Clinical and Microbiological Characteristics of a Community-Acquired Carbapenem-Resistant Escherichia coli ST410 Isolate Harbouring blaNDM-5-Encoding IncX3-Type Plasmid From Blood

Objectives: The aim of this research was to investigate the clinical and microbiological characteristics of a case of community-acquired carbapenem-resistant Escherichia coli isolated from a patient with a bloodstream infection in China.Methods:Escherichia coli Huamei202001 was recovered from the first blood culture from a patient hospitalised in China. An antimicrobial susceptibility test was performed, and the genome was sequenced on an Illumina HiSeq X 10 platform with a 150-bp paired-end approach. The generated sequence reads were assembled using Unicycler, and the whole genome sequence data were analysed using bioinformatics tools. Moreover, the patient and her main family members obtained a faecal sample screening test for CRE, the positive strain was further isolated and the identification and antimicrobial susceptibility testing was performed.Results:Escherichia coli Huamei202001 belonged to sequence type 410. In addition, a blaNDM-5-encoding IncX3-type plasmid was responsible for the spreading of carbapenem resistance. Only the patient was detected as having a positive faecal sample screening test for CRE. Strain Fec01 was identified as E. coli, and the antibiotic susceptibility profile was the same as that of E. coli Huamei202001.Conclusions:Escherichia coli Huamei202001 is defined as community-acquired carbapenem-resistant Enterobacteriaceae. The clone ST410 that harbours the blaNDM-5-encoding IncX3-type plasmid is causing new high-risk clones globally. Thus, infection control measures should be strengthened to curb the dissemination of IncX3.

Download Full-text

Emergence of IncHI2 Plasmid-Harboring blaNDM-5 from Porcine Escherichia coli Isolates in Guangdong, China

Pathogens ◽

10.3390/pathogens10080954 ◽

2021 ◽

Vol 10 (8) ◽

pp. 954

Author(s):

Zhenbao Ma ◽

Zhenling Zeng ◽

Jiao Liu ◽

Chang Liu ◽

Yu Pan ◽

...

Keyword(s):

Escherichia Coli ◽

Susceptibility Testing ◽

Carbapenem Resistance ◽

Guangdong Province ◽

Whole Genome Sequence ◽

Molecular Characteristics ◽

E Coli ◽

Carbapenem Resistant ◽

Genetic Feature ◽

Plasmid Backbone

Carbapenem resistance has posed potential harmful risks to human and animals. The objectives of this study were to understand the prevalence of blaNDM-5 in pigs and investigate the molecular characteristics of NDM-5-producing Escherichia coli isolates in Guangdong province in China. Carbapenem-resistant E. coli isolates were isolated from pigs and obtained using MacConkey plates containing 0.5 mg/L meropenem. Conjugation assay and antimicrobial susceptibility testing were conducted for the isolates and their transconjugants. Whole-genome sequence (WGS) was used to analyze the plasmid genetic feature. A total of five blaNDM-5-carrying E. coli isolates were obtained in the present investigations. They belonged to five ST types. The blaNDM-5 genes were found to be in IncX3 and IncHI2 plasmid. The IncX3 plasmid was 46,161 bp in size and identical to other reports. IncHI2 plasmid was 246,593 bp in size and similar to other IncHI2-ST3 plasmids. It consisted of a typical IncHI2 plasmid backbone region and a multiresistance region (MRR). The blaNDM-5 was closely associated with the IS3000-ISAba125-blaNDM-5-bleMBL-trpF-tat-IS26 unit. We first reported the blaNDM-5-carrying IncHI2 in E. coli isolates recovered from pigs and revealed the molecular characterization. Continued surveillance for the dissemination of blaNDM-5 among food-producing animals is required.

Download Full-text

Susceptibility of Tigecycline against Carbapenem Resistant Enterobacteriaceae

Pakistan Journal of Medicine and Dentistry ◽

10.36283/pjmd10-3/004 ◽

2021 ◽

Keyword(s):

