| 1. |
- Ahlstrom, Christina A., et al.
(författare)
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Environmental antimicrobial resistance gene detection from wild bird habitats using two methods : A commercially available culture-independent qPCR assay and culture of indicator bacteria followed by whole-genome sequencing
- 2023
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 33, s. 186-193
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: A variety of methods have been developed to detect antimicrobial resistance (AMR) in differ-ent environments to better understand the evolution and dissemination of this public health threat. Com-parisons of results generated using different AMR detection methods, such as quantitative PCR (qPCR) and whole-genome sequencing (WGS), are often imperfect, and few studies have analysed samples in parallel to evaluate differences. In this study, we compared bacterial culture and WGS to a culture-independent commercially available qPCR assay to evaluate the concordance between methods and the utility of each in answering research questions regarding the presence and epidemiology of AMR in wild bird habitats.Methods: We first assessed AMR gene detection using qPCR in 45 bacterial isolates from which we had existing WGS data. We then analysed 52 wild bird faecal samples and 9 spatiotemporally collected water samples using culture-independent qPCR and WGS of phenotypically resistant indicator bacterial isolates.Results: Overall concordance was strong between qPCR and WGS of bacterial isolates, although concor-dance differed among antibiotic classes. Analysis of wild bird faecal and water samples revealed that more samples were determined to be positive for AMR via qPCR than via culture and WGS of bacterial isolates, although qPCR did not detect AMR genes in two samples from which phenotypically resistant isolates were found.Conclusions: Both qPCR and culture followed by sequencing may be effective approaches for characteris-ing AMR genes harboured by wild birds, although data streams produced using these different tools may have advantages and disadvantages that should be considered given the application and sample matrix.Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )
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| 2. |
- Ahlstrom, Christina A., et al.
(författare)
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Genomic comparison of carbapenem-resistant Enterobacteriaceae from humans and gulls in Alaska
- 2021
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier Science Ltd. - 2213-7165 .- 2213-7173. ; 25, s. 23-25
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Wildlife may harbour clinically important antimicrobial-resistant bacteria, but the role of wildlife in the epidemiology of antimicrobial-resistant bacterial infections in humans is largely unknown. In this study, we aimed to assess dissemination of the bla(KPC) carbapenemase gene among humans and gulls in Alaska. Methods: We performed whole-genome sequencing to determine the genetic context of bla(KPC) in bacterial isolates from all four human carbapenemase-producing Enterobacteriaceae (CPE) infections reported in Alaska between 2013-2018 and to compare the sequences with seven previously reported CPE isolates from gull faeces within the same region and time period. Results: Genomic analysis of CPE isolates suggested independent acquisition events among humans with no evidence for direct transmission of bla(KPC) between people and gulls. However, some isolates shared conserved genetic elements surrounding bla(KPC), suggesting possible exchange between species. Conclusion: Our results highlight the genomic plasticity associated with bla(KPC) and demonstrate that sampling of wildlife may be useful for identifying clinically relevant antimicrobial resistance not observed through local passive surveillance in humans. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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| 3. |
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| 4. |
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| 5. |
- Börjesson, Stefan, 1979-, et al.
(författare)
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A link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 20, s. 285-289
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The aim of this study was to investigate the occurrence of the newly described transferable colistin resistance gene mcr-9 in extended-spectrum β-lactamase (ESBL)-producing clinical Enterobacteriaceae isolates from horses in Sweden.METHODS: A total of 56 whole-genome sequenced ESBL-producing Enterobacteriaceae isolates from horses were subjected to in silico detection of antimicrobial resistance genes and identification of plasmid replicons types. The colistin minimum inhibitory concentration (MIC) for mcr-positive isolates was determined by broth microdilution. Relatedness between Enterobacteriaceae carrying mcr genes was determined by multilocus sequence typing (MLST) and core genome MLST.RESULTS: Thirty ESBL-producing Enterobacteriaceae isolates from horses were positive for the colistin resistance gene mcr-9. These isolates included Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca and Citrobacter freundii and belonged to diverse MLST sequence types within each species. Two of the mcr-9-containing isolates originated from the same horse. All mcr-9-positive isolates had colistin MICs below or equal to the EUCAST epidemiological cut-off value of 2 mg/L and were negative for the two potential regulatory genes qseB-like and qseC-like for mcr-9. Except for one isolate carrying only blaTEM-1B, all of the isolates carried blaSHV-12 and blaTEM-1B, and were all considered multidrug-resistant as they harboured genes encoding resistance to aminoglycosides, chloramphenicol, fosfomycin, macrolides, quinolones, sulfonamides, trimethoprim and tetracyclines. Plasmid replicon types IncHI2 and IncHI2A were detected in all mcr-9-positive isolates.CONCLUSION: The occurrence of mcr-9 was common among clinical ESBL-producing Enterobacteriaceae isolates from horses in Sweden and was linked to the ESBL-encoding gene blaSHV-12 and plasmid replicon types IncHI2 and IncHI2A.
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| 6. |
- Chen, Baoli, et al.
