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1.
Antibiotics (Basel) ; 12(11)2023 Nov 02.
Article in English | MEDLINE | ID: mdl-37998787

ABSTRACT

Infections caused by extended-spectrum ß-lactamase-producing Enterobacterales have increased rapidly and are mainly attributed to the production of CTX-M enzymes. This study evaluated the NG-Test® CTX-M MULTI lateral flow assay (CTX-M LFA) and the Rapid ESBL NP® test (ESBL NP test) for rapid detection of CTX-M-producing Enterobacterales directly in midstream urine (MSU) samples. Testing was performed on 277 clinical MSU samples in a hospital microbiology laboratory from November 2022 to January 2023; 60 of these samples (30 positive for ESBL producers and 30 positive for non-ESBL producers) were tested retrospectively after the identification and susceptibility results were obtained, and 217 samples were tested prospectively immediately after a Gram stain showing the presence of Gram-negative bacilli. The results were compared against phenotypic detection of ESBL and molecular testing as the reference methods. Overall, 67 of the 277 samples were culture-positive for ESBL-producing Enterobacterales. PCR for the blaCTX-M gene was positive for all ESBL-producing Enterobacterales isolates. All CTX-M LFA results were interpretable, while three of the ESBL NP test results were noninterpretable. The sensitivity of the CTX-M LFA (100%, 95% CI 94.6-100%) was higher than that of the ESBL NP test (86.6%, 95% CI 76.0-93.7%). Both tests had high specificities (CTX-M LFA, 99.1%, 95% CI 96.6-99.9% and ESBL NP test, 100%, 95% CI 98.2-100%). In conclusion, both the CTX-M LFA and the ESBL NP test can deliver rapid results that could improve antimicrobial stewardship for urinary tract infections.

2.
Anaerobe ; 82: 102756, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37429411

ABSTRACT

OBJECTIVES: This retrospective study analyzed the susceptibility levels of Bacteroides fragilis group (BFG) in a hospital-based laboratory where disk diffusion test (DDT) was routinely performed. Isolates non-susceptible to imipenem and metronidazole by DDT were further investigated using a gradient method. METHODS: The DDT and MIC susceptibility data of clindamycin, metronidazole, moxifloxacin and imipenem obtained on Brucella blood agar for 1264 non-duplicated isolates during 2020-2021 were analyzed. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry and 16S rRNA sequencing. Interpretative agreement of DDT results using the 2015 EUCAST tentative and 2021 CA-SFM breakpoints was compared against MIC as the reference. RESULTS: The dataset included 604 B. fragilis (483 division I, 121 division II isolates), 415 non-fragilis Bacteroides, 177 Phocaeicola and 68 Parabacteroides. Susceptibility rates for clindamycin (22.1-62.1%) and moxifloxacin (59.9-80.9%) were low and many had no inhibition zones. At the EUCAST and CA-SFM breakpoints, 83.0 and 89.4% were imipenem-susceptible, and 89.6% and 97.4 were metronidazole-susceptible. MIC testing confirmed 11.4% and 2.8% isolates as imipenem-non-susceptible and metronidazole-resistant, respectively. Significant numbers of false-susceptibility and/or false-resistance results were observed at the CA-SFM breakpoint but not the EUCAST breakpoint. Higher rates of imipenem and/or metronidazole resistance were detected in B. fragilis division II, B. caccae, B. ovatus, B. salyersiae, B. stercoris and Parabacteroides. Co-resistance to imipenem and metronidazole was detected in 3 B. fragilis division II isolates. CONCLUSIONS: The data demonstrated emerging BFG resistance to several important anti-anaerobic antibiotics and highlights the importance of anaerobic susceptibility testing in clinical laboratories to guide therapy.


Subject(s)
Bacteroides fragilis , Bacteroides , Clindamycin , Metronidazole , Moxifloxacin , Hong Kong , Retrospective Studies , RNA, Ribosomal, 16S/genetics , Microbial Sensitivity Tests , Anti-Bacterial Agents/pharmacology , Imipenem/pharmacology
3.
mSystems ; 7(6): e0077522, 2022 12 20.
Article in English | MEDLINE | ID: mdl-36218363

ABSTRACT

The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread. IMPORTANCE Antimicrobial resistance (AMR) has proven to be a global public health concern. To conquer this increasingly worrying trend, an overarching, One Health approach has been used that brings together different sectors, but the fundamental knowledge of the relationship between humans, food animals, and their environments is not mature yet or is lacking in some aspect. With swine and chicken as examples of food animals, a large global data set of over 1,000 human and food animal gut metagenomes was analyzed with a focus on acquired antibiotic resistance genes (ARGs) associated with mobile genetic elements (MGEs) to answer this question. Outputs from this work open a new avenue to further our understanding of ARG transferability in food animals. It is a necessary milestone to better equip governmental agencies to monitor and pre-empt antibiotic resistance hot spots. This work will assist and give guidance on how to decipher other links within any One Health initiatives with expected positive feedback to human health.


Subject(s)
Anti-Bacterial Agents , Drug Resistance, Bacterial , Humans , Animals , Swine/genetics , Anti-Bacterial Agents/pharmacology , Drug Resistance, Bacterial/genetics , Bacteria/genetics , Genes, Bacterial , Metagenome
4.
Int J Med Microbiol ; 312(6): 151559, 2022 Aug.
Article in English | MEDLINE | ID: mdl-35961233

ABSTRACT

INTRODUCTION: The emergence of multidrug resistance in Bacteroides fragilis, especially the phylogenetic lineage carrying the carbapenemase gene cfiA, represents an increasing threat to human health. However, knowledge on the diversity of the multidrug-resistant strains and the genetic elements carrying the antibiotic resistance genes (ARGs) remains limited. AIM: The objective of the study was to describe the resistome in cfiA-positive B. fragilis. METHODS: A collection of cfiA-positive B. fragilis from diverse human (8 bacteremias, 15 wound infections) and animal (2 chickens, 2 pigs, 6 dogs, 3 cats) sources in Hong Kong, 2015-2017 was analysed by whole genome sequencing. RESULTS: In the 36 isolates, 13 distinct ARGs (total number 83, median 2, range 0-7 per isolate) other than cfiA were detected. ARGs encoding resistance to aminoglycosides, ß-lactams, macrolides, sulphonamides and tetracyclines were carried by CTn341-like, CTnHyb-like, Tn5220-like, Tn4555-like and Tn613-like transposons and were detected in phylogenetically diverse isolates of different host sources. Only few ARGs encoding resistance to metronidazole and tetracyclines were localized on plasmids. In two chicken isolates, a novel transposon (designated as Tn6994) was found to be involved in the dissemination of multiple ARGs mediating resistance to multiple antibiotics, including metronidazole and linezolid that are critically important for treatment of anaerobic infections. In mating experiments, Tn6994 and the associated phenotypic resistance could be transferred to Bacteroides nordii recipient. CONCLUSION: This study illustrates the importance of transposons in the dissemination of ARGs in the cfiA-positive division of B. fragilis. One Health approach is necessary to track the dissemination of ARGs.


Subject(s)
Bacterial Infections , Bacteroides Infections , Aminoglycosides , Animals , Anti-Bacterial Agents/pharmacology , Bacterial Proteins/genetics , Bacteroides fragilis/genetics , Chickens , Dogs , Drug Resistance, Microbial , Humans , Linezolid , Macrolides , Metronidazole , Microbial Sensitivity Tests , Phylogeny , Sulfonamides , Swine , Tetracyclines , Whole Genome Sequencing , beta-Lactamases/genetics , beta-Lactams
5.
Anaerobe ; 75: 102567, 2022 Jun.
Article in English | MEDLINE | ID: mdl-35427784

ABSTRACT

OBJECTIVES: To compare the phylogeny of cfiA-positive Bacteroides fragilis isolates from diverse human and animal sources. METHOD: Complete genome sequences were obtained from 42 cfiA-positive B. fragilis isolates (Hong Kong, 2015-2017) and additional 24 genomes deposited in the GenBank (multiple countries, 1985-2019) were included. The genomic clusters were constructed using PopPUNK. The CfiA alleles and polymorphism in the cfiA locus were analyzed in silico. RESULTS: The 66 isolates were grouped into 12 genomic clusters (BFSC-1 to 12). Human infection isolates were distributed in diverse clusters, being many of them common to fecal isolates from both human and animals. Thirteen CfiA alleles including 2 novel ones were identified. CfiA-1 (n = 28) is the predominating allele, following by CfiA-13 (n = 8), CfiA-4 (n = 7) and CfiA-14 (n = 6). The other CfiA alleles were identified in 1-3 isolates. Six patterns of gene context were identified in the regions flanking cfiA locus. No consistent association between genomic clusters and CfiA alleles could be detected. Similarly, markedly elevated imipenem MIC was linked to the integration, immediately upstram of cfiA of an IS element but not the CfiA allele or gene context. CONCLUSION: The phylogeny of cfiA-positive B. fragilis isolates causing human diseases was diverse and overlaped with those from human and animal carriage.


Subject(s)
Bacterial Infections , Bacteroides Infections , Alleles , Animals , Anti-Bacterial Agents , Bacterial Proteins/genetics , Bacteroides fragilis/genetics , Genomics , Humans , Microbial Sensitivity Tests , beta-Lactamases/genetics
6.
Int J Med Microbiol ; 311(8): 151543, 2021 Dec.
Article in English | MEDLINE | ID: mdl-34864352

ABSTRACT

Pneumococcal conjugate vaccines (PCVs) successfully decreased the incidence of invasive pneumococcal disease in children. However, many countries have reported serotype replacement and a rebound in diseases from non-vaccine serotypes. Here, we report the genomic investigation of a Streptococcus pneumoniae strain M215 that caused severe meningoencephalitis in an infant in 2019. The strain was assigned to serotype 24F using the bioinformatic pipeline SeroBA and pneumococcal type specific anti-sera. The strain was resistant to cotrimoxazole from mutations in both folA and folP genes. It was susceptible to penicillin and other non-ß-lactam antibiotics. Phylogenetically, it belongs to Global Pneumococcal Sequence Cluster (GPSC) 6 and multi-locus sequence type 162. A total of 38 virulence genes were detected in the genome of M215. Upon comparison of the profile of virulence genes, GPSC6 but not non-GPSC6 strains of serotype 24F and related serotypes were found to possess the major virulence determinant, pilus islet-1, comprising genes encoding sortases (srtB, srtC, srtD), pilus proteins (rrgA, rrgB and rrgC) and one transcriptional regulator (rlrA), which was previously described to be characteristic feature of international clones in the pre-PCV era. In our locality, this represented the first detection of serotype 24F and GPSC6/ST162 causing serious pneumococcal disease. The emergence of the non-vaccine serotype 24F GPSC6/ST162 lineage with molecular feature of high virulence is concerning and emphasizes the need for full characterization of strains causing severe disease.


Subject(s)
Meningoencephalitis , Streptococcus pneumoniae , Child , Genomics , Hong Kong , Humans , Serogroup , Streptococcus pneumoniae/genetics
7.
Front Microbiol ; 12: 704552, 2021.
Article in English | MEDLINE | ID: mdl-34421864

ABSTRACT

Oxacillin resistance mediated by mecA in Staphylococcus lugdunensis is emerging in some geographic areas. We evaluated cefoxitin disk diffusion (DD) and a new oxacillin agar (supplemented with 2 µg/ml oxacillin and 2% sodium chloride) screen for the detection of mecA-mediated resistance in S. lugdunensis. A total of 300 consecutive, non-duplicated clinical S. lugdunensis isolates from diverse sources in Hong Kong in 2019 were tested. The categorical agreement and errors obtained between cefoxitin DD test, oxacillin agar screen and mecA PCR were analyzed. Isolates with discordant results were further tested by MIC, penicillin binding protein 2a (PBP2a) assays, population analysis and molecular typing. PCR showed that 62 isolates were mecA-positive and 238 isolates were mecA-negative. For cefoxitin DD results interpreted using S. aureus/S. lugdunensis breakpoints, the categorical agreement (CA) for two brands of Muller-Hinton agars, MH-II (Becton Dickinson) and MH-E (bioMérieux) were both 96.0%; MEs were both 0%; and VMEs were 19.4 and 12.9%, respectively. The new oxacillin agar reliably differentiated mecA-positive and mecA-negative isolates (100% CA) without any ME or VME results. The 8 isolates with false susceptibility in the cefoxitin DD testing had cefoxitin and oxacillin MICs in the susceptible range. The isolates showed heterogeneous oxacillin resistance with resistant subpopulations at low frequencies. All had positive PBP2a results and were typed as sequence type 27/SCCmec V. The findings highlight the inability of cefoxitin DD and MIC tests for reliable detection of some mecA-positive S. lugdunensis isolates.

8.
J Glob Antimicrob Resist ; 20: 260-265, 2020 03.
Article in English | MEDLINE | ID: mdl-31493529

ABSTRACT

OBJECTIVES: This study evaluated disc diffusion tests and agar screening for detecting mecA-mediated oxacillin resistance in Staphylococcus lugdunensis (S. lugdunensis). METHODS: Staphylococcus lugdunensis isolates (n = 179) from diverse sources in Hong Kong during 1998-2018 were investigated by disc diffusion tests (cefoxitin and oxacillin) and inoculation onto oxacillin (1 µg/mL and 2 µg/mL) and chromID methicillin-resistant Staphylococcus aureus (MRSA) agars. The results were compared with mecA PCR as the reference. Isolates with discordant results were further tested by MIC and penicillin-binding protein 2a (PBP2a) assays. RESULTS: Cefoxitin and oxacillin zone diameters were not distributed in ways that allowed reliable division of the mecA-positive (n = 52) and mecA-negative (n = 127) isolates. On applying the 2019 Clinical Laboratory Standards Institute (CLSI) M100 breakpoints for cefoxitin disc results, there was 88% categorical agreement (CA) and 40% very major error (VME). Screening using 2 µg/mL oxacillin agar reliably differentiated mecA-positive and mecA-negative isolates (100% CA) without any major error (ME) or VME results. The performance of screening using 1 µg/mL oxacillin agar or ChromID MRSA agar was variable (74-89% CA, 0-38% ME and 0-37% VME). The mecA-positive isolates (n = 21) that could not be detected by the cefoxitin disc test were further characterised. The cefoxitin MIC for all 21 isolates was ≤4 µg/mL. Twenty isolates had an oxacillin MIC of 1-2 µg/mL and one had an oxacillin MIC of 4 µg/mL. All had positive PBP2a results and were typed as clonal cluster 27/SCCmec V. CONCLUSIONS: These findings highlight the need to evaluate phenotypic methods using mecA-positive S. lugdunensis with different oxacillin resistance phenotypes.


Subject(s)
Bacterial Proteins/genetics , Cefoxitin/pharmacology , Methicillin Resistance , Staphylococcal Infections/microbiology , Staphylococcus lugdunensis/classification , Agar , Bacterial Load , Carrier State/microbiology , Cefoxitin/therapeutic use , Disk Diffusion Antimicrobial Tests , Humans , Microbial Sensitivity Tests , Oxacillin/pharmacology , Phenotype , Staphylococcal Infections/drug therapy , Staphylococcus lugdunensis/drug effects , Staphylococcus lugdunensis/growth & development
9.
J Med Microbiol ; 68(9): 1367-1372, 2019 Sep.
Article in English | MEDLINE | ID: mdl-31329093

ABSTRACT

Methicillin-resistant Staphylococcus lugdunensis (MRSL) is increasingly recognized in healthcare and community settings. To obtain a better understanding of the emergence of MRSL, this study characterized the structure and content of the SCCmec elements harboured by 36 MRSL isolates obtained from diverse sources in Hong Kong from 2008 to 2017. The isolates were investigated by whole-genome sequencing. SCCmec types and subtypes were assigned according to the guidelines from the International Working Group on the Classification of Staphylococcal Cassette Chromosome Elements. The sequence type (ST)-SCCmec combinations in the 36 MRSL isolates were as follows: ST3-SCCmec IV (n=2), ST3-SCCmec V (n=28), ST27-SCCmec V (n=5) and ST42-SCCmec V (n=1). The two SCCmec IV elements were highly similar to the SCCmec IV element harboured by the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain, JCSC6668. The J3-mec complex-J2 regions in the SCCmec V elements were highly similar to the corresponding regions in the CA-MRSA strains PM1 (n=13) or WIS (n=21). Based on the J1 to J3 sequences, the SCCmec V elements can be categorized into nine different subtypes. Our findings highlight the diversified structures of SCCmec elements among MRSL strains and their close relationship with SCCmec elements harboured by CA-MRSA.


Subject(s)
Chromosomes, Bacterial/genetics , Community-Acquired Infections/microbiology , Genes, Bacterial/genetics , Methicillin-Resistant Staphylococcus aureus/genetics , Staphylococcal Infections/microbiology , Staphylococcus lugdunensis/genetics , Anti-Bacterial Agents/pharmacology , Community-Acquired Infections/epidemiology , DNA, Bacterial/genetics , Genome, Bacterial/genetics , Hong Kong/epidemiology , Humans , Methicillin-Resistant Staphylococcus aureus/classification , Methicillin-Resistant Staphylococcus aureus/drug effects , Methicillin-Resistant Staphylococcus aureus/isolation & purification , Microbial Sensitivity Tests , Molecular Epidemiology , Sequence Analysis, DNA , Staphylococcal Infections/epidemiology , Students, Medical
10.
Int J Med Microbiol ; 309(5): 270-273, 2019 Jul.
Article in English | MEDLINE | ID: mdl-31113737

ABSTRACT

In 2017, we identified a Clostridium difficile strain HKCD4 that caused community-acquired fulminant colitis in a previously healthy child. Phylogenetically, it belonged to clade 2, sequence type 67 and was resistant to fluoroquinolone and tetracycline. The strain was pathogenicity locus and binary toxin positive. It has a mutation in the trehalose repressor treR leading to the L172I substitution that was previously reported in the epidemic ribotype 027 lineage. HKCD4 has a tcdB sequence that shared very high identities with 3 highly virulent reference strains. It has a CpG depleted genome that is characteristic of hypervirulent C. difficile. The emergence of ST67 lineage with molecular feature of hypervirulence in the community is concerning and emphasizes the need for full characterization of strains causing severe disease in patients without classical risk factors.


Subject(s)
Clostridioides difficile/genetics , Clostridioides difficile/pathogenicity , Colitis/microbiology , Cross Infection/microbiology , Genome, Bacterial , Bacterial Proteins/genetics , Child , Clostridium Infections/diagnosis , Clostridium Infections/microbiology , Colon/diagnostic imaging , Colon/microbiology , Female , Genomics , Hong Kong , Humans , Ribotyping , Tomography, X-Ray Computed , Virulence
11.
Access Microbiol ; 1(10): e000072, 2019.
Article in English | MEDLINE | ID: mdl-32975531

ABSTRACT

[This corrects the article DOI: 10.1099/acmi.ac2019.po0040.].

12.
Front Microbiol ; 9: 2272, 2018.
Article in English | MEDLINE | ID: mdl-30294321

ABSTRACT

The emergence of New Delhi metallo-ß-lactamase (NDM) in common enterobacterial species is a major concern for healthcare. Early reports have revealed that the spread of NDM involved diverse and heterogeneous plasmids. Recently, the involvement of a rare, IncX3 subtype plasmid has been increasingly recognized. Here, we studied the prevalence of IncX plasmid subtypes in 198 carbapenem-resistant Enterobacteriaceae, originating from a territory-wide active surveillance in Hong Kong in 2016. The complete sequences and biological features of the bla NDM-carrying plasmids were investigated. A total of 62 NDM-type, 21 OXA-48 type, 14 IMP-type, 8 KPC-type, 4 IMI-type producers, and 89 non-carbapenemase-producers were tested for presence of IncX subtypes. IncX3 (n = 60) was the most common subtype, followed by IncX4 (n = 6) and IncX1 (n = 2). The prevalence of IncX3 subtype in isolates producing NDM, other carbapenemase types and non-carbapenemase producers were 75.8, 21.3, and 3.4%, respectively (P < 0.001). An IncX3 plasmid (size ∼50 kb) was confirmed to carry bla NDM in 47 isolates of different enterobacterial species. Thirteen IncX3 plasmids originating from six healthcare regions in Hong Kong were completely sequenced. The results showed that the IncX3 plasmids carrying bla NDM share a high degree of sequence identity with a previously reported plasmid, pNDM-HN380 (GenBank accession JX104760), over the backbone and genetic load regions. A blast search further revealed the occurrence of identical or nearly identical IncX3 plasmids carrying bla NDM in other part of China, Korea, Myanmar, India, Oman, Kuwait, Italy, and Canada. Two IncX3 carrying bla NDM were investigated further. Conjugation experiments demonstrated that the IncX3 plasmids could be efficiently transferred to multiple enterobacterial species at frequencies that are comparable or higher than the epidemic IncFII plasmid carrying bla CTX-M (pHK01). In addition, efficient transfer of the NDM plasmids occurred over a range of temperatures. In conclusion, this study demonstrated the important role played by IncX3 in the dissemination of NDM and the occurrence of pNDM-HN380-like plasmids in geographically widespread areas. The high mobility of IncX3 plasmid across different enterobacterial species highlights the ability of this plasmid replicon to be an important vehicle in worldwide dissemination of NDM.

13.
Article in English | MEDLINE | ID: mdl-29311058

ABSTRACT

Six imported pigs originating from Guangdong, Henan, and Hunan provinces in China during October 2015 to February 2017 were cultured and found to be positive for meropenem-resistant Escherichia coli The samples yielded 9 E. coli isolates of diverse sequence types carrying blaNDM-5 on IncX3 (8 isolates from 5 farms) or IncFII (1 isolate from 1 farm) plasmids. The mcr-1 gene was coharbored by 4 isolates. The IncX3 plasmids (∼46 kb) carrying blaNDM-5 were identical or nearly identical to each other.


Subject(s)
Escherichia coli Infections/veterinary , Escherichia coli/genetics , Plasmids/chemistry , beta-Lactamases/genetics , Animal Husbandry , Animals , Anti-Bacterial Agents/pharmacology , Carbapenems/pharmacology , China/epidemiology , Colistin/pharmacology , Drug Resistance, Multiple, Bacterial , Escherichia coli/drug effects , Escherichia coli/enzymology , Escherichia coli/isolation & purification , Escherichia coli Infections/drug therapy , Escherichia coli Infections/epidemiology , Escherichia coli Infections/microbiology , Escherichia coli Proteins/genetics , Escherichia coli Proteins/metabolism , Farms , Gene Expression , Plasmids/metabolism , Replicon , Swine , beta-Lactamases/metabolism
15.
J Clin Pathol ; 70(10): 868-873, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28360188

ABSTRACT

AIMS: Carbapenem resistance in Bacteroides fragilis is emerging and is mainly attributed to insertion sequence (IS)-mediated activation of the carbapenemase gene cfiA. We investigated the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) and the CarbaNP assay for the rapid identification of these strains. METHODS: This study used the Bruker MALDI Biotype system and the mass spectra models generated by 20 B. fragilis reference strains (10 cfiA-positive and 10 cfiA-negative) in the ClinProTools software to identify 404 B. fragilis (71 cfiA-positive and 333 cfiA-negative) clinical isolates. The ability of the CarbaNP assay to detect IS-mediated activation of the cfiA gene was assessed and the results obtained by molecular analysis were used as reference methods. RESULTS: The support vector machine model generated by ClinProTools was found to be the most reliable algorithm for differentiation of cfiA-positive and cfiA-negative B. fragilis subgroups. Using the direct transfer method, all but one cfiA-negative isolates were correctly identified to the two subgroups by the model. The correct identification of the cfiA-negative isolate was obtained upon retesting by the extraction method. Of the 81 cfiA-positive isolates, PCR and sequencing showed that 30 had an IS element providing the promoter for activation of cfiA. With regard to the presence of the IS element, the CarbaNP test in the cfiA upstream region had 100% sensitivity, 80.4% specificity, 75.0% positive predictive value and 100% negative predictive value. CONCLUSIONS: The combination of MALDI-TOF MS and the CarbaNP assay can be applied in diagnostic clinical laboratory for rapid identification of B. fragilis with IS element-activated cfiA gene.


