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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.

ABSTRACT: Objectives: Enterobacteriaceae are common pathogens causing bloodstream infection (BSI) in sub-Saharan Africa and frequently express third-generation cephalosporin (3GC) resistance; however, the impact of 3GC resistance on clinical outcomes is rarely studied. Methods: We conducted a single-site prospective cohort study at Tygerberg Hospital, Cape Town, South Africa to examine the feasibility of measuring impacts of 3GC resistance in Enterobacteriaceae BSI. We included patients with 3GC-susceptible and 3GC-resistant BSIs and matched each BSI patient to two uninfected patients. We determined the concordance of initial antibiotic treatment with the corresponding isolate's susceptibility profile. We performed exploratory impact analysis using multivariable regression models. Results: Between 1 June 2017 and 31 January 2018, we matched 177 Enterobacteriaceae BSI patients to 347 uninfected patients. Among these BSIs, 35% were phenotypically 3GC resistant. Parameters describing clinical comorbidity showed strong associations with mortality. We found that 18% of 3GC-R and 3% of 3GC-S BSI patient received non-concordant initial therapy. In multivariable Cox regression, we found a mortality impact over their matched patients for both 3GC-R (cause-specific hazard ratio 23.77; 95% CI 5.12–110.3) and 3GC-S (HR 7.49; 95%CI 3.08–18.19) BSI. There was a nonsignificant ratio of these ratios (HR 3.18; 95% CI 0.54–18.70), limited by the small sample size. Conclusion: This form of impact estimation was feasible in one hospital in South Africa where 3GC-R status was associated with non-concordant initial antibiotic treatment. There was a possible increase in mortality among individuals with 3GC-resistant Enterobacteriaceae, but with broad confidence intervals. These analytical approaches could be applied to larger datasets to improve precision of estimates.

ABSTRACT: Objectives: This study aimed to develop and evaluate a novel air-dried high-resolution melt (HRM) assay to detect eight major extended-spectrum β-lactamase (ESBL) (blaSHV and blaCTX-M groups 1 and 9) and carbapenemase (blaNDM, blaIMP, blaKPC, blaVIM and blaOXA-48-like) genes that confer resistance to cephalosporins and carbapenems. Methods: The assay was evaluated using 439 DNA samples extracted from bacterial isolates from Nepal, Malawi and the UK and 390 clinical isolates from Nepal with known antimicrobial susceptibility. Assay reproducibility was evaluated across five different real-time quantitative PCR (qPCR) instruments [Rotor-Gene® Q, QuantStudioTM 5, CFX96, LightCycler® 480 and Magnetic Induction Cycler (Mic)]. Assay stability was also assessed under different storage temperatures (6.2 ± 0.9°C, 20.4 ± 0.7°C and 29.7 ± 1.4°C) at six time points over 8 months. Results: The sensitivity and specificity (with 95% confidence intervals) for detecting ESBL and carbapenemase genes was 94.7% (92.5–96.5%) and 99.2% (98.8–99.5%) compared with the reference gel-based PCR and sequencing and 98.3% (97.0–99.3%) and 98.5% (98.0–98.9%) compared with the original HRM wet PCR mix format. Overall agreement was 91.1% (90.0–92.9%) when predicting phenotypic resistance to cefotaxime and meropenem among Enterobacteriaceae isolates. We observed almost perfect inter-machine reproducibility of the air-dried HRM assay, and no loss of sensitivity occurred under all storage conditions and time points. Conclusion: We present a ready-to-use air-dried HRM PCR assay that offers an easy, thermostable, fast and accurate tool for the detection of ESBL and carbapenemase genes in DNA samples to improve antimicrobial resistance detection.

ABSTRACT: Objectives: Fluoroquinolone (FQ)- and third-generation cephalosporin-resistant Escherichia coli are increasing in Japan. In the early 2000s, the FQ-resistant E. coli clone ST131 increased in clinical settings worldwide. It frequently produces extended-spectrum β-lactamases (ESBLs) such as CTX-M. This study aimed to explore the characteristics of FQ-resistant E. coli isolated in Japan during 2008–2009 and 2020. Methods: We compared FQ-resistant E. coli clinical isolates from urine samples collected in 2020 (151 isolates) with a FQ-resistant E. coli collection isolated in 2008–2009 (42 isolates). Identification of E. coli ST131 clades and blaCTX-M were determined by multiplex PCR. Sequence types of non-ST131 isolates were determined by whole-genome sequencing. Results: Although the prevalence of ST131 was comparable in 2020 (74.2%) and 2008–2009 (78.6%), the subclades differed during the two time periods (C1-nM27: 40.2% in 2008–2009 vs. 78.8% in 2020; C1-M27: 32.1% in 2008–2009 vs. 9.1% in 2020). The incidence of blaCTX-M among ST131 isolates increased from 27.3% in 2008–2009 to 64.3% in 2020. blaCTX-M was found in 80.6% and 93.8% of C1-M27 and C2 in 2020, respectively, and blaCTX-M possession in C1-nM27 increased from 19.2% in 2008–2009 to 40% in 2020. FQ-resistant ST1193 was detected only in 2020 (17.9% of 151 isolates, of which 14.8% possessed blaCTX-M). Conclusion: Increased resistance of E. coli to FQs and third-generation cephalosporins in Japan can be attributed to the accumulation of blaCTX-M in C1-nM27 and the increase of C1-M27 and C2 clades with high blaCTX-M possession, alongside the spread of ST1193.

ABSTRACT: Objectives: Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are an increasingly significant cause of hospital- and community-acquired infections worldwide. Whereas several reports have highlighted their increased prevalence also in North African countries, genomic data on isolates associated with these infections are still scarce. This study aimed to provide data on ESBL-producing E. coli isolates from patients with extraintestinal infections at the Military Teaching Hospital Mohamed V of Rabat, Morocco. Methods: Whole-genome sequencing was carried out on 18 ESBL-producing extraintestinal pathogenic E. coli (ExPEC) isolates for analysis of phylogenomic evolution, virulence factors and antimicrobial resistance genes. Data were compared with ExPEC lineages from several surrounding countries using multilocus sequence typing (MLST) and single nucleotide polymorphism-based phylogenetic approaches. Results: The majority of E. coli isolates were ST131 (n = 15), followed by ST617 (n = 2) and a novel sequence type (ST10703) that is closely related to the pandemic ST405 clone. All ST131 isolates belonged to the O25b-ST131 pandemic clone. They harboured more virulence genes than their non-ST131 counterparts. IncF plasmid replicons and the blaCTX-M-15 β-lactamase gene were identified in all isolates. No ESBL-producing E. coli isolates carried any known carbapenemase gene. Conclusion: Our findings underscore the pre-eminence of ST131 as the major factor driving the expansion of ExPEC in the Rabat region while highlighting the potential links with isolates circulating in other neighbouring countries.

ABSTRACT: Objectives: The aim of this study was to investigate the genetic context of expanded-spectrum β-lactam resistance in a Klebsiella pneumoniae strain causing a hard-to-treat nasal infection in a domestic cat. Methods: A K. pneumoniae isolate was recovered from a 4-year-old male cat hospitalised in a veterinary hospital in Paraíba, Northeastern Brazil. Following phenotypic confirmation of multidrug resistance by the disk diffusion method, the genome was sequenced using an Illumina MiSeq system. Multilocus sequence typing (MLST) and structural features related to antimicrobial resistance were determined by downstream bioinformatics analyses. Results: The strain was confirmed as sequence type 273 (ST273) K. pneumoniae harbouring a variety of genes conferring antimicrobial resistance to phenicols tetracyclines, aminoglycosides, β-lactams, fosfomycin, sulfonamides and quinolones. Two plasmids were identified. Plasmid p114PB_I co-harboured a set of plasmid-borne resistance genes [blaCTX-M−15, blaTEM−1, qnrS1, tetD, tetR, sul2, aph(6)-Id, aph(3′') and cat2]. Notably, the multiresistance region was characterised as a chimeric plasmid structure sharing high sequence homology with several plasmids from Enterobacteriaceae. The second plasmid (p114PB_II) was characterised as a plasmid present in many genomes belonging to K. pneumoniae. Conclusion: The genetic context of the plasmid sequences harboured by a veterinary pathogenic K. pneumoniae isolate reveals the high complexity of horizontal gene transfer mechanisms in the acquisition of antimicrobial resistance genes. The emergence, dissemination and evolution of antimicrobial resistance must be investigated from a One Health perspective.

ABSTRACT: Objectives: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have become a cause for great concern. Although some studies have reported the prevalence of ESBL-producing bacteria and ESBL-encoding genes in horses worldwide, the genetic structure surrounding the ESBL gene has not been analysed in detail. In the present study, we isolated two ESBL-producing Escherichia coli strains from diseased racehorses in Japan and demonstrated the mechanisms underlying the acquisition of their antimicrobial resistance (AMR) genes. Methods: Two ESBL-producing E. coli strains (E148 and E189) were isolated from the heart and liver of horses with endocarditis and sepsis in 2014 and 2016, respectively, in Japan. Complete genomic sequences of the two strains were analysed using a PacBio RSII sequencer. Antimicrobial susceptibility testing was performed by the agar dilution method. Results: The two isolates possessed a chromosomal AMR gene cluster containing blaCTX-M-1 that was similar to the pEQ1 plasmid found in E. coli isolated from a racehorse in the Czech Republic. In one of the two strains, tandem duplication of the 16-kb region containing blaCTX-M-1 and a class 1 integron, which occurred via IS26-mediated recombination, increased minimum inhibitory concentrations (MICs) associated with the duplicated AMR genes. Conclusion: Chromosomal blaCTX-M-1 possibly derived from the pEQ1 or pEQ1-like plasmid was found in Japanese equine E. coli isolates. In Japanese strains, many AMR genes containing blaCTX-M-1 and the class 1 integron are highly accumulated in one region on the chromosome, and the AMR of E. coli was enhanced via the IS26-mediated duplication of the AMR gene cluster.

Objectives: In this study, the genetic diversity, phylogenetic grouping, antimicrobial resistance and extended-spectrum β-lactamase (ESBL) types of Escherichia coli isolates from chickens, dogs, pigs and yaks in six prefectures of Gansu and Qinghai Provinces, China, were investigated. Methods: E. coli was isolated from diarrhoeic and healthy faecal samples. Multilocus sequence typing (MLST), phylogenetic grouping, antimicrobial resistance and ESBL profiles were investigated. Results: A total of 142 MLST sequence types (STs) were identified from 400 E. coli isolates. eBURST clustering analysis resolved the 142 STs into 19 clonal complexes (CCs) and 67 singletons. PCR phylogenetic typing determined the isolation rate of potentially pathogenic B2/D group isolates among all E. coli to be 12.5% from healthy animal samples and 17.5% from diarrhoeic samples. Antimicrobial susceptibility testing revealed 78 antimicrobial resistance patterns. E. coli resistance rates were highest to doxycycline, ampicillin and tetracycline, whereas polymyxin B and meropenem had the lowest resistance rates. All polymyxin B-resistant E. coli isolates were positive for the mcr-1 gene. A total of 62 ESBL-producing isolates were identified. The ESBL prevalence was 55.0% in diarrhoeic samplings and 5.6% in healthy animals. TEM (82.3%) was the predominant ESBL type, followed by CTM (43.5%) and SHV (19.4%). Conclusion: E. coli isolates in the study area have a high diversity of genetic and antimicrobial resistance patterns but a relatively low isolation rate of potentially pathogenic phylogroups. However, the somewhat high isolation rate of multidrug-resistant E. coli, particularly ESBL-producing isolates, requires continual surveillance of E. coli from animals in these areas.

Objectives: Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria. Methods: ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for blaKPC, blaCTX-M, blaCMY-2, blaNDM, blaVIM, blaIMP, blaOXA-181 and blaOXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing. Results: The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried blaNDM (n = 30; 62.5%), blaNDM + blaOXA-181 (n = 10; 20.8%), blaOXA-181 (n = 2; 4.2%) and blaNDM + blaOXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae. Conclusion: Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with blaNDM. Genotyping suggested that the observed clones possibly originated from Southeast Asia.

Objectives: Extended-spectrum β-lactamase/AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-E. coli) are common in developing countries and travellers represent potential reservoirs for their dissemination. The aim of this study was to quantify cefotaxime (CTX)-resistant E. coli harboured by travellers to Vietnam and to conduct a follow-up study. Methods: In total, 19 travellers and 34 travel events were investigated. After confirming that travellers were not colonised with CTX-resistant E. coli before travel, 15 travellers and 20 travel events were studied to quantify travellers harbouring CTX-resistant E. coli after travel. A stool sample (0.1 g) in 10 mL of PBS was diluted and plated. Selected colonies were identified, genotyped and further verified by pulsed-field gel electrophoresis (PFGE). Results: After travel, travellers harboured an average of 3.6 × 107 CFU/g faeces of CTX-resistant E. coli, which continued to be detected for an average of 14 weeks. In the follow-up study, travellers from two travel events had ESBL-E. coli for 12 months. Multiplex PCR showed blaCTX-M-55 and blaCTX-M-27, with replicon types FIA and F, and FIB and F, respectively. PFGE showed that two travellers harboured a single clonal ESBL-E. coli strain for 12 months. By PFGE, the follow-up study showed that a single type of ESBL/AmpC-E. coli was only detected in individuals living in Japan. Moreover, the same clonal ESBL-E. coli isolate was detected in a group that travelled to Ho Chi Minh City. Conclusion: ESBL/AmpC-E. coli colonised the gut of travellers to Vietnam with CTX-resistant E. coli (>107 CFU/g faeces) lasting for 14 weeks.

Objectives: Escherichia coli is one of the most prevalent bacterial pathogens causing urinary tract infections (UTIs). The increasing dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli in the community renders clinical treatment difficult. Here we report the complete genome sequence of a blaCTX-M-15-carrying E. coli strain (EC28) isolated from a urine sample of a female outpatient with UTI. Methods: The whole genome sequence of E. coli strain EC28 was determined using both a MinION™ sequencer and an Illumina NovaSeq 6000 system. De novo hybrid assembly of the short Illumina reads and long MinION reads was performed using Unicycler. Multilocus sequence typing (MLST), antimicrobial resistance genes (ARGs), plasmid replicons and phylogenetic relationship were analysed using the BacWGSTdb database. Results: The genome sequence of E. coli strain EC28 consists of six contigs comprising 5260 133 bp, including one chromosome and five plasmids. According to MLST analysis, EC28 belongs to ST429. Six ARGs were identified, including blaCTX-M-15 located on a 63,295-bp IncI2-type plasmid. Twenty-three phylogenetically related E. coli ST429 strains were identified in the NCBI GenBank database, none recovered from China. The closest relative was an isolate recovered from Japan in 2009 that differed by 146 cgMLST loci. Conclusion: Here we report the first complete genome sequence of an ESBL-producing E. coli ST429 strain isolated from the community in China. The genome sequence of EC28 can be used as a reference sequence for comparative analysis, including acquisition and mobilisation of blaCTX-M genes in community-acquired E. coli strains.

Objectives: Enterobacteriaceae are common pathogens causing bloodstream infection (BSI) in sub-Saharan Africa and frequently express third-generation cephalosporin (3GC) resistance; however, the impact of 3GC resistance on clinical outcomes is rarely studied., Methods: We conducted a single-site prospective cohort study at Tygerberg Hospital, Cape Town, South Africa to examine the feasibility of measuring impacts of 3GC resistance in Enterobacteriaceae BSI. We included patients with 3GC-susceptible and 3GC-resistant BSIs and matched each BSI patient to two uninfected patients. We determined the concordance of initial antibiotic treatment with the corresponding isolate's susceptibility profile. We performed exploratory impact analysis using multivariable regression models., Results: Between 1 June 2017 and 31 January 2018, we matched 177 Enterobacteriaceae BSI patients to 347 uninfected patients. Among these BSIs, 35% were phenotypically 3GC resistant. Parameters describing clinical comorbidity showed strong associations with mortality. We found that 18% of 3GC-R and 3% of 3GC-S BSI patient received non-concordant initial therapy. In multivariable Cox regression, we found a mortality impact over their matched patients for both 3GC-R (cause-specific hazard ratio 23.77; 95% CI 5.12-110.3) and 3GC-S (HR 7.49; 95%CI 3.08-18.19) BSI. There was a nonsignificant ratio of these ratios (HR 3.18; 95% CI 0.54-18.70), limited by the small sample size., Conclusion: This form of impact estimation was feasible in one hospital in South Africa where 3GC-R status was associated with non-concordant initial antibiotic treatment. There was a possible increase in mortality among individuals with 3GC-resistant Enterobacteriaceae, but with broad confidence intervals. These analytical approaches could be applied to larger datasets to improve precision of estimates., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

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 bla CTX-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 bla CTX-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., Competing Interests: Declaration of Competing Interest None declared., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: The aim of this study was to investigate the genetic context of expanded-spectrum β-lactam resistance in a Klebsiella pneumoniae strain causing a hard-to-treat nasal infection in a domestic cat., Methods: A K. pneumoniae isolate was recovered from a 4-year-old male cat hospitalised in a veterinary hospital in Paraíba, Northeastern Brazil. Following phenotypic confirmation of multidrug resistance by the disk diffusion method, the genome was sequenced using an Illumina MiSeq system. Multilocus sequence typing (MLST) and structural features related to antimicrobial resistance were determined by downstream bioinformatics analyses., Results: The strain was confirmed as sequence type 273 (ST273) K. pneumoniae harbouring a variety of genes conferring antimicrobial resistance to phenicols tetracyclines, aminoglycosides, β-lactams, fosfomycin, sulfonamides and quinolones. Two plasmids were identified. Plasmid p114PB_I co-harboured a set of plasmid-borne resistance genes [bla CTX-M-15 , bla TEM-1 , qnrS1, tetD, tetR, sul2, aph(6)-Id, aph(3'') and cat2]. Notably, the multiresistance region was characterised as a chimeric plasmid structure sharing high sequence homology with several plasmids from Enterobacteriaceae. The second plasmid (p114PB_II) was characterised as a plasmid present in many genomes belonging to K. pneumoniae., Conclusion: The genetic context of the plasmid sequences harboured by a veterinary pathogenic K. pneumoniae isolate reveals the high complexity of horizontal gene transfer mechanisms in the acquisition of antimicrobial resistance genes. The emergence, dissemination and evolution of antimicrobial resistance must be investigated from a One Health perspective., (Copyright © 2022 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: Extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have become a cause for great concern. Although some studies have reported the prevalence of ESBL-producing bacteria and ESBL-encoding genes in horses worldwide, the genetic structure surrounding the ESBL gene has not been analysed in detail. In the present study, we isolated two ESBL-producing Escherichia coli strains from diseased racehorses in Japan and demonstrated the mechanisms underlying the acquisition of their antimicrobial resistance (AMR) genes., Methods: Two ESBL-producing E. coli strains (E148 and E189) were isolated from the heart and liver of horses with endocarditis and sepsis in 2014 and 2016, respectively, in Japan. Complete genomic sequences of the two strains were analysed using a PacBio RSII sequencer. Antimicrobial susceptibility testing was performed by the agar dilution method., Results: The two isolates possessed a chromosomal AMR gene cluster containing bla CTX-M-1 that was similar to the pEQ1 plasmid found in E. coli isolated from a racehorse in the Czech Republic. In one of the two strains, tandem duplication of the 16-kb region containing bla CTX-M-1 and a class 1 integron, which occurred via IS26-mediated recombination, increased minimum inhibitory concentrations (MICs) associated with the duplicated AMR genes., Conclusion: Chromosomal bla CTX-M-1 possibly derived from the pEQ1 or pEQ1-like plasmid was found in Japanese equine E. coli isolates. In Japanese strains, many AMR genes containing bla CTX-M-1 and the class 1 integron are highly accumulated in one region on the chromosome, and the AMR of E. coli was enhanced via the IS26-mediated duplication of the AMR gene cluster., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: Fluoroquinolone (FQ)- and third-generation cephalosporin-resistant Escherichia coli are increasing in Japan. In the early 2000s, the FQ-resistant E. coli clone ST131 increased in clinical settings worldwide. It frequently produces extended-spectrum β-lactamases (ESBLs) such as CTX-M. This study aimed to explore the characteristics of FQ-resistant E. coli isolated in Japan during 2008-2009 and 2020., Methods: We compared FQ-resistant E. coli clinical isolates from urine samples collected in 2020 (151 isolates) with a FQ-resistant E. coli collection isolated in 2008-2009 (42 isolates). Identification of E. coli ST131 clades and bla CTX-M were determined by multiplex PCR. Sequence types of non-ST131 isolates were determined by whole-genome sequencing., Results: Although the prevalence of ST131 was comparable in 2020 (74.2%) and 2008-2009 (78.6%), the subclades differed during the two time periods (C1-nM27: 40.2% in 2008-2009 vs. 78.8% in 2020; C1-M27: 32.1% in 2008-2009 vs. 9.1% in 2020). The incidence of bla CTX-M among ST131 isolates increased from 27.3% in 2008-2009 to 64.3% in 2020. bla CTX-M was found in 80.6% and 93.8% of C1-M27 and C2 in 2020, respectively, and bla CTX-M possession in C1-nM27 increased from 19.2% in 2008-2009 to 40% in 2020. FQ-resistant ST1193 was detected only in 2020 (17.9% of 151 isolates, of which 14.8% possessed bla CTX-M )., Conclusion: Increased resistance of E. coli to FQs and third-generation cephalosporins in Japan can be attributed to the accumulation of bla CTX-M in C1-nM27 and the increase of C1-M27 and C2 clades with high bla CTX-M possession, alongside the spread of ST1193., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: This study aimed to develop and evaluate a novel air-dried high-resolution melt (HRM) assay to detect eight major extended-spectrum β-lactamase (ESBL) (bla SHV and bla CTX-M groups 1 and 9) and carbapenemase (bla NDM , bla IMP , bla KPC , bla VIM and bla OXA-48-like ) genes that confer resistance to cephalosporins and carbapenems., Methods: The assay was evaluated using 439 DNA samples extracted from bacterial isolates from Nepal, Malawi and the UK and 390 clinical isolates from Nepal with known antimicrobial susceptibility. Assay reproducibility was evaluated across five different real-time quantitative PCR (qPCR) instruments [Rotor-Gene® Q, QuantStudio TM 5, CFX96, LightCycler® 480 and Magnetic Induction Cycler (Mic)]. Assay stability was also assessed under different storage temperatures (6.2 ± 0.9°C, 20.4 ± 0.7°C and 29.7 ± 1.4°C) at six time points over 8 months., Results: The sensitivity and specificity (with 95% confidence intervals) for detecting ESBL and carbapenemase genes was 94.7% (92.5-96.5%) and 99.2% (98.8-99.5%) compared with the reference gel-based PCR and sequencing and 98.3% (97.0-99.3%) and 98.5% (98.0-98.9%) compared with the original HRM wet PCR mix format. Overall agreement was 91.1% (90.0-92.9%) when predicting phenotypic resistance to cefotaxime and meropenem among Enterobacteriaceae isolates. We observed almost perfect inter-machine reproducibility of the air-dried HRM assay, and no loss of sensitivity occurred under all storage conditions and time points., Conclusion: We present a ready-to-use air-dried HRM PCR assay that offers an easy, thermostable, fast and accurate tool for the detection of ESBL and carbapenemase genes in DNA samples to improve antimicrobial resistance detection., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli are an increasingly significant cause of hospital- and community-acquired infections worldwide. Whereas several reports have highlighted their increased prevalence also in North African countries, genomic data on isolates associated with these infections are still scarce. This study aimed to provide data on ESBL-producing E. coli isolates from patients with extraintestinal infections at the Military Teaching Hospital Mohamed V of Rabat, Morocco., Methods: Whole-genome sequencing was carried out on 18 ESBL-producing extraintestinal pathogenic E. coli (ExPEC) isolates for analysis of phylogenomic evolution, virulence factors and antimicrobial resistance genes. Data were compared with ExPEC lineages from several surrounding countries using multilocus sequence typing (MLST) and single nucleotide polymorphism-based phylogenetic approaches., Results: The majority of E. coli isolates were ST131 (n = 15), followed by ST617 (n = 2) and a novel sequence type (ST10703) that is closely related to the pandemic ST405 clone. All ST131 isolates belonged to the O25b-ST131 pandemic clone. They harboured more virulence genes than their non-ST131 counterparts. IncF plasmid replicons and the bla CTX-M-15 β-lactamase gene were identified in all isolates. No ESBL-producing E. coli isolates carried any known carbapenemase gene., Conclusion: Our findings underscore the pre-eminence of ST131 as the major factor driving the expansion of ExPEC in the Rabat region while highlighting the potential links with isolates circulating in other neighbouring countries., (Copyright © 2021 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: In this study, the genetic diversity, phylogenetic grouping, antimicrobial resistance and extended-spectrum β-lactamase (ESBL) types of Escherichia coli isolates from chickens, dogs, pigs and yaks in six prefectures of Gansu and Qinghai Provinces, China, were investigated., Methods: E. coli was isolated from diarrhoeic and healthy faecal samples. Multilocus sequence typing (MLST), phylogenetic grouping, antimicrobial resistance and ESBL profiles were investigated., Results: A total of 142 MLST sequence types (STs) were identified from 400 E. coli isolates. eBURST clustering analysis resolved the 142 STs into 19 clonal complexes (CCs) and 67 singletons. PCR phylogenetic typing determined the isolation rate of potentially pathogenic B2/D group isolates among all E. coli to be 12.5% from healthy animal samples and 17.5% from diarrhoeic samples. Antimicrobial susceptibility testing revealed 78 antimicrobial resistance patterns. E. coli resistance rates were highest to doxycycline, ampicillin and tetracycline, whereas polymyxin B and meropenem had the lowest resistance rates. All polymyxin B-resistant E. coli isolates were positive for the mcr-1 gene. A total of 62 ESBL-producing isolates were identified. The ESBL prevalence was 55.0% in diarrhoeic samplings and 5.6% in healthy animals. TEM (82.3%) was the predominant ESBL type, followed by CTM (43.5%) and SHV (19.4%)., Conclusion: E. coli isolates in the study area have a high diversity of genetic and antimicrobial resistance patterns but a relatively low isolation rate of potentially pathogenic phylogroups. However, the somewhat high isolation rate of multidrug-resistant E. coli, particularly ESBL-producing isolates, requires continual surveillance of E. coli from animals in these areas., (Copyright © 2020 Lanzhou Veterinary research institute ,CAAS. Published by Elsevier Ltd.. All rights reserved.)

Objectives: Escherichia coli is one of the most prevalent bacterial pathogens causing urinary tract infections (UTIs). The increasing dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli in the community renders clinical treatment difficult. Here we report the complete genome sequence of a bla CTX-M-15- carrying E. coli strain (EC28) isolated from a urine sample of a female outpatient with UTI., Methods: The whole genome sequence of E. coli strain EC28 was determined using both a MinION™ sequencer and an Illumina NovaSeq 6000 system. De novo hybrid assembly of the short Illumina reads and long MinION reads was performed using Unicycler. Multilocus sequence typing (MLST), antimicrobial resistance genes (ARGs), plasmid replicons and phylogenetic relationship were analysed using the BacWGSTdb database., Results: The genome sequence of E. coli strain EC28 consists of six contigs comprising 5260 133 bp, including one chromosome and five plasmids. According to MLST analysis, EC28 belongs to ST429. Six ARGs were identified, including bla CTX-M-15 located on a 63,295-bp IncI2-type plasmid. Twenty-three phylogenetically related E. coli ST429 strains were identified in the NCBI GenBank database, none recovered from China. The closest relative was an isolate recovered from Japan in 2009 that differed by 146 cgMLST loci., Conclusion: Here we report the first complete genome sequence of an ESBL-producing E. coli ST429 strain isolated from the community in China. The genome sequence of EC28 can be used as a reference sequence for comparative analysis, including acquisition and mobilisation of bla CTX-M genes in community-acquired E. coli strains., (Copyright © 2020 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

Objectives: Carbapenem-resistant Enterobacterales are a global problem, however little is known about the burden and origin of carbapenem resistance in Africa. The objectives of this study were to determine the proportion of carbapenem-resistant isolates among extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E), to identify the underlying mechanisms of resistance and to assess the population structure of carbapenem-resistant isolates from Nigeria., Methods: ESBL-E isolates (n = 175) from infections were collected at four hospitals in Lagos, Nigeria, from July 2016 to January 2018 and were screened for carbapenem resistance using a VITEK®2 automated system. All carbapenem-resistant ESBL-E (CRE) were screened for bla KPC , bla CTX-M , bla CMY-2 , bla NDM , bla VIM , bla IMP , bla OXA-181 and bla OXA-48 genes. Genotyping of randomly selected isolates was performed by whole-genome sequencing., Results: The isolates included Escherichia coli (n = 113; 64.6%) and Klebsiella pneumoniae (n = 62; 35.4%). Of the 175 ESBL-E isolates, 48 (27.4%) were resistant to carbapenems (15 E. coli and 33 K. pneumoniae). CRE isolates carried bla NDM (n = 30; 62.5%), bla NDM + bla OXA-181 (n = 10; 20.8%), bla OXA-181 (n = 2; 4.2%) and bla NDM  + bla OXA-48 (n = 1; 2.1%); no carbapenemase gene was detected in 5 isolates (10.4%). The isolates showed low diversity and were mainly associated with multilocus sequence typing (MLST) sequence types ST410 for E. coli and ST395 and ST147 for K. pneumoniae., Conclusion: Carbapenem resistance is frequent among ESBL-E in Nigeria and is mainly associated with bla NDM . Genotyping suggested that the observed clones possibly originated from Southeast Asia., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: Extended-spectrum β-lactamase/AmpC β-lactamase-producing Escherichia coli (ESBL/AmpC-E. coli) are common in developing countries and travellers represent potential reservoirs for their dissemination. The aim of this study was to quantify cefotaxime (CTX)-resistant E. coli harboured by travellers to Vietnam and to conduct a follow-up study., Methods: In total, 19 travellers and 34 travel events were investigated. After confirming that travellers were not colonised with CTX-resistant E. coli before travel, 15 travellers and 20 travel events were studied to quantify travellers harbouring CTX-resistant E. coli after travel. A stool sample (0.1 g) in 10 mL of PBS was diluted and plated. Selected colonies were identified, genotyped and further verified by pulsed-field gel electrophoresis (PFGE)., Results: After travel, travellers harboured an average of 3.6 × 10 7 CFU/g faeces of CTX-resistant E. coli, which continued to be detected for an average of 14 weeks. In the follow-up study, travellers from two travel events had ESBL-E. coli for 12 months. Multiplex PCR showed bla CTX-M-55 and bla CTX-M-27 , with replicon types FIA and F, and FIB and F, respectively. PFGE showed that two travellers harboured a single clonal ESBL-E. coli strain for 12 months. By PFGE, the follow-up study showed that a single type of ESBL/AmpC-E. coli was only detected in individuals living in Japan. Moreover, the same clonal ESBL-E. coli isolate was detected in a group that travelled to Ho Chi Minh City., Conclusion: ESBL/AmpC-E. coli colonised the gut of travellers to Vietnam with CTX-resistant E. coli (>10 7 CFU/g faeces) lasting for 14 weeks., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: Maternal colonisation with extended-spectrum β-lactamase (ESBL)-producing micro-organisms can lead to transmission of such pathogens to neonates, resulting in considerable morbidity. The aim of this study was to determine the global prevalence of maternal colonisation with ESBL-producing Enterobacteriaceae (ESBL-E)., Methods: A systematic review of PubMed, Embase, Scopus, Web of Science and ProQuest databases as well as the grey literature was performed. Studies reporting the prevalence of ESBL-E colonisation during pregnancy or postpartum period were included. Prevalence data were grouped by geographic region. The pooled prevalence and 95% confidence interval (CI) was estimated by meta-analysis using a random-effects model., Results: Nineteen studies with reports from 16 countries (seven studies from Africa, one study from South America, two studies from Asia and nine studies from Europe) reporting data for 7352 pregnant/postpartum women were included. The pooled prevalence of ESBL-E colonisation was 8% (95% CI 5-10%). Prevalence estimates were 15% (95% CI 5-24%) in Africa, 6% (95% CI 4-10%) in South America, 5% (95% CI 4-6%) in Asia and 4% (95% CI 2-5%) in Europe. The pooled prevalence was higher in studies with low risk of bias (10%; 95% CI 7-13%) compared with those with high risk of bias (3%; 95% CI 2-3%)., Conclusion: There was heterogeneity regarding ESBL-E colonisation rates in different continents. The pooled prevalence rate was higher in Africa compared with other areas. Given that the highest rate was observed in Africa, implementing screening efforts for ESBL-E colonisation during pregnancy may be justified., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: Klebsiella pneumoniae sequence type 307 (ST307) has emerged as a new high-risk clone worldwide. The aim of this study was to report the draft genome sequence of a multidrug-resistant CTX-M-15-positive K. pneumoniae strain causing urinary tract infection in a companion animal in Brazil., Methods: Whole-genome sequencing was performed on an Illumina NextSeq platform and the genome was de novo assembled using SPAdes. Data analysis was performed using online tools from the Center for Genomic Epidemiology., Results: The genome size of K. pneumoniae strain PRETA was calculated at 5 450 575 bp, containing a total of 5355 protein-coding sequences. The strain was assigned to the high-risk ST307 and carried the clinically relevant bla CTX-M-15 gene, besides other genes conferring resistance to aminoglycosides, tetracyclines, quinolones, trimethoprim and fosfomycin., Conclusion: These data offer novel information for comparative genomic analyses in order to track the transmission dynamics and epidemiology of the newly emerging high-risk clone ST307., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: This study was conducted to examine the molecular mechanisms responsible for the evolution of TEM-type extended-spectrum β-lactamases (ESBLs) following selective pressure from four third-generation cephalosporins, namely ceftazidime, cefotaxime, ceftriaxone and ceftibuten. In addition, selective enrichment for ESBL detection in environmental samples was investigated., Methods: Using experimental evolution, resistant variants were isolated and mutations in TEM-1 were examined by DNA sequencing. Resistance levels and the development of cross-resistance were determined for ESBL-producing isolates by Etest and disk diffusion assay. Selective plating with or without prior growth in selective broth was used to examine the approach of selective enrichment for ESBL detection., Results: The third-generation cephalosporins ceftazidime, cefotaxime and ceftriaxone selected for ESBLs, whereas ceftibuten did not. All ESBL variants additionally remained susceptible to ceftibuten. DNA sequencing of the TEM-1 coding sequence of mutants revealed mutations not previously isolated through selection. This indicates that the potential for ESBL evolution is much broader than can be inferred from sequence analysis of clinical samples alone. The results also indicate that selective enrichment for enhanced detection of ESBL-producers may give unreliable results owing to the selection of spontaneous mutations in narrow-spectrum β-lactamases resulting in TEM-type ESBL-producers., Conclusion: These results help explain the molecular changes responsible for evolution of TEM-type ESBLs and meanwhile question the appropriate use of selective enrichment for detection of ESBLs in environmental samples., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: This study investigated the prevalence of Escherichia coli (E. coli) colistin resistance and mcr-1 and mcr-2 genes among extended-spectrum β-lactamase (ESBL)/AmpC-producing E. coli isolates recovered from chicken feces in Canada (Quebec), Senegal and Vietnam, and evaluated the susceptibility pattern of the colistin-resistant E. coli isolates to other clinically relevant antimicrobials., Methods: A total of 327 potential ESBL/AmpC-producing E. coli isolates from chicken farms in Canada (Quebec), Senegal and Vietnam were analysed for colistin susceptibility by broth microdilution method and for the presence of mcr (1-2) genes by PCR. The pmrA and pmrB genes of colistin-resistant E. coli isolates, in the absence of mcr (1-2) genes, were sequenced. Antimicrobial resistance phenotypes of colistin-resistant E. coli isolates were determined by disk diffusion., Results: None of the 108 potential ESBL/AmpC-producing E. coli isolates from seven farms in Canada were colistin-resistant or possessed mcr-1 or mcr-2 gene. A low prevalence of 2.2% of colistin resistance was observed in 93 Senegalese isolates from the 15 sampled farms, although neither mcr-1 nor mcr-2 gene was found. A prevalence of 8.7% of colistin resistance was observed among 126 Vietnamese isolates from two of the four sampled farms. The mcr-1 gene was detected in 85% of the 13 phenotypically colistin-resistant isolates. Moreover, all colistin-resistant isolates presented a multidrug-resistant phenotype., Conclusions: The co-existence of the mcr-1 and ESBL/AmpC genes and the very high level of multiple drug resistance in all colistin-resistant E. coli isolates obtained from sampled chicken farms in Vietnam is a major concern., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: Proteus mirabilis is ubiquitous in soil and water. It is an important catheter-associated urinary tract pathogen and has reportedly been associated with antimicrobial-resistant infections. This study reports the draft genome of a multidrug-resistant P. mirabilis isolated from raw retail chicken meat in Singapore., Methods: The P. mirabilis strain was isolated on Brilliance TM ESBL Agar and was screened for antimicrobial susceptibility against 29 antimicrobial agents using a MicroScan® Neg MIC Panel Type 44. The double-disk synergy test (DDST) was used for confirmation of extended-spectrum β-lactamase (ESBL) production. Genomic DNA from the pure culture isolate was extracted and was sent for sequencing based on Illumina HiSeq 2500 technology. Further bioinformatics analysis was performed using online tools available at the Center for Genomic Epidemiology., Results: Species identification of the isolate was performed by KmerFinder. Antimicrobial susceptibility testing of the isolate showed multidrug resistance to broad-spectrum β-lactams, fluoroquinolones and aminoglycosides, among others. ESBL production was confirmed by the DDST. A total of 29 antimicrobial resistance genes were detected by ResFinder., Conclusion: To the best of our knowledge, this is the first report of the whole-genome sequence of a multidrug-resistant P. mirabilis producing an ESBL from raw chicken meat in Singapore. This indicates that raw meat in Singapore can be a reservoir for drug-resistant pathogens., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: The aim of this study was to characterise the molecular drivers of multidrug resistance in Proteus mirabilis isolated from Algerian community and hospital patients., Methods: A total of 166 P. mirabilis isolates were collected from two hospitals and eight private laboratories from four cities (Khemis Miliana, Aïn Defla, Oran and Chlef) located in northwestern Algeria. All isolates were identified by matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF/MS). Antimicrobial susceptibility testing was performed by the disk diffusion and Etest methods. Genes encoding AmpC β-lactamases, extended-spectrum β-lactamases (ESBLs), quinolone resistance and aminoglycoside-modifying enzymes (AMEs) as well as plasmid replicon typing were characterised by PCR. Clonal relationships were also determined by enterobacterial repetitive intergenic consensus PCR (ERIC-PCR) typing and were compared with MALDI-TOF/MS proteomic typing., Results: Of the 166 P. mirabilis isolates, 14 (8.4%) exhibited resistance to important antibiotics, including amoxicillin, amoxicillin/clavulanic acid, cefotaxime, gentamicin and ciprofloxacin, of which 4/14 (28.6%) had an ESBL genotype (bla CTX-M-2 ) and 10 (71.4%) had an AmpC/ESBL genotype (bla CMY-2 /bla TEM-1 ). AME genes were detected in all isolates, including ant(2'')-I, aac(3)-I, aac(6')-Ib-cr and aac(3)-IV. The qnrA gene was identified in 13 isolates (7.8%). ERIC-PCR showed one predominant clone, with eight bla CMY-2 -producing isolates from UHC Oran belonging to profile A clustering together in the MALDI-TOF/MS dendrogram., Conclusion: Here we report the first description of AME and plasmid-mediated quinolone resistance genes among ESBL- and/or AmpC β-lactamase-producing P. mirabilis isolates from community- and hospital-acquired infections in northwestern Algeria., (Copyright © 2019 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Extended-spectrum β-lactamase-producing Klebsiella pneumoniae (ESBL-KP) have emerged as an important pathogen causing severe infections worldwide. Infections due to ESBL-KP are associated with high morbidity and mortality, especially in developing countries such as Iran. The aim of this study was to assess the pooled prevalence of ESBL-KP with different gene variants in Iran., Methods: A literature search of Medline (via PubMed), Embase, Web of Science and Iranian Database was performed. A meta-analysis was conducted using Comprehensive Meta-Analysis Software (version 2.2, Biostat). A fixed- or random-effects model was used based on the heterogeneity test. Publication bias was determined using Begg's rank correlation and Egger's weighted regression methods., Results: Among 783 articles identified, 43 studies met the eligibility criteria. The pooled prevalence of ESBL-KP was 43.5% (95% CI 39.3-47.9%) among clinical K. pneumoniae isolates. Among genes encoding ESBLs during 2000-2009, SHV, CTX-M and TEM were found with prevalences of 23.3%, 15.2% and 12.3%, respectively, whilst the prevalences of SHV, CTX-M, TEM and VEB were 24%, 28.1%, 25.2% and 8.3%, respectively, during the period 2010-2018., Conclusion: The prevalence of ESBL-KP has increased steadily in recent years among clinical K. pneumoniae isolates in Iran. Thus, initial identification of ESBL-KP according to Clinical and Laboratory Standards Institute (CLSI) guidelines, proper molecular approaches, and implementation of antimicrobial stewardship programmes in Iranian hospitals together with comprehensive infection control measures are urgently needed to control the dissemination of these strains., (Copyright © 2019 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-EC) are a serious public health concern worldwide. The aim of this study was to characterise ESBL-EC isolated from raw retail chicken in South Korea., Methods: The antimicrobial resistance, phylogenetic group and virulence gene prevalence of 67 ESBL-EC isolated from retail chicken in South Korea were investigated., Results: All of the isolates possessed bla CTX-M genes, predominantly bla CTX-M-65 (52.2%) and bla CTX-M-55 (25.4%), and three isolates harboured both bla CTX-M-65 and bla CTX-M-55 . More than one-half of the ESBL-EC strains also carried bla TEM . Antimicrobial susceptibility testing revealed that 98.5% of the strains were multidrug-resistant (MDR). Phylogenetic analysis showed that group A was predominant (56.7%), followed by B1 (19.4%), E (8.9%), B2 (6.0%) and D (6.0%). Virulence genes associated with extraintestinal pathogenic E. coli (ExPEC) were frequently detected in isolates of phylogenetic groups B1, B2, D and E., Conclusion: The results in this study demonstrate that retail chicken in South Korea is highly contaminated with MDR ESBL-EC and may serve as a reservoir for transmitting ExPEC to humans., (Copyright © 2019 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objectives: Escherichia coli and Enterobacter cloacae are two major pathogens causing urinary tract infection (UTI). Here we characterised the genome of an NDM-1-producing E. cloacae strain and an extended-spectrum β-lactamase (ESBL)-producing E. coli strain that were co-isolated from a UTI., Methods: The genomes of E. cloacae strain EC32 and E. coli strain EC33 were sequenced using an Illumina HiSeq TM platform. The whole genome sequences were assembled using CLC Genomics Workbench and were annotated by the NCBI Prokaryotic Genome Annotation Pipeline (PGAP) server. Genomic analysis was further performed., Results: The draft genome sequences of E. cloacae EC32 (ST66) and E. coli EC33 (ST1139) consisted of 89 contigs comprising 5 178 393 bp and 62 contigs comprising 5 057 666 bp, respectively. Including the bla NDM-1 gene, in total 13 resistance genes were identified in E. cloacae EC32 conferring resistance to β-lactams, rifampicin, phenicols, fosfomycin, macrolides, quinolones, sulfonamides and tetracycline. Nine resistance genes were identified in E. coli EC33 including the ESBL-encoding gene bla CTX-M-27 ., Conclusion: To our knowledge, this is the first report of genomic characterisation of NDM-1-producing E. cloacae and ESBL-producing E. coli co-isolated from a UTI in China. The two strains inhabiting in the same environment may allow the possibility of horizontal transfer of bla NDM-1 and bla CTX-M-27 , making clinical treatment even difficult. This report also sheds light on geographically distinct Enterobacteriaceae strains from China enabling a comparative analysis of NDM-1- or ESBL-producing strains., (Copyright © 2019 International Society for Antimicrobial Chemotherapy. Published by Elsevier Ltd. All rights reserved.)

Objectives: The aim of this study was to identify and characterise probable extended-spectrum β-lactamase (ESBL)-, AmpC lactamase- and/or metallo-β-lactamase (MBL)-producing Escherichia coli variants circulating in the livestock and poultry environment to establish their epidemiological significance, genetic diversity, antimicrobial resistance (AMR) trends and virulence., Methods: The culture method and E. coli-specific multiplex PCR identified 78 E. coli strains from faecal samples of healthy livestock and poultry. The antibiogram was determined by the disk diffusion and minimum inhibitory concentration (MIC) methods. Antimicrobial-resistant E. coli isolates were screened for the presence of ESBL, AmpC and MBL genes. Isolates were further characterised by plasmid replicon typing, integron assay and virulence gene analysis. Genetic diversity was assessed by random amplification of polymorphic DNA (RAPD) analysis and multilocus sequence typing (MLST)., Results: ESBL (CTX-M group 1, CTX-M group 4, TEM), AmpC (EBC, FOX, CMY, DHA) and MBL (IMP, SIM) resistance determinants were identified in 75%, 19% and 6% of isolates, respectively. Nine plasmid replicon types were distributed among resistant E. coli strains, with the most common plasmid replicon types being L/M and Y. Integrons were detected in 19% of E. coli isolates. RAPD analysis categorised the E. coli isolates into three clusters. MLST revealed seven different sequence types (STs), with ST10 being the most common., Conclusions: This study demonstrated a high prevalence of animals carrying potential ESBL- and AmpC-producing E. coli and emphasises the need for rigorous surveillance in the animal sector to identify critical control points conducive to prevent the rapid dissemination of AMR., (Copyright © 2019 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objective: The aim of this study was to determine whether Clinton River water is contaminated with antibiotics and is a reservoir of antimicrobial-resistant bacteria., Methods: Water samples were taken from two sites of Clinton River. Antimicrobial-resistant bacteria were enumerated on agar plates supplemented with six commonly used antibiotics. Extended-spectrum β-lactamase (ESBL)-producing bacteria were identified using a BD Phoenix™ System and by 16S rRNA gene sequencing. Antimicrobial resistance gene transfer was performed by conjugation studies and the location of genes was determined by Southern hybridisation. Virulence properties of ESBL-producing isolates were determined by assessing their biofilm-forming ability, cellular toxicity, and induction of an inflammatory response in intestinal epithelial (Caco-2) cells., Results: 16S rRNA analysis of water samples showed the presence of potentially pathogenic bacteria (e.g. Shigella flexneri, Klebsiella pneumoniae, Aeromonas punctata and Pseudomonas aeruginosa). Among 64 biochemically identified bacterial isolates tested, 42% were resistant to cefotaxime, 34% to chloramphenicol, 9% to tetracycline, 11% to ciprofloxacin and 9% to gentamicin. Of 27 cefotaxime-resistant isolates, 11 (41%) were ESBL-positive and possessed either bla CTX-M (n=9), bla TEM (n=1) or bla KPC (n=1). Comparative analysis of ESBL gene sequences from Clinton River water bacteria showed 98-100% identity with clinical isolates. ESBL-producing isolates from Clinton River water were found to form biofilms, induced inflammatory cytokines and caused toxicity to epithelial cells., Conclusions: Clinton River water contains isolates with ESBL genes identical to clinical isolates and possessing virulence properties, thus it could be a potential reservoir in causing human infections., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: The aim of this study was to assess the prevalence of Shigella flexneri resistance to third-generation cephalosporins (3GCs) and to characterise the underlying resistance mechanisms., Methods: A total of 282 S. flexneri strains isolated in 2013-2015 in Jiangsu Province, China, were identified, serotyped and analysed for their susceptibility to 3GCs. The bla TEM , bla SHV , bla OXA-1-like and bla CTX-M-type extended-spectrum β-lactamase (ESBL) genes were amplified and sequenced by PCR., Results: Of the 282 S. flexneri strains, 97 (34.4%) were resistant to cefotaxime, from which 68 (24.1%) were also resistant to ceftazidime. ESBL genes were detected in 73/97 isolates (75.3%), of which 66/73 (90.4%) showed resistance to 3GCs. Of the 73 ESBL-positive isolates, 32 (43.8%) were positive for CTX-M-1 group (17 for CTX-M-55, 4 for CTX-M-3, 1 for CTX-M-15, 3 for CTX-M-79 and 7 for CTX-M-123), 31 (42.5%) were positive for CTX-M-9 group (29 for CTX-M-14, 1 for CTX-M-24 and 1 for CTX-M-27), 25 (34.2%) were positive for TEM-types (21 for TEM-1 and 4 for TEM-1b) and 1 (1.4%) was positive for SHV-type (SHV-12); none were positive for CTX-M-2 group, CTX-M-8 group and OXA-type., Conclusion: ESBLs play an important role in Shigella resistance to 3GCs. CTX-M-14 and CTX-M-55 appeared to be the dominant ESBLs in 13 cities of Jiangsu Province. Therefore, it is time to regularly monitor resistance of S. flexneri to 3GCs and to take appropriate measures to manage this problem., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: The widespread dissemination of extended-spectrum β-lactamase-producing Enterobacteriaceae has become a major issue in veterinary medicine. However, until now, there has been no report of bacteria with such a phenotype in infected snakes. The aim of this study was to report the first draft genome sequence of an Enterobacter cloacae isolate (SERP1) recovered from a snake with infectious stomatitis., Methods: The whole genome of E. cloacae strain SERP1 was sequenced on an Illumina NextSeq platform and was de novo assembled using CLC NGS Cell v.10. Data analysis was performed using online tools from the Center of Genomic Epidemiology., Results: The genome size was calculated at 4966856bp, containing a total of 4796 protein-coding sequences. The strain was assigned to sequence type 279 (ST279) and, besides the clinically relevant bla CTX-M-15 and aac(6')-Ib-cr genes, it also presented resistance genes to β-lactams, aminoglycosides, phenicols, sulphonamides, tetracyclines, trimethoprim, quinolones and fosfomycin., Conclusion: These data offer novel information regarding multidrug-resistant E. cloacae dissemination in wild animals and might contribute to further comparative genomic analysis., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Genomic surveillance studies monitoring the dissemination of multidrug-resistant Enterobacteriaceae in polluted aquatic ecosystems are urgently required. The aim of this study was to report the draft genome sequence of an MCR-1 and CTX-M-8 co-producing Escherichia coli isolated from a polluted mangrove ecosystem in Northeast Brazil., Methods: Total genomic DNA was sequenced on an Illumina NextSeq platform and was assembled using CLC Genomics Workbench. The whole-genome sequence was evaluated through bioinformatics tools available from the Center of Genomic Epidemiology as well as additional in silico analysis., Results: The genome size was calculated at 5089467bp, comprising a total of 5068 protein-coding sequences. The strain was assigned to sequence type 58 (ST58) and revealed the presence of mcr-1, bla CTX-M-8 and other clinically significant genes responsible for conferring resistance to colistin, β-lactams, trimethoprim and quinolones. In addition, genes conferring resistance to silver (silR) and quaternary ammonium compounds (sugE) were identified., Conclusion: These data provide valuable information for comparative genomic analysis regarding the dissemination of MCR-1-producing E. coli at the human-animal-environment interface., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Escherichia coli strains producing extended-spectrum β-lactamases (ESBLs), especially CTX-M-type, have been largely described in companion animals; however, genomic data are lacking to clarify the clinical impact of ESBL-producing isolates in these hosts. The aim of this study was to present the genomic features of a highly virulent, ceftiofur-resistant, CTX-M-8-producing E. coli isolate from a case of pneumonia in a domestic cat with fatal outcome., Methods: Genomic DNA was sequenced using an Illumina NextSeq 500 platform and was assembled using CLC Genomic Workbench. Genomic data were analysed using online bioinformatics tools., Results: The genome size was evaluated at 5.1Mb, with 5334 protein-coding sequences. The strain was assigned to sequence type 224 (ST224) and presented genes conferring resistance to β-lactams (bla CTX-M-8 ), sulphonamides (sul2), tetracycline (tetA) and trimethoprim (dfrA14) as well as chromosomal point mutations in ParC (S80I), GyrA (S83L) and GyrB (D87N). In addition, the presence of the virulence genes cba, gad, ipfA, iroN, iss, mchF and tsh was detected., Conclusion: This draft genome sequence might provide important data for a better understanding of genomic aspects regarding the dissemination of CTX-M-8-producing E. coli in the human-animal-environment interface., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: The draft genome sequences of two Enterobacter aerogenes strains (HN503E2II and PN108E5IIB) isolated from two Cameroonian abattoirs are reported., Methods: Bacterial genomic DNA of the two isolates was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors and plasmids were identified., Results: Whole-genome sequencing revealed that both strains were similar, with genomes of 4878638bp and 4794257bp, encoding several resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, fosfomycin, phenicols, sulphonamides, trimethoprim, macrolides and tetracycline. In silico analysis also revealed chromosomal integration of one plasmid in the genome of PN108E5IIB., Conclusion: The genome sequences reported here will provide useful information for a better understanding of the genetic structure of E. aerogenes in Africa., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Here we report the draft genome sequence of Escherichia coli strain HN503E1II isolated from a nasal sample of an abattoir worker in Cameroon., Methods: Bacterial genomic DNA of E. coli HN503E1II was sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench. The assembled contigs were annotated and antibiotic resistance genes, virulence factors, plasmids and the sequence type (ST) were identified., Results: The genome comprised a circular chromosome of 4 674201bp, with a 50.78% G+C content and several resistance genes associated with resistance to β-lactams, fluoroquinolones, aminoglycosides, sulphonamides, trimethoprim, macrolides and tetracycline. The isolate was assigned to ST10 with 100% identity among the seven housekeeping genes. In silico analysis also revealed the presence six plasmid types and one virulence factor., Conclusion: The genome sequence reported here will provide valuable information for a better understanding of the genetic structure of the E. coli genome in Africa., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

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., (Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: Extended-spectrum β-lactamase (ESBL)-producing Escherichia coli have disseminated worldwide. This study investigated bla CTX-M -positive E. coli on a large-scale Vietnamese chicken farm and analysed whether there was any difference in prevalence and molecular characteristics of bla CTX-M -positive E. coli between the farm and the Vietnamese community., Methods: Faecal samples were collected from 24 human individuals and 38 chickens from the large-scale chicken farm as well as 51 humans and 36 chickens from the community. All samples were collected between June 2013 and June 2014 in Bavi Province in the Red River Delta region of Vietnam. Molecular characterisation of CTX-M-producing E. coli and genetic relatedness among the isolates were evaluated by conventional typing methods. Antimicrobial susceptibility of the isolates was evaluated by the disk diffusion method., Results: The prevalence of bla C TX-M -positive E. coli was 83.3%, 71.1%, 54.9% and 13.9% in farm workers, farm chickens, community individuals and community backyard chickens, respectively. On average, bla CTX-M -positive E. coli isolates from farm chickens were resistant to 8.3 different antibiotics. The average number of detected aminoglycoside-modifying enzyme genes (3.4 genes) and the detection rate of the plasmid-mediated colistin resistance gene mcr-1 (33.3%) were higher in bla CTX-M -positive E. coli isolated from farm chickens compared with other sampling groups. In addition, two types of indistinguishable pulsed-field gel electrophoresis (PFGE) patterns were observed in six bla CTX-M-65 -positive E. coli and three bla CTX-M-55 -positive E. coli from farm chickens., Conclusions: These results suggest a more frequent transmission opportunity of bla CTX-M -positive E. coli on the large-scale Vietnamese chicken farm., (Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: The aim of this study was to evaluate the prevalence of extended-spectrum β-lactamase (ESBL)- and carbapenemase-encoding genes in poultry from Algeria and Marseille, France., Methods: Samples consisted of faeces collected from broilers in France and Algeria between 2014 and 2015. DNA extraction and quantitative PCR were performed on 833 faecal samples to screen for the presence of genes encoding ESBLs (bla TEM , bla SHV and bla CTX-M ) and carbapenemases (bla NDM , bla VIM , bla KPC , bla OXA-23 , bla OXA-24 , bla OXA-48 and bla OXA-58 ). To characterise bacteria carrying antimicrobial resistance genes, positive results were simultaneously sequenced., Results: All chicken faeces from Marseille were negative for ESBL- and carbapenemase-encoding genes. However, of the 503 faecal samples collected in Algeria, 128 (25.4%) were positive for bla TEM , 83 (16.5%) for bla SHV , 46 (9.1%) for bla CTX-M and 132 (26.2%) for bla OXA-58 . Using a sequencing reaction, a high diversity of ESBL genes was observed throughout the sites studied., Conclusions: This study shows a high prevalence and diversity of ESBL and carbapenemase genes in poultry faeces from Algeria, whereas none of the samples from Marseille were positive for these genes. The high prevalence of ESBLs in Algeria is in contrast to the observation that no chickens were found to be positive in France., (Copyright © 2017 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.)

Objectives: High rates of antimicrobial resistance (AMR) are seen throughout Southeast Asia. However, limited AMR data exist for Timor-Leste, which is situated on the south-eastern portion of the Malay Archipelago. The purpose of this study was to identify AMR in bacteria isolated from urine and skin swabs from patients in Dili, the capital of Timor-Leste., Methods: Urine and skin swabs were collected from symptomatic patients in Timor-Leste and were processed for bacterial culture. Isolates were processed in Australia using a VITEK ® 2 system for bacterial identification and to determine antimicrobial susceptibility according to Clinical and Laboratory Standards Institute (CLSI) guidelines., Results: A total of 154 urine isolates and 57 skin isolates were analysed. Of the Enterobacteriaceae, 35% were resistant to ceftriaxone with an extended-spectrum β-lactamase (ESBL)-producing phenotype. Carbapenem resistance was not observed in any of the Gram-negative isolates. Of the Staphylococcus aureus isolates, 11% were of the community-associated methicillin-resistant S. aureus (CA-MRSA) phenotype., Conclusions: A moderately high proportion of Gram-negative urine isolates in Timor-Leste demonstrate phenotypic ESBL production, and a relatively low proportion of S. aureus isolates were methicillin-resistant. Improved understanding of AMR rates in Timor-Leste can help guide antimicrobial prescribing and inform antimicrobial stewardship strategies., (Copyright © 2017 The Author(s). Published by Elsevier Ltd.. All rights reserved.)