(författare)
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Rapid increase in occurrence of carbapenem-resistant Enterobacteriaceae in healthy rural residents in Shandong Province, China, from 2015 to 2017
- 2022
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 28, s. 38-42
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVES: The global increase in carbapenem-resistant Enterobacteriaceae (CRE) is a growing health concern. Infections caused by CRE are associated with increased mortality and length of hospital stay, emphasising the health and economic burden posed by these pathogens. Although CRE can inhabit the human gut asymptomatically, colonisation with CRE is associated with an increased risk of CRE infection and mortality. In this study, we investigated the occurrence and characteristics of CRE in faecal samples from healthy persons in 12 villages in Shandong Province, China.METHODS: Screening for CRE in faecal samples was performed by selective cultivation. Minimum inhibitory concentrations (MICs) of meropenem were determined by the agar dilution method. Multilocus sequence typing (MLST) and carbapenemase gene carriage of the isolates were determined by whole-genome sequencing. Genetic relatedness of Escherichia coli isolates was determined by core genome MLST.RESULTS: CRE carriage increased from 2.4% in 2015 to 13.4% in 2017. Most CRE isolates (93.0%) were E. coli and all carried NDM-type carbapenemases. Sequence types (STs) among the E. coli isolates were diverse. The single most common ST was the highly epidemic strain ST167, which was only observed in 2017.CONCLUSION: We report a rapid increase in occurrence of CRE (from 2.4% to 13.4%) among faecal samples collected from healthy rural residents of Shandong Province from 2015 to 2017. Colonisation with CRE is known to increase the risk of CRE infection, and the worrying deterioration of the epidemiological situation in the region reported here indicates a need for further monitoring and possible interventions.
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| 7. |
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| 8. |
- El Zowalaty, Mohamed E., et al.
(författare)
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Draft genome sequence of Cronobacter sakazakii strain MEZCS99 sequence type 3 isolated from chicken in South Africa
- 2022
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 31, s. 292-294
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Cronobacter sakazakii is an emerging opportunistic foodborne pathogen that is frequently as-sociated with life-threatening infections such as infantile septicemia, meningitis, and necrotizing entero-colitis. The emergence of antimicrobial-resistant, livestock-associated C. sakazakii is a great public health concern. Here, we report on the first draft genome sequence of C. sakazakii strain MEZCS99 sequence type 3 (ST3) isolated from feces from a healthy chicken in KwaZulu-Natal Province, South Africa.Methods: The genomic DNA of C. sakazakii was sequenced using an Illumina MiSeq platform (Illumina Inc., San Diego, CA). Generated reads were trimmed and de novo assembled. The assembled contigs were analyzed for virulence and antimicrobial resistance genes, extra-chromosomal plasmids, and multi -locus sequence type (MLST). To compare the sequenced strains to other previously sequenced C. sakazakii strains, available raw read sequences of C. sakazakii were downloaded and all sequence files were treated identically to generate a core genome phylogenetic tree.Results: Intrinsic beta-lactam resistance gene blaCSA-1 was detected in MEZCS99. No colistin or other antibiotic resistance genes were detected. MEZCS99 belonged to ST3 and harbored an extra-chromosomal plasmid (IncFIB (pCTU3)). The genome of MEZCS99 strain showed two CRISPR/Cas cluster arrays of I-E (n = 1) and I-F (n = 1) type.Conclusion: The genome sequence of strain MEZCS99 will serve as a reference point for molecular epi-demiological studies of livestock-associated C. sakazakii in Africa. In addition, this study allows in-depth analysis of the genomic structure and will provide valuable information that helps understand the patho-genesis and antimicrobial resistance of livestock-associated C. sakazakii.
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| 9. |
- El Zowalaty, Mohamed E., et al.
(författare)
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Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - OXFORD ENGLAND : Elsevier BV. - 2213-7165 .- 2213-7173. ; 23, s. 445-449
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa. Methods: Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree. Results: Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844. Conclusion: The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli. (C) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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| 10. |
- El Zowalaty, Mohamed E., et al.
(författare)
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Genome sequences of two Salmonella enterica strains (MEZSAL74 and MEZSAL81) harbouring multiple antimicrobial resistance genes isolated from livestock in South Africa
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 21, s. 396-398
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Objectives: Antimicrobial-resistant livestock-associated Salmonella enterica infections pose a significant public-health threat worldwide. Here we report for the first time the draft genome sequences of two multidrug-resistant livestock-associated S. enterica strains isolated from a chicken and a cow in South Africa. Methods: Genomic DNA of S. enterica strains MEZSAL74 and MEZSAL81 was sequenced using an Illumina MiSeq platform. The generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids. Multilocus sequence typing (MLST) was also performed. In order to compare isolates MEZSAL74 and MEZSAL81 with other previously sequenced S. enterica isolates, raw read sequences were downloaded and all sequence files were treated identically to generate a bootstrapped maximum likelihood phylogenetic tree. Results: Extrachromosomal plasmids and genetic determinants of antimicrobial resistance were detected in both sequenced bacterial isolates to aminoglycosides and fluoroquinolones. By MLST, strain MEZSAL74 belonged to an unknown sequence type (ST) and strain MEZSAL81 belonged to ST33. Conclusion: The genome sequences of strains MEZSAL74 and MEZSAL81 reported here will serve as a reference for molecular epidemiological studies of antimicrobial-resistant livestock-associated S. enterica in Africa. (c) 2020 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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| 11. |
- Eze, Emmanuel C., et al.
(författare)
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Antibiotic resistance and biofilm formation of Acinetobacter baumannii isolated from high-risk effluent water in tertiary hospitals in South Africa
- 2021
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 27, s. 82-90
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Discharge of drug-resistant, biofilm-forming pathogens from hospital effluent water into mu-nicipal wastewater treatment plants poses a public health concern. This study examined the relationship between antibiotic resistance levels and biofilm formation of Acinetobacter baumannii strains isolated from hospital effluents.Methods: Antibiotic susceptibility of 71 A. baumannii isolates was evaluated by the Kirby-Bauer disk dif-fusion method. Minimum inhibitory concentrations (MICs) were determined by the agar dilution method, while the minimum biofilm eradication concentration (MBEC) was determined by the broth dilution method. Genotyping was performed for plasmid DNA. Biofilm formation was evaluated by the microtitre plate method and was quantified using crystal violet. A P-value of < 0.05 was regarded as statistically significant in all tests.Results: Extensively drug-resistant (XDR) strains made up 58% of the isolates, while multidrug-resistant (MDR) and pandrug-resistant (PDR) strains made up 50% of the isolates from final effluent. The MBEC of ciprofloxacin increased by 255-fold, while that of ceftazidime was as high as 63-1310-fold compared with their respective MICs. Isolates were classified into four plasmid pattern groups with no association between biofilm formation and plasmid type ( P = 0.0921). The degree of biofilm formation was inde-pendent of the level of antibiotic resistance, although MDR, XDR and PDR isolates produced significant biofilm biomass ( P = 0.2580).Conclusion: These results suggest that hospital effluent is a potential source of MDR biofilm-forming A. baumannii strains. Appropriate treatment and disposal of effluents are essential to prevent the presence of drug-resistant pathogens in wastewater.
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| 12. |
- Eze, Emmanuel C., et al.
(författare)
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Draft genome sequences of extensively drug resistant and pandrug resistant Acinetobacter baumannii strains isolated from hospital wastewater in South Africa
- 2022
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 31, s. 286-291
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Acinetobacter baumannii is a significant opportunistic pathogen causing nosocomial infections. Infections caused by A. baumannii are often difficult to treat because this bacterium is often multidrug-resistant and shows high environmental adaptability. Here, we report on the analysis of three A. bauman-nii strains isolated from hospital effluents in South Africa.Methods: Strains were isolated on Leeds Acinetobacter agar and were identified using VITEK (R) 2 platform. Antibiotic susceptibility testing was performed using the Kirby-Bauer Disk diffusion method. Whole-genome sequencing was performed. The assembled contigs were annotated. Multilocus sequence type, antimicrobial resistance, and virulence genes were identified.Results: The strains showed two multilocus sequence types, ST231 (FA34) and ST1552 (PL448, FG116). Based on their antibiotic susceptibility profiles, PL448 and FG116 were classified as extensively drug -resistant and FA34 as pandrug-resistant. FA34 harbored mutations in LpxA, LpxC, and PmrB, conferring resistance to colistin, but not mcr genes. All three strains encoded virulence genes for immune evasion (capsule, lipopolysaccharide [LPS]), iron uptake, and biofilm formation. FA34 was related to human strains from South Africa; PL448 and FG116 were related to a strain isolated in the United States from a human wound.Conclusions: The detection of extensively drug-and pandrug-resistant A. baumannii strains in hospital effluents is of particular concern. It indicates that wastewater might play a role in the spread of these bacteria. Our data provide insight into the molecular epidemiology, resistance, pathogenicity, and distri-bution of A. baumannii in South Africa.
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| 13. |
- Eze, Emmanuel C., et al.
(författare)
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Genome sequence of a carbapenemase-encoding Acinetobacter baumannii isolate of the sequence type 231 isolated from hospital wastewater in South Africa
- 2022
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 29, s. 150-154
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Tidskriftsartikel (refereegranskat)abstract
- ObjectivesThe resistome, virulome, mobilome and phylogenetic relationship of the Acinetobacter baumannii isolate FG121 depicting the multilocus sequence type (ST) 231 isolated from hospital effluent water in South Africa was determined using whole-genome sequence analysis.MethodA. baumannii FG121 was isolated on Leed Acinetobacter Medium (LAM) agar and the bacterial isolate was identified using the VITEK®2 platform. Antibiotic susceptibility testing was performed using Kirby–Bauer Disk diffusion method. A whole genome sequencing library was constructed from DNA extracted from the isolate using the Illumina Nextera XT library preparation kit and was sequenced using the Illumina NextSeq500 platform. Generated reads were de novo assembled using SpAdes v.3.9. The assembled contigs were annotated, and multilocus sequence type, antimicrobial resistance, and virulence genes were identified.ResultsThe resistome was consistent with the resistance phenotype of the isolate with resistance determinants for beta-lactams, aminoglycosides, and tetracycline (blaADC-25, blaOXA-23, blaOXA-51, blaNDM-1, aph[3’]-VIa and tet[B]). Global phylogenomic analysis using BacWGSTdb revealed that the isolate belonged to the multilocus sequence type ST-231, similar to previously reported isolates from South Africa, the United States, and related to the invasive KR3831 isolate identified from Oman in 2012, suggesting the isolate might be imported from abroad. Virulome analysis predicted both virulence and biofilm-determinants of A. baumannii, which may help to establish infections in adverse conditions.ConclusionThis is the first report on a carbapenemase-encoding A. baumannii ST-231 isolated from hospital effluent water. Our data will offer insight into the global phylogenetic, pathogenicity and distribution of A. baumannii in South Africa.
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| 14. |
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| 15. |
- Falcone, Marco, et al.
(författare)
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Considerations for the optimal management of antibiotic therapy in elderly patients
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - : ELSEVIER SCI LTD. - 2213-7165 .- 2213-7173. ; 22, s. 325-333
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Forskningsöversikt (refereegranskat)abstract
- Objectives: To maximise efficacy and minimise toxicity, special considerations are required for antibiotic prescription in elderly patients. This review aims to provide practical suggestions for the optimal management of antibiotic therapy in elderly patients. Methods: This was a narrative review. A literature search of published articles in the last 15 years on antibiotics and elderly patients was performed using the Cochrane Library and PubMed electronic databases. The three priority areas were identified: (i) pharmacokinetics/pharmacodynamics (PK/PD) for optimising dosage regimens and route of administration; (ii) antibiotic dosages in some special subpopulations; and (iii) treatment considerations relating to different antibiotic classes and their adverse events. Results: Clinicians should understand the altered PK/PD of drugs in this population owing to co-morbid conditions and normal physiological changes associated with ageing. The body of evidence justifies the need for individualised dose selection, especially in patients with impaired renal and liver function. Clinicians should be aware of the major drug-drug interactions commonly observed in the elderly as well as potential side effects. Conclusion: Antibiotic therapy in the elderly requires a comprehensive approach, including strategies to improve appropriate antibiotic prescribing, limit their use for uncomplicated infections and ensure the attainment of an optimal PK/PD target. To this purpose, further studies involving the elderly are needed to better understand the PK of antibiotics. Moreover, it is necessary to assess the role therapeutic drug monitoring in guiding antibiotic therapy in elderly patients in order to evaluate its impact on clinical outcome.
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| 16. |
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| 17. |
- Gavier-Widén, Dolores
(författare)
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In vitro activity of ceftaroline against mecC-positive MRSA isolates
- 2016
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier BV. - 2213-7165 .- 2213-7173. ; 5, s. 3-6
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Tidskriftsartikel (refereegranskat)abstract
- Ceftaroline is a new cephalosporin with activity against methicillin-resistant Staphylococcus aureus (MRSA). A collection of 17 clinical and veterinary mecC-positive MRSA isolates was tested to evaluate the in vitro efficacy of ceftaroline against recently emerged mecC-MRSA isolates. Minimum inhibitory concentrations (MICs) and minimum bactericidal concentrations (MBCs) of ceftaroline for the 17 isolates were determined by broth microdilution using the methodology and interpretive criteria of the Clinical and Laboratory Standards Institute (CLSI). Additional susceptibility tests were performed using ceftaroline M.I.C. Evaluator (M.I.C.E.(TM)) strips. All isolates showed susceptibility according to CLSI breakpoints, with MICs of ceftaroline ranging from 0.125 mg/L to 0.25 mg/L. MBCs were identical or up to a twofold dilution step higher. In conclusion, all tested isolates, from various sources and belonging to several clonal complexes (CCs), but predominantly to CC130, were found to be susceptible to ceftaroline. Ceftaroline could thus be an option for the treatment of mecC-MRSA infections. (C) 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.
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| 18. |
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| 19. |
- Kenyon, Chris, et al.
(författare)
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Gonorrhoea treatment combined with population-level general cephalosporin and quinolone consumption may select for Neisseria gonorrhoeae antimicrobial resistance at the levels of NG-MAST genogroup : an ecological study in Europe
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 23, s. 377-384
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Tidskriftsartikel (refereegranskat)abstract
- OBJECTIVE: The prevalence of Neisseria gonorrhoeae NG-MAST genogroup G1407, associated with decreased susceptibility to extended-spectrum cephalosporins and fluoroquinolone resistance, has declined in Europe and it switched from circulating predominantly in men who have sex with men (MSM) in 2009-10 to heterosexuals in 2013. We hypothesized that changes to gonorrhoea treatment guidelines combined with differences in country-level consumption of cephalosporins and quinolones contributed to this shift.METHODS: Linear regression was used to evaluate associations between changes in prevalence of G1407 from 2009-10 to 2013 and country-level consumption of quinolones and cephalosporins in 2011/12 in 20 European countries.RESULTS: Whilst the prevalence of G1407 declined from 2009-10 to 2013 in the EU/EEA, its absolute prevalence increased by 10% or more in 3 countries. The national prevalence of G1407 in 2013 was positively associated with population-level general cephalosporin and quinolone consumption in the preceding two years. The association between the prevalence of G1407 and proportion of the national sample derived from MSM was non-significant in 2009-10 and negative in 2013.CONCLUSIONS: Our results are broadly compatible with the hypothesis that changes in gonorrhoea therapy to the more efficacious ceftriaxone (plus azithromycin) from 2010-11 and onwards resulted in a reduced prevalence of the resistance associated-G1407 overall but in MSM in particular. High population-level consumption of quinolones and cephalosporins in certain countries then contributed to the selection of G1407 predominantly in heterosexuals in these countries.
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| 20. |
- Lagunas-Rangel, Francisco Alejandro
(författare)
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Antimicrobial susceptibility profiles of bacteria causing urinary tract infections in Mexico : Single-centre experience with 10 years of results
- 2018
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier BV. - 2213-7165 .- 2213-7173. ; 14, s. 90-94
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The aim of this retrospective study was to describe urinary tract infections (UTIs) diagnosed in a single centre in Mexico through 10 years of results, with a particular emphasis on the aetiology, patterns of antimicrobial susceptibility and incidence of extended-spectrum β-lactamase (ESBL)-producing strains.Methods: This study involved all urine samples analysed during the period March 2007 to September 2017 in a single centre in Mexico. Isolated uropathogens were identified to species level using routine laboratory methods, and antimicrobial susceptibility was determined by the disk diffusion method.Results: Overall, 859 urinary isolates were identified, including 582 (67.8%) Escherichia coli, 69 (8.0%) Enterococcus faecalis, 29 (3.4%) Klebsiella pneumoniae, 24 (2.8%) Proteus mirabilis, 24 (2.8%) Pseudomonas aeruginosa, 23 (2.7%) Candida albicans, 18 (2.1%) Streptococcus agalactiae and 10 (1.2%) Candida glabrata. Patient sex and age were the main risk factors associated with UTI in this population. Nitrofurantoin together with fosfomycin and amikacin had the highest percentages of susceptibility. Of the 859 isolates, 213 (24.8%) presented a positive double-disk synergy test indicating the presence of an ESBL phenotype, with E. coli showing a gradual increase in ESBL-producing isolates over time.Conclusions: These results provide additional evidence in relation to the role of different bacterial species as aetiological agents of UTI as well as antimicrobial susceptibility information that will help to guide the selection of antimicrobial treatment for UTIs and the prevalence of ESBL-producing strains over a 10-year period in a Mexican centre.
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| 21. |
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| 22. |
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| 23. |
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| 24. |
- Osman, Marwan, et al.
(författare)
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Multidrug-resistant pathogens contaminate river water used in irrigation in disenfranchised communities
- 2024
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier. - 2213-7165 .- 2213-7173. ; 36, s. 175-180
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The contamination of fresh surface waters poses a significant burden on human health and prosperity, especially in marginalized communities with limited resources and inadequate infrastructure. Here, we performed in-depth genomic analyses of multidrug-resistant bacteria (MDR-B) isolated from Al-Oueik river water that is used for irrigation of agricultural fields in a disenfranchised area that also hosts a makeshift Syrian refugee camp.Methods: A composite freshwater sample was filtered. Faecal coliforms were counted and extended spectrum cephalosporins and/or ertapenem resistant bacteria were screened. Isolates were identified using MALDI-TOF-MS and analysed using whole-genome sequencing (WGS) to identify the resistome, sequence types, plasmid types, and virulence genes.Results: Approximately 106 CFU/100 mL of faecal coliforms were detected in the water. Four drug-resistant Gram-negative bacteria were identified, namely Escherichia coli, Klebsiella pneumoniae, Enterobacter hormaechei, and Pseudomonas otitidis. Notably, the E. coli isolate harboured blaNDM-5 and a YRIN-inserted PBP3, representing an emerging public health challenge. The K. pneumoniae isolate carried blaSHV-187 as well as mutations in the gene encoding the OmpK37 porin. Enterobacter hormaechei and P. otitidis harboured blaACT-16 and blaPOM-1, respectively.Conclusion: This report provides comprehensive genomic analyses of MDR-B in irrigation water in Lebanon. Our results further support that irrigation water contaminated with faecal material can be a reservoir of important MDR-B, which can spread to adjacent agricultural fields and other water bodies, posing both public health and food safety issues. Therefore, there is an urgent need to implement effective water quality monitoring and management programs to control the proliferation of antibiotic-resistant pathogens in irrigation water in Lebanon.
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| 25. |
- Radisic, Vera, et al.
(författare)
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Tigecycline-resistant Klebsiella pneumoniae strains from sewage in Norway carry heavy-metal resistance genes encoding conjugative plasmids
- 2024
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Ingår i: JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE. - 2213-7165 .- 2213-7173. ; 36, s. 482-484
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Tigecycline is a last-resort antibiotic used for treatment of infections with carbapenemresistant Klebsiella pneumoniae . The aim of the study was to understand the genetic mechanism of resistance and the genetic context of resistance genes in two tigecycline-resistant K. pneumoniae strains isolated from sewage in Bergen, Norway. Methods: Complete genome sequencing of the two strains was accomplished using a combination of short-read Illumina MiSeq-based and long-read Oxford Nanopore MinION-based sequencing. Conjugation experiments were performed using filter mating and a green fluorescent protein (GFP)-tagged Escherichia coli strain. Results: The complete genome sequences of strain K6-320.1 and strain K7-325 were assembled into two contigs for each strain, one contig representing the complete circular chromosomes of 5 223 440 bp (K6320.1) and 5 263 092 bp (K7-325), respectively, and the other representing plasmids with sizes of 276 509 bp (pK6-320.1) and 246 731 bp (pK7-325). Strain K6-320.1 belonged to sequence type (ST)869, whereas strain K7-325 belonged to the pathogenic ST307. Both plasmids belonged to the IncFIB(K)/IncFII(K) group and carried several antibiotic resistance genes (ARGs), including tet (A) and blaCTX-M . Both plasmids (pK6320.1 and pK7-325) were transferred to a GFP-tagged E. coli strain, leading to the acquisition of resistance against multiple classes of antibiotics. Several heavy-metal resistance genes (HMRGs) encoding resistance against silver ( sil ), copper ( pco ), and arsenic ( ars ) were also present on both plasmids. Conclusions: Our study demonstrates the presence of multidrug-resistant K. pneumoniae strains carrying conjugative plasmids encoding both ARGs and HMRGs that have potential for persistence in the environment and human microbiota. (c) 2023 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
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| 26. |
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| 27. |
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| 28. |
- Sewunet, Tsegaye, et al.
(författare)
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Polyclonal spread of bla CTX-M-15 through high-risk clones of Escherichia coli at a tertiary hospital in Ethiopia
- 2022
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier BV. - 2213-7173 .- 2213-7165. ; 29, s. 405-412
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The burden of antimicrobial resistance and spread of epidemic clones are rarely reported from low-income countries. We aimed to investigate the genome-based epidemiology of extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) at a tertiary hospital in Jimma, Ethiopia. Methods: Bacteria were isolated from clinical specimens at Jimma Medical Center and subjected to species identification (MALDI-TOF), antimicrobial susceptibility testing (disk diffusion) and whole-genome sequencing (Illumina, HiSeq2500). Genomic data analysis was performed using EnteroBase and Center for Genomic Epidemiology bioinformatics pipelines. A maximum likelihood tree was generated using FastTree/2.1.8 based on single nucleotide polymorphisms (SNPs) in shared genomic regions to identify transmission clusters. Results: Escherichia coli isolates (n = 261) were collected from 1087 single non-duplicate clinical specimens over a 5-month period in 2016. The prevalence of ESBL-EC was 54.8% (143/261), 96% of which were resistant to multiple antibiotic classes. The blaCTX-M-15 ESBL gene was present in 88.4.% of isolates (122/138). Genes conferring resistance to aminoglycosides and ciprofloxacin [aac(6′)-Ib-cr, 62.3% (86/138)], phenicols [catB3, 56.5% (78/138)], sulfonamides [sul1, 68.1% (94/138), trimethoprim [dfrA17, 58.0% (80/138)] and macrolides [mph(A), 67.4% (93/138) were detected. The most prevalent sequence types were ST410 (23%), ST648 (17%), ST131 (10%) and ST167 (7%). Isolates of the same sequence type collected from different units of the hospital were highly similar in the SNP analysis. Conclusion: A high prevalence of ESBLs and dissemination of blaCTX-M-15 through multiple high-risk E. coli clones was detected. Nosocomial spread of multidrug-resistant ESBL-EC within the hospital puts vulnerable patients at risk of difficult-to-treat infections.
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| 29. |
- Tien Viet Dung, Vu, et al.
(författare)
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Antimicrobial susceptibility testing and antibiotic consumption results from 16 hospitals in Viet Nam: The VINARES project 2012-2013
- 2019
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Ingår i: Journal of Global Antimicrobial Resistance. - : ELSEVIER SCI LTD. - 2213-7165 .- 2213-7173. ; 18, s. 269-278
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Tidskriftsartikel (refereegranskat)abstract
- Objective: To establish a hospital-based surveillance network with national coverage for antimicrobial resistance (AMR) and antibiotic consumption in Viet Nam. Methods: A 16-hospital network (Viet Nam Resistance: VINARES) was established and consisted of national and provincial-level hospitals across the country. Antimicrobial susceptibility testing results from routine clinical diagnostic specimens and antibiotic consumption data in Defined Daily Dose per 1000 bed days (DDD/1000 patient-days) were prospectively collected and analysed between October 2012 and September 2013. Results: Data from a total of 24 732 de-duplicated clinical isolates were reported. The most common bacteria were: Escherichia coli (4437 isolates, 18%), Klebsiella spp. (3290 isolates, 13%) and Acinetobacter spp. (2895 isolates, 12%). The hospital average antibiotic consumption was 918 DDD/1000 patient-days. Third-generation cephalosporins were the most frequently used antibiotic class (223 DDD/1000 patient-days, 24%), followed by fluoroquinolones (151 DDD/1000 patient-days, 16%) and second-generation cephalosporins (112 DDD/1000 patient-days, 12%). Proportions of antibiotic resistance were high: 1098/1580 (69%) Staphylococcus aureus isolates were methicillin-resistant (MRSA); 115/344 isolates (33%) and 90/358 (25%) Streptococcus pneumoniae had reduced susceptibility to penicillin and ceftriaxone, respectively. A total of 180/2977 (6%) E. coli and 242/1526 (16%) Klebsiella pneumoniae were resistant to imipenem, respectively; 602/1826 (33%) Pseudomonas aeruginosa were resistant to ceftazidime and 578/1765 (33%) to imipenem. Of Acinetobacter spp. 1495/2138 (70%) were resistant to carbapenems and 2/333 (1%) to colistin. Conclusions: These data are valuable in providing a baseline for AMR among common bacterial pathogens in Vietnamese hospitals and to assess the impact of interventions. (C) 2019 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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| 30. |
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| 33. |
- Bobis Camacho, Julián, 1997, et al.
(författare)
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Evaluation of culture conditions for sewage-based surveillance of antibiotic resistance in Klebsiella pneumoniae.
- 2024
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Ingår i: Journal of global antimicrobial resistance. - 2213-7173.
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies have shown promise in predicting clinical antibiotic resistance rates from sewage data. Few have focused on Klebsiella pneumoniae, despite its virulence and importance as carrier of antibiotic resistance. Several media have been suggested for the isolation of K. pneumoniae from complex samples. However, comprehensive evaluations of culture protocols for isolation of K. pneumoniae from sewage are lacking.Here, influent samples from a major Swedish sewage treatment plant were used to evaluate ten culture conditions in parallel: cultivation on Brilliant green containing Inositol-Nitrate-Deoxycholate agar (BIND), Bruce agar, Klebsiella ChromoSelect Selective agar®, MacConkey-Inositol-Carbenicillin, or Simmons Citrate Agar with Inositol (SCAI) incubated at either 37˚C or 42˚C for 44 h. The culture conditions were compared based on colony counts of presumed K. pneumoniae and identification precision assessed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.The sensitivity was lowest for BIND, whereas it was similar for the other media irrespective of incubation temperature. For four media, a better precision was observed after incubation at 42˚C compared to 37˚C, to a large extent explained by a lower frequency of captured Klebsiella oxytoca. SCAI incubated at 42˚C showed the highest precision (84.4%). By combining this protocol with subsequent antibiotic resistance screening of collected isolates, low resistance rates in sewage K. pneumoniae were revealed, potentially reflecting the local resistance landscape.When combined with downstream analyses, SCAI incubated at 42˚C could be a valuable culture protocol for sewage-based studies on various aspects of K. pneumoniae epidemiology including antibiotic resistance prevalence.
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| 34. |
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| 35. |
- Garau, Javier, et al.
(författare)
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Antibiotic stewardship challenges in the management of community-acquired infections for prevention of escalating antibiotic resistance
- 2014
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier BV. - 2213-7165. ; 2:4, s. 245-253
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Forskningsöversikt (refereegranskat)abstract
- Community-acquired infections, including respiratory tract infections (RTIs) and urinary tract infections (UTIs), represent a major burden for most healthcare systems, partially due to ineffective or inappropriate antibiotic treatment leading to clinical failure, which often requires alternative antibiotics for cure. Appropriate antimicrobial use not only maximises clinical success in the treatment of community-acquired infections, but also minimises unintended consequences such as resistance development or collateral damage. This article outlines a range of antibiotic stewardship strategies and other preventative approaches that support the management of community-acquired infections, based on existing antibiotic use for community-acquired infections and the current resistance patterns among common RTI and UTI pathogens. (C) 2014 The Authors. Published by Elsevier Ltd on behalf of International Society for Chemotherapy of Infection and Cancer.
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| 36. |
- Grevskott, D. H., et al.
(författare)
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Complete sequence of a new conjugative multidrug-resistance encoding IncFII/IncFIA/IncFIB plasmid carrying NDM-6 metallo-beta-lactamase from pathogenic Escherichia coli sequence type 167 isolated from sewage in Norway
- 2023
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Ingår i: Journal of Global Antimicrobial Resistance. - 2213-7165. ; 33, s. 291-293
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: The aim of the current study was to determine the genomic map of resistance genes and to understand the potential for mobility of a new NDM-6-carrying plasmid from a pathogenic Escherichia coli strain. A complete and closed genome sequence of the E. coli strain was obtained by applying a combination of short-read Illumina and long-read Nanopore-based sequencing.Methods: Isolation of E. coli was performed, using ECC CHROMagarTM, and antibiotic sensitivity pat-terns were determined, using SensititreTM EUVSEC3 plates. Whole-genome sequencing was performed, using Illumina MiSeq-and Oxford Nanopore MinION-based sequencing. Conjugation experiments were performed, using filter-mating and a green fluorescent protein (GFP)-tagged E. coli strain.Results: Two carbapenem-resistant E. coli strains were isolated from sewage. These strains (2-331 and 2-333) belonged to sequence type (ST) 167 and carried an NDM-6 carbapenemase. The complete genome of strain 2-331 (GenBank accession no.: CP110117-22.1) was assembled into six contigs, representing a complete circular chromosome of 4 947 178 bp and five plasmids, ranging from 143 596 bp to 1549 bp. Plasmid p2-331_1 ( similar to 144 kb), belonging to the IncFII/IncFIA/IncFIB group, carried multiple antibiotic resistance genes, including mph(A), mrx(A), blaTEM-1, rmtB1, blaNDM-6, ble, sul1, qacEA1, aadAA, dfrA12, and tet(A). Plasmid p2-331_1 was transferred from strain 2-331, via conjugation, conferring resistance against eight different classes of antibiotics to a GFP-tagged E. coli strain.Conclusions: Our study showed the emergence of a new conjugative plasmid-carrying NDM-6 carbapen-emase from pathogenic E. coli ST167 for the first time in Norway. The importance of population-based sewage-surveillance for understanding the antimicrobial resistance situation within the community is highlighted.(c) 2023 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy. This is an open access article under the CC BY license ( http://creativecommons.org/licenses/by/4.0/ )
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| 37. |
- Karami, Nahid, 1959, et al.
(författare)
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Recurrence of urinary tract infections with extended-spectrum beta-lactamase-producing Escherichia coli caused by homologous strains among which clone ST131-O25b is dominant
- 2020
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Ingår i: Journal of Global Antimicrobial Resistance. - : Elsevier BV. - 2213-7165. ; 22, s. 126-132
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Tidskriftsartikel (refereegranskat)abstract
- Objectives: Bacterial features associated with recurrent urinary tract infections (RUTIs) due to extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli) are not well understood. In this study, phylogenetic groups and ST131 subclones were investigated to assess strain homology of ESBL-E. coli isolates in patients with RUTIs in inpatient and outpatient settings in western Sweden. Methods: Almost all isolates (319/356) from 123 patients with 2-7 episodes (median 2 episodes) of ESBL-E. coli UTI within 1 year were examined for seven E. coli phylogroups, the ST131-O25b clone and its subclonefimH30-Rx. Antimicrobial resistance and ESBL genes were determined for the index isolates. A subset of isolates was typed using pulsed-field gel electrophoresis (PFGE). Results: The same phylogroup and ST131 subclones were seen for all recurrences in 119/123 patients, and PFGE confirmed strain homology in recurrences for 43/44 patients tested. Phylogroup B2 dominated (56%), followed by D (19%) and F (10%). ST131-O25b andfimH30-Rx isolates were detected in 44% and 30%, respectively. CTX-M group 1 (71%) predominated. Elderly patients were in the majority. There were no associations between patient demographics or time to recurrence and bacterial characteristics. The fimH30-Rx subclone was associated with a higher number of recurrences (P= 0.015) compared with the remaining B2 isolates. Conclusion: In ESBL-E. coli RUTI, most recurrences were caused by the initial infecting strain. The high frequency of the multidrug-resistant fimH30-Rx subclone and its association with multiple recurrences warrants further attention and early detection of this subclone in patients at risk of developing RUTI with ESBL-E. coli. (C) 2020 The Authors. Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.
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| 38. |
- Sun, Jing, et al.
(författare)
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Changes in patterns of antibiotic use in Chinese public hospitals (2005-2012) and a benchmark comparison with Sweden in 2012
- 2015
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Ingår i: JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE. - : Elsevier BV. - 2213-7165. ; 3:2, s. 95-102
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Tidskriftsartikel (refereegranskat)abstract
- Changes in patterns of antibiotic use in Chinese hospitals before and after intensive nationwide interventions are reported and compared with Chinese national targets and antibiotic use in Swedish hospitals. Chinese data were collected quarterly and yearly from selected patient prescriptions/medical records and medicines inventory control systems from 15 hospitals (2005-2012). Swedish data were extracted from a 2010-point prevalence survey and 2009-2012 sales data from seven university hospitals. An interrupted time series with segmented regression analysis was used to measure changes in patterns of antibiotic use in Chinese hospitals before and after the interventions. Following the 2011 interventions, significant reductions in antibiotic use in Chinese hospitals were seen: the proportion of prescriptions with antibiotics decreased 4.7% (P=0.03) and the proportion of medical records with antibiotic prescription decreased 73% (P=0.04). The proportions of prescriptions and medical records with antibiotics in Chinese hospitals in 2012 were 10% and 50%, respectively, and remained much higher than Swedish hospitals (1.1% in DDD for outpatients and 34% in number of patients for inpatients). Inpatient consumption in Chinese hospitals dropped significantly from 910 DDD/1000 inpatient days in 2008 to 473 in 2012 (588 in Swedish hospitals). Antibiotics are being used less frequently in Chinese hospitals, broad-spectrum antibiotics are still preferred, and overall usage is higher than Sweden. A significant reduction in overall inpatient antibiotic consumption was observed after the interventions. It is not possible to identify whether the-changes have resulted in less inappropriate antibiotic use. Further studies are needed.
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| 39. |
- Wertheim, Heiman, et al.
(författare)
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Global survey of polymyxin use : A call for international guidelines
- 2013
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Ingår i: JOURNAL OF GLOBAL ANTIMICROBIAL RESISTANCE. - : Elsevier BV. - 2213-7165. ; 1:3, s. 131-134
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Tidskriftsartikel (refereegranskat)abstract
- Polymyxins (polymyxin B and colistin) are older bactericidal antibiotics that are increasingly used to treat infections caused by multidrug-resistant (MDR) Gram-negative bacteria. However, dosing and clinical use of these drugs vary widely. This survey was undertaken to reveal how polymyxins are used worldwide. Data were collected through a structured online questionnaire consisting of 24 questions regarding colistin usage patterns and indications as well as colistin dosage for adult patients. The questionnaire was disseminated in 2011 to relevant experts worldwide and was completed by 284 respondents from 56 different countries. Respondents from 11/56 countries (20%) had no access to colistin; 58/284 respondents (20.4%) reported that in 2010 they experienced that colistin was not available when needed. Formulations of polymyxins used were reported as: colistimethate sodium (48.6%); colistin sulfate (14.1%); both (1.4%); polymyxin B (1.4%); and unknown. Intravenous formulations were used by 84.2%, aerosolised or nebulised colistin by 44.4% and oral colistin for selective gut decontamination by 12.7%. Common indications for intravenous colistin were ventilator-associated pneumonia, sepsis and catheter-related infections with MDR Gram-negative bacteria. Only 21.2% of respondents used a colistin-loading dose, mainly in Europe and North America. This survey reveals that the majority of respondents use colistin and a few use polymyxin B. The survey results show that colistin is commonly underdosed. Clear guidance is needed on indications, dosing and antibiotic combinations to improve clinical outcomes and delay the emergence of resistance. Colistin should be considered a last-resort drug and its use should be controlled. International guidelines are urgently needed. (C) 2013 International Society for Chemotherapy of Infection and Cancer.
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