Escherichia Coli ◽

Respiratory Tract ◽

Antimicrobial Susceptibility ◽

Bacterial Infections ◽

Large Family ◽

Klebsiella Species ◽

Cross Sectional ◽

E Coli ◽

Carbapenem Resistant ◽

Carbapenem Resistant Enterobacteriaceae

Background: Enterobacteriaceae, a large family of Gram-negative bacteria, are one of the commonest etiological agents causing serious bacterial infections to humans. Carbapenems are the group of antibiotics with a broad spectrum of antimicrobial action. Infections caused due to Carbapenem resistant Enterobacteriaceae (CRE) are a huge challenge for existing medical practice. Therefore, this project aimed to find out the antimicrobial susceptibility pattern of Tigecycline against CRE. Methods: This cross-sectional study with non-probability consecutive sampling was done at Ziauddin Hospital Microbiology Laboratory from 15th August 2017 to 15th April 2018. Accordingly, 151 isolates of CRE were collected from cultures of blood, respiratory tract, wound pus and other body fluids. The growth inhibition zones were measured following the Food and Drug Administration (FDA) disk diffusion breakpoint criteria. Frequencies and percentages were computed for gender, microorganism, and antimicrobial susceptibility. Chi-squared test was applied and p≤ 0.05 was considered as statistically significant. Results: Klebsiella species were most commonly isolated pathogen, 67.5% (n=102) followed by Escherichia coli (E. coli) 23.2% (n=35), Enterobacter 7.3% (n=11) and Serratia species 2% (n=3). Tigecycline was 97% (34 /35) sensitive for E. coli, 86.3% (88/102) for Klebsiella species), 91% (10/11) for Enterobacter species, and 100% for Serratia species. Klebsiella species showed the highest rate of resistance to tigecycline i.e., 13.7% of the total Klebsiella isolates. Conclusion: Among the Enterobacteriaceae family, Klebsiella species have the greatest ability to acquire resistance. Tigecycline showed good activity against isolates of CRE recovered from infections of skin, soft tissue, intra-abdomen, lower respiratory tract and blood stream. Keywords: Carbapenems; beta-Lactamases; Anti-Bacterial Agents; Tigecycline; Klebsiella; Escherichia coli.

Download Full-text

Dissemination of Blandm-5 in Escherichia Coli via the Incx3 Plasmid From Different Regions in China

10.21203/rs.3.rs-254667/v1 ◽

2021 ◽

Author(s):

Xiaofeng Hu ◽

Lang Yang ◽

Nian Dong ◽

Yanfeng Lin ◽

Ling Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Blot Hybridization ◽

Carbapenem Resistance ◽

Southern Blot Hybridization ◽

Control Measures ◽

Rrna Gene ◽

Limited Information ◽

E Coli ◽

Carbapenem Resistant ◽

Antimicrobial Resistance Genes

Abstract Background: Recently, the spread of NDM-5-producing Escherichia coli has become a severe challenge in clinical therapy, which necessitates reliable detection and surveillance methods. However, limited information is available regarding the prevalence and dissemination of the blaNDM-5 gene in Escherichia coli in China. Therefore, we investigated the dissemination of the blaNDM-5 gene in carbapenem-resistant Escherichia coli isolates from different regions in China.Methods: A total of 1,180 carbapenem-resistant enterobacteriaceae strains were obtained from patients admitted to the 20 sentinel hospitals in eight cities. Strains positive for blaNDM-5 were detected using the Vitek 2 compact system, 16S rRNA gene sequencing, PCR, the S1-pulsed-field gel electrophoresis assay, and Southern blot hybridization. The horizontal-transfer capability of the blaNDM gene was assessed by filter mating with a standard E. coli J53 azide-resistant strain as the recipient. Genotyping, susceptibility testing, and whole genome sequencing were performed. Results: Seven strains of blaNDM-5-positive E.coli was detected in 1180 clinical strains from different regions in China. The blaNDM-5-carrying strains showed resistance to multiple tested antibiotics and belonged to two widespread sequence types, ST167 and ST405. Antimicrobial resistance genes including blaCTX-M, blaOXA, blaCMY, and two novel blaTEM variants (blaTEM-230 and blaTEM-231) were also identified. Southern blotting located the blaNDM-5 gene on 46-kb IncX3 plasmids in all isolates, which showed only two single nucleotide differences between EJN003 and the other strains. Conclusions: This study further confirms the increasing occurrence of blaNDM-5-carrying IncX3 plasmids and the dissemination of carbapenem resistance in E. coli isolates via the plasmid from different parts in China, which warrants stringent surveillance and control measures.

Download Full-text

Genomic characterization of carbapenem resistant Escherichia coli from multiple hospitals in Nanjing, China: focusing on frequent co-occurrence of blaNDM and blaKPC-2

10.21203/rs.3.rs-37813/v2 ◽

2020 ◽

Author(s):

Xiaoli Cao ◽

Jie Zheng ◽

Li Cheng ◽

Wanqing Zhou ◽

Zhifeng Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Control Measures ◽

Potential Threat ◽

E Coli ◽

Infection Control Measures ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Drum Tower Hospital ◽

