Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing

Cao, Huiluo; Liu, Chunjiao; Tong, Man-Ki; Jiang, Shuo; Chow, Kam-Pui; To, Kelvin Kai‐Wang; Tse, Cindy Wing-Sze; Ho, Pak‐Leung

doi:10.1016/j.ijmm.2022.151559

Cited by 14 publications

(9 citation statements)

References 48 publications

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“…This plasmid was also detected in 4/5 MDR B. fragilis isolates from the Netherlands and 2/23 cfiA -harbouring B. fragilis isolates from Hong Kong. 12 , 21 The P. melaninogenica isolate resistant to metronidazole harboured a nimA gene in its chromosome. The nimA gene can be present on plasmids and in the chromosome.…”

Section: Discussionmentioning

confidence: 99%

Antimicrobial susceptibility profile of clinically relevantBacteroides,Phocaeicola,ParabacteroidesandPrevotellaspecies, isolated by eight laboratories in the Netherlands

Boiten,

Notermans,

Rentenaar

et al. 2024

Journal of Antimicrobial Chemotherapy

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Objectives Recently, reports on antimicrobial-resistant Bacteroides and Prevotella isolates have increased in the Netherlands. This urged the need for a surveillance study on the antimicrobial susceptibility profile of Bacteroides, Phocaeicola, Parabacteroides and Prevotella isolates consecutively isolated from human clinical specimens at eight different Dutch laboratories. Methods Each laboratory collected 20–25 Bacteroides (including Phocaeicola and Parabacteroides) and 10–15 Prevotella isolates for 3 months. At the national reference laboratory, the MICs of amoxicillin, amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem, metronidazole, clindamycin, tetracycline and moxifloxacin were determined using agar dilution. Isolates with a high MIC of metronidazole or a carbapenem, or harbouring cfiA, were subjected to WGS. Results Bacteroides thetaiotaomicron/faecis isolates had the highest MIC90 values, whereas Bacteroides fragilis had the lowest MIC90 values for amoxicillin/clavulanic acid, piperacillin/tazobactam, meropenem, imipenem and moxifloxacin. The antimicrobial profiles of the different Prevotella species were similar, except for amoxicillin, for which the MIC50 ranged from 0.125 to 16 mg/L for Prevotella bivia and Prevotella buccae, respectively. Three isolates with high metronidazole MICs were sequenced, of which one Bacteroides thetaiotaomicron isolate harboured a plasmid-located nimE gene and a Prevotella melaninogenica isolate harboured a nimA gene chromosomally. Five Bacteroides isolates harboured a cfiA gene and three had an IS element upstream, resulting in high MICs of carbapenems. The other two isolates harboured no IS element upstream of the cfiA gene and had low MICs of carbapenems. Conclusions Variations in resistance between species were observed. To combat emerging resistance in anaerobes, monitoring resistance and conducting surveillance are essential.

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Section: Discussionmentioning

confidence: 99%

Antimicrobial susceptibility profile of clinically relevantBacteroides,Phocaeicola,ParabacteroidesandPrevotellaspecies, isolated by eight laboratories in the Netherlands

Boiten,

Notermans,

Rentenaar

et al. 2024

Journal of Antimicrobial Chemotherapy

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“…Genomic DNA of each strain was extracted and qualified as was done in our previous studies [ 19 , 20 ]. All genomes were sequenced using the Illumina NovaSeq platform (Illumina, CA, USA) at the Novogene Bioinformatics Institute, Beijing.…”

Section: Methodsmentioning

confidence: 99%

“…All genomes were sequenced using the Illumina NovaSeq platform (Illumina, CA, USA) at the Novogene Bioinformatics Institute, Beijing. The workflow from raw reads to generate annotated genomes employed in our previous studies was performed [ 19 , 20 ]. Databases of CTX-M and CTX-M-like protein sequences were curated after comprehensively screening all available databases including the updated Bacterial Antimicrobial Resistance Reference Gene Database ( , accessed on 1 November 2022), BLDB ( , accessed on 1 November 2022), ResFinder (upon the date of September 2022) and HMD-ARG-DB [ 21 ].…”

Section: Methodsmentioning

confidence: 99%

Evaluation of a Lateral Flow Immunoassay for Rapid Detection of CTX-M Producers from Blood Cultures

et al. 2023

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Bacteremia caused by extended-spectrum β-lactamases-producing Enterobacterales has increased rapidly and is mainly attributed to CTX-M enzymes. This study aimed to evaluate the NG-Test® CTX-M MULTI lateral flow assay (CTX-M LFA) for rapid detection of CTX-M producers in blood cultures (BCs) positive for Gram-negative bacilli in spiked and clinical BCs. Retrospective testing was performed on BC bottles spiked with a collection of well-characterized Enterobacterales isolates producing CTX-M (n = 15) and CTX-M-like (n = 27) β-lactamases. Prospective testing of clinical, non-duplicate BCs (n = 350) was performed in two hospital microbiology laboratories from April 2021 to March 2022 following detection of Gram-negative bacilli by microscopic examination. Results were compared against molecular testing as the reference. In the spiked BCs, the CTX-M LFA correctly detected all CTX-M producers including 5 isolates with hybrid CTX-M variants. However, false-positive results were observed for several CTX-M-like β-lactamases, including OXY-1-3, OXY-2-8, OXY-5-3, FONA-8, -9, -10, 11, 13 and SFO-1. In clinical BCs, the CTX-M LFA showed 100% (95% CI, 96.0–100%) sensitivity and 99.6% (97.9–100%) specificity. In conclusion, this study showed that rapid detection of CTX-M producers in BC broths can be reliably achieved using the CTX-M LFA, thus providing an opportunity for early optimization of antibiotics.

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“…The Illumina short reads were then trimmed with Trimmomatic v0.39 and the Nanopore long reads were trimmed by Porechop version 0.2.4. The trimmed reads proceeded to de novo assembly using Unicycler v0.4.9, as in our previous studies [ 25 , 26 ]. In the case of an incomplete genome generated from Unicycler, CANU v2.2 [ 27 ] or Flye v2.9.1 [ 28 ] was used to assemble the Nanopore reads and corrected with Pilon v1.24 [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

“…In the case of an incomplete genome generated from Unicycler, CANU v2.2 [ 27 ] or Flye v2.9.1 [ 28 ] was used to assemble the Nanopore reads and corrected with Pilon v1.24 [ 29 ]. Quality evaluations, fixations of the start position with dnaA , and annotations of genomes were performed as described in our previous studies [ 25 , 26 ].…”

Section: Methodsmentioning

confidence: 99%

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

Cao

Chen

et al. 2023

Microorganisms

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Typhoid fever is a notable disease in Hong Kong. We noticed two local cases of typhoid fever caused by Salmonella Typhi within a two-week period in late 2022, which had no apparent epidemiological linkage except for residing in the same region of Hong Kong. A phylogenetic study of Salmonella Typhi isolates from Hong Kong Island from 2020 to 2022 was performed, including a whole-genome analysis, the typing of plasmids, and the analysis of antibiotic-resistance genes (ARGs), to identify the dominant circulating strain and the spread of ARGs. A total of seven isolates, from six local cases and an imported case, were identified from positive blood cultures in two hospitals in Hong Kong. Five antibiotic-sensitive strains of genotype 3.2.2 were found, which clustered with another 30 strains originating from Southeast Asia. Whole-genome sequencing revealed clonal transmission between the two index cases. The remaining two local cases belong to genotype 2.3.4 and genotype 4.3.1.1.P1 (also known as the H58 lineage). The genotype 4.3.1.1.P1 strain has an extensively drug-resistant (XDR) phenotype (co-resistance to ampicillin, chloramphenicol, ceftriaxone, ciprofloxacin, and co-trimoxazole). Although the majority of local strains belong to the non-H58 genotype 3.2.2 with a low degree of antibiotic resistance, the introduction of XDR strains with the global dissemination of the H58 lineage remains a concern.

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Comprehensive investigation of antibiotic resistance gene content in cfiA-harboring Bacteroides fragilis isolates of human and animal origins by whole genome sequencing

Cited by 14 publications

References 48 publications

Antimicrobial susceptibility profile of clinically relevantBacteroides,Phocaeicola,ParabacteroidesandPrevotellaspecies, isolated by eight laboratories in the Netherlands

Antimicrobial susceptibility profile of clinically relevantBacteroides,Phocaeicola,ParabacteroidesandPrevotellaspecies, isolated by eight laboratories in the Netherlands

Evaluation of a Lateral Flow Immunoassay for Rapid Detection of CTX-M Producers from Blood Cultures

Genomic Investigation of Salmonella Typhi in Hong Kong Revealing the Predominance of Genotype 3.2.2 and the First Case of an Extensively Drug-Resistant H58 Genotype

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