Subject(s)
Bacterial Proteins/analysis , Bacteriological Techniques , Bacteroides fragilis/enzymology , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods , beta-Lactamases/analysis , Drug Resistance, Microbial/physiology , Microbial Sensitivity Tests , Polymerase Chain Reaction , Sensitivity and Specificity , Support Vector Machine
16.
Anaerobe ; 47: 51-56, 2017 Oct.
Article in English | MEDLINE | ID: mdl-28414107

ABSTRACT

This study used a recently developed EUCAST disc diffusion method to measure the susceptibility of 741 B. fragilis group isolates to six antibiotics. Isolates nonsusceptible to imipenem and metronidazole by the disc method were further investigated by E-test. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR assays and 16S rRNA sequencing. The most common species were B. fragilis (n = 424, including 81 division II and 343 division I isolates), B. thetaiotaomicron (n = 111), B. ovatus (n = 53) and B. vulgatus (n = 46). Overall, metronidazole following by imipenem and amoxicillin-clavulanate are the most active agents with over 90% of all the isolates being susceptible at the tentative disc breakpoints. Susceptibility rates for moxifloxacin (69.5%), piperacillin-tazobactam (58.2%) and clindamycin (37.2%) were much lower. Metronidazole is the only agent active against >90% of B. fragilis, non-fragilis Bacteroides and Parabacteroides isolates. With the exception of B. fragilis division II, imipenem was active against 88.0%-98.3% of isolates of the other species. Susceptibility rates for clindamycin (14.4%-54.3%) and moxifloxacin (33.3%-80.6%) were low across all species and many isolates had no inhibition zone around the discs. E-test testing confirmed 8.2% (61/741) and 1.6% (12/741) isolates as nonsusceptible to imipenem and metronidazole, respectively with B. fragilis and B. thetaoiotaomicron accounting for a large share of the observed resistance to both agents. Two imipenem-resistant and one metronidazole-resistant B. dorei were misidentified as B. vulgatus by MALDI-TOF MS. These data highlights the importance anaerobic susceptibility testing in clinical laboratories to guide therapy.


Subject(s)
Anti-Bacterial Agents/pharmacology , Bacteroides/drug effects , Disk Diffusion Antimicrobial Tests , Bacteroides/classification , Bacteroides/isolation & purification , DNA, Bacterial/chemistry , DNA, Bacterial/genetics , DNA, Ribosomal/chemistry , DNA, Ribosomal/genetics , Drug Resistance, Bacterial , Hong Kong , Humans , Polymerase Chain Reaction , RNA, Ribosomal, 16S/genetics , Sequence Analysis, DNA , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
J Antimicrob Chemother ; 72(1): 99-103, 2017 01.
Article in English | MEDLINE | ID: mdl-27609049

ABSTRACT

OBJECTIVES: To characterize blaIMP-4-carrying plasmids originating from inpatients in Hong Kong. METHODS: Sixteen blaIMP-4-carrying plasmids identified among Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae, two Citrobacter freundii and one Enterobacter cloacae) recovered from 15 patients were characterized. The isolates, collected during January 2010 to December 2013, were retrospectively investigated by plasmid sequencing, molecular and fitness studies. RESULTS: The blaIMP-4-carrying plasmids belonged to the IncN ST7 lineage (∼50 kb). Twelve of the 16 plasmids were epidemiologically linked to seven different regions in China. Alignment of the complete plasmid sequences showed identical plasmid backbones and two highly similar resistance regions, each carrying one of two resistance genes (blaIMP-4 and qnrS1). The blaIMP-4 was detected in a class 1 integron (containing blaIMP-4 and intron Kl.pn.13) that is part of an IS6100-IS26 transposon-like structure. The nine E. coli carrying the epidemic plasmid belonged to multiple multilocus STs (six ST542, one ST131, one ST657 and one ST3177). Fitness assays performed on E. coli J53 recipients showed that the presence of the epidemic plasmid did not have a significant biological cost. CONCLUSIONS: This study identified a blaIMP-4-carrying IncN ST7 plasmid disseminated among multiple enterobacterial species originating from patients with epidemiological links to different regions in China.


Subject(s)
Cross Infection/microbiology , Enterobacteriaceae Infections/microbiology , Enterobacteriaceae/enzymology , Plasmids/analysis , Topography, Medical , Aged , Aged, 80 and over , Cross Infection/epidemiology , Enterobacteriaceae/genetics , Enterobacteriaceae/isolation & purification , Enterobacteriaceae Infections/epidemiology , Female , Gene Transfer, Horizontal , Hong Kong/epidemiology , Humans , Infant , Male , Middle Aged , Plasmids/classification , Retrospective Studies , Sequence Alignment , Sequence Analysis, DNA
19.
J Clin Microbiol ; 55(2): 384-390, 2017 02.
Article in English | MEDLINE | ID: mdl-27852672

ABSTRACT

A novel Bacteroides fragilis selective (BFS) medium, consisting of a brain heart infusion agar base supplemented with yeast extract, cysteine hydrochloride, bile salts, vitamin K, hemin, glucose, esculin, ferric ammonium citrate, bromothymol blue, gentamicin, kanamycin, and novobiocin, was evaluated. When BFS agar was tested with a collection of 303 bacteria of different genera, it allowed the growth of B. fragilis as large yellow colonies, with blackening of the medium after 48 h of anaerobic incubation, while the growth of most other anaerobes, facultative anaerobes, and aerobes was inhibited. In a prospective comparison of BFS agar with a routinely used medium (neomycin blood agar) in 1,209 clinical specimens, 60 B. fragilis bacteria were detected on BFS agar while 46 were detected on the routine agar (McNemar's test, P = 0.008). In conclusion, this novel medium may be added to improve the recovery of B. fragilis in clinical specimens and to facilitate surveillance of antimicrobial-resistant strains.


Subject(s)
Bacteriological Techniques/methods , Bacteroides Infections/diagnosis , Bacteroides fragilis/growth & development , Bacteroides fragilis/isolation & purification , Culture Media/chemistry , Anaerobiosis , Bacteroides Infections/microbiology , Humans , Selection, Genetic
20.
Antimicrob Agents Chemother ; 60(10): 6411-4, 2016 10.
Article in English | MEDLINE | ID: mdl-27503649

ABSTRACT

Of 137 Staphylococcus lugdunensis isolates collected from two nephrology centers in Hong Kong, 10 (7.3%) and 3 (2.2%) isolates had high-level and low-level mupirocin resistance, respectively. Isolates with high-level resistance contained the plasmid-mediated ileS2 gene, while isolates with low-level resistance contained the mutation V588F within the chromosomal ileS gene. All but one of the ileS2-positive isolates belong to the predominating clone HKU1. Plasmids carrying the ileS2 gene were mosaic and also cocarry multiple other resistance determinants.


Subject(s)
Drug Resistance, Multiple, Bacterial/genetics , Genes, Bacterial , Staphylococcus lugdunensis/drug effects , Staphylococcus lugdunensis/genetics , Drug Resistance, Multiple, Bacterial/drug effects , Hong Kong , Humans , Methicillin Resistance/genetics , Microbial Sensitivity Tests , Mupirocin/pharmacology , Mupirocin/therapeutic use , Mutation , Plasmids , Staphylococcus lugdunensis/isolation & purification
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