Genomic Characterization

Abstract Background: The increasing emergence of carbapenem resistant Escherichia coli (CREC) poses a potential threat to public health, hence genomic characterization of isolates is needed for a better understanding of its transmission and implementation of infection control measures. Materials and methods：Eleven CREC isolates were collected in 2015 from 6 hospitals in Nanjing, China, and analyzed using whole genome sequencing. Resistance determinants, virulence elements, multi-locus sequence type (MLST), serotypes, phylogeny and fimH types were determined. Results: All of the CREC carried at least one carbapenemase. NDM-5 (n=9) was the most frequent carbapenemase, followed by KPC-2 (n=3) and NDM-1 (n=2); three isolates produced NDM-5 and KPC-2. Ten out of the 11 isolates co-carried blaCTX-M variants. MLST analysis found 7 distinct STs, including ST410 (n=2), ST3489 (n=1), ST156 (n=1), ST683 (n=1), ST297 (n=1), ST167 (n=1), and ST361 (n=1). Six distinct serotypes and 8 Fim types were identified. A great diversity of plasmid profiles was observed with plasmid replicon IncX3 being the most frequent (n=11). Phylogenetic analysis showed great diversity between the 11 CREC isolates and also between 6 additional isolates co-carrying blaNDM and blaKPC which were selected from the strains collection of Nanjing Drum Tower Hospital for comparison. Conjugation assays demonstrated that blaNDM was transferable. Conclusion: NDM is the major carbapenemase among CREC, with NDM-5 being the main variant which can be horizontally disseminated by IncX3 plasmids. These isolates displayed genetic diversity by MLST, Fim typing and serotyping. We herein provided the first report on emergence of NDM-5 producing E. coli ST297, ST683, ST3489, and NDM-1 producing E. coli ST361.

Download Full-text

Extensive Gene Amplification as a Mechanism for Piperacillin-Tazobactam Resistance in Escherichia coli

mBio ◽

10.1128/mbio.00583-18 ◽

2018 ◽

Vol 9 (2) ◽

Cited By ~ 19

Author(s):

Lisa M. Schechter ◽

David P. Creely ◽

Cherilyn D. Garner ◽

Dee Shortridge ◽

Hoan Nguyen ◽

...

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Copy Number ◽

Sequence Data ◽

Gene Dosage ◽

Clinical Isolates ◽

Whole Genome Sequence ◽

Content Type ◽

E Coli ◽

Protein Levels

ABSTRACT Although the TEM-1 β-lactamase (Bla TEM-1 ) hydrolyzes penicillins and narrow-spectrum cephalosporins, organisms expressing this enzyme are typically susceptible to β-lactam/β-lactamase inhibitor combinations such as piperacillin-tazobactam (TZP). However, our previous work led to the discovery of 28 clinical isolates of Escherichia coli resistant to TZP that contained only bla TEM-1 . One of these isolates, E. coli 907355, was investigated further in this study. E. coli 907355 exhibited significantly higher β-lactamase activity and Bla TEM-1 protein levels when grown in the presence of subinhibitory concentrations of TZP. A corresponding TZP-dependent increase in bla TEM-1 copy number was also observed, with as many as 113 copies of the gene detected per cell. These results suggest that TZP treatment promotes an increase in bla TEM-1 gene dosage, allowing Bla TEM-1 to reach high enough levels to overcome inactivation by the available tazobactam in the culture. To better understand the nature of the bla TEM-1 copy number proliferation, whole-genome sequence (WGS) analysis was performed on E. coli 907355 in the absence and presence of TZP. The WGS data revealed that the bla TEM-1 gene is located in a 10-kb genomic resistance module (GRM) that contains multiple resistance genes and mobile genetic elements. The GRM was found to be tandemly repeated at least 5 times within a p1ESCUM/p1ECUMN-like plasmid when bacteria were grown in the presence of TZP. IMPORTANCE Understanding how bacteria acquire resistance to antibiotics is essential for treating infected patients effectively, as well as preventing the spread of resistant organisms. In this study, a clinical isolate of E. coli was identified that dedicated more than 15% of its genome toward tandem amplification of a ~10-kb resistance module, allowing it to escape antibiotic-mediated killing. Our research is significant in that it provides one possible explanation for clinical isolates that exhibit discordant behavior when tested for antibiotic resistance by different phenotypic methods. Our research also shows that GRM amplification is difficult to detect by short-read WGS technologies. Analysis of raw long-read sequence data was required to confirm GRM amplification as a mechanism of antibiotic resistance.

Download Full-text

Genomic characterization of carbapenem resistant Escherichia coli from multiple hospitals in Nanjing, China: focusing on frequent co-occurrence of blaNDM and blaKPC-2

10.21203/rs.3.rs-37813/v1 ◽

2020 ◽

Author(s):

Xiaoli Cao ◽

Jie Zheng ◽

Li Cheng ◽

Wanqing Zhou ◽

Zhifeng Zhang ◽

...

Keyword(s):

Escherichia Coli ◽

Control Measures ◽

Potential Threat ◽

E Coli ◽

Infection Control Measures ◽

Carbapenem Resistant ◽

Plasmid Replicon ◽

Drum Tower Hospital ◽

Genomic Characterization

Abstract Background The increasing emergence of carbapenem resistant Escherichia coli (CREC) poses a potential threat to public health, hence genomic characterization of isolates is needed for a better understanding of its transmission and implementation of infection control measures. Materials and methods Eleven CREC isolates were collected in 2015 from 6 hospitals in Nanjing, China, and analyzed using whole genome sequencing. Resistance determinants, virulence elements, multi-locus sequence type (MLST), serotypes, phylogeny and fimH types were determined. Results All of the CREC carried at least one carbapenemase. NDM-5 (n = 9) was the most frequent carbapenemase, followed by KPC-2 (n = 3) and NDM-1 (n = 2); three isolates produced NDM-5 and KPC-2. Ten out of the 11 isolates co-carried blaCTX-M variants. MLST analysis found 7 distinct STs, including ST410 (n = 2), ST3489 (n = 1), ST156 (n = 1), ST683 (n = 1), ST297 (n = 1), ST167 (n = 1), and ST361 (n = 1). Six distinct serotypes and 8 Fim types were identified. A great diversity of plasmid profiles was observed with plasmid replicon IncX3 being the most frequent (n = 11). Phylogenetic analysis showed great diversity between the 11 CREC isolates and also between 6 additional isolates co-carrying blaNDM and blaKPC which were selected from the strains collection of Nanjing Drum Tower Hospital for comparison. Conjugation assays demonstrated that blaNDM was transferable. Conclusion NDM is the major carbapenemase among CREC, with NDM-5 being the main variant which can be horizontally disseminated by IncX3 plasmids. These isolates displayed genetic diversity by MLST, Fim typing and serotyping. We herein provided the first report on emergence of NDM-5 producing E. coli ST297, ST683, ST3489, and NDM-1 producing E. coli ST361.

Download Full-text

Hospital outbreak of carbapenem-resistant Enterobacteriales associated with an OXA-48 plasmid carried mostly by Escherichia coli ST399

10.1101/2020.06.15.148189 ◽

2020 ◽

Author(s):

Alice Ledda ◽

Martina Cummins ◽

Liam P. Shaw ◽

Elita Jauneikaite ◽

Kevin Cole ◽

...

Keyword(s):

Escherichia Coli ◽

Sequence Data ◽

Hospital Setting ◽

E Coli ◽

Hospital Outbreak ◽

Carbapenem Resistant ◽

Routine Surveillance ◽

Key Driver ◽

Unique Clade ◽

Plasmid Conjugation

AbstractA hospital outbreak of carbapenem-resistant Enterobacteriales was detected by routine surveillance. Whole genome sequencing and subsequent analysis revealed a conserved promiscuous OXA-48 carrying plasmid as the defining factor within this outbreak. Four different species of Enterobacteriales were involved in the outbreak. Escherichia coli ST399 accounted for 20/55 of all the isolates. Comparative genomics with publicly available E. coli ST399 sequence data showed that the outbreak isolates formed a unique clade. The OXA-48 plasmid identified in the outbreak differed from other known plasmids by an estimated five homologous recombination events. We estimated a lower bound to the plasmid conjugation rate to be 0.23 conjugation events per lineage per year. Our analysis suggests co-evolution between the plasmid and its main bacterial host to be a key driver of the outbreak. This is the first study to report carbapenem-resistant E. coli ST399 carrying OXA48 as the main cause of a plasmid-borne outbreak within a hospital setting. This study supports complementary roles for both plasmid conjugation and clonal expansion in the emergence of this outbreak.

Download Full-text

Phenotypic Antimicrobial Susceptibility of Escherichia coli from Raw Meats, Ready-to-Eat Meats, and Their Related Samples in One Health Context

Microorganisms ◽

10.3390/microorganisms9020326 ◽

2021 ◽

Vol 9 (2) ◽

pp. 326

Author(s):

Frederick Adzitey ◽

Nurul Huda ◽

Amir Husni Mohd Shariff

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Antimicrobial Susceptibility ◽

Resistance Index ◽

Diffusion Method ◽

Resistant Bacteria ◽

Disk Diffusion Method ◽

E Coli ◽

The Usa ◽

Raw Meats

Meat is an important food source that can provide a significant amount of protein for human development. The occurrence of bacteria that are resistant to antimicrobials in meat poses a public health risk. This study evaluated the occurrence and antimicrobial resistance of E. coli (Escherichia coli) isolated from raw meats, ready-to-eat (RTE) meats and their related samples in Ghana. E. coli was isolated using the USA-FDA Bacteