime 94 (88.7%), cotrimoxazole 58 (88.1%), ceftazidime 40 (83.3%), ciprofloxacin 47 (77.1%), nitrofurantoin 35 (70.0%), gentamycin 71 (65.7%), with high level of resistance. However, piperacillin-tazobactam 41 (48.8%), chloramphenicol 25 (47.2%), meropenem 13 (11.7%), and amikacin 9 (8.5%) were with low rates of resistance. In this study, there were no variables statically associated with carbapenem resistance that is p > 0.05. ...

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Opening Pandora’s box: high level resistance to antibiotics of last resort in Gram negative bacteria from Nigeria

Cited by 4 publications

References 47 publications

An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

An ST131 clade and a Phylogroup A clade bearing a novel Escherichia coli O-antigen cluster predominate among bloodstream E. coli isolates from southwest Nigeria hospitals

An ST131 clade and a phylogroup A clade bearing an O101-like O-antigen cluster predominate among bloodstream Escherichia coli isolates from South-West Nigeria hospitals

Phenotypic Detection of Carbapenem-Resistant Gram-Negative Bacilli from a Clinical Specimen in Sidama, Ethiopia: A Cross-Sectional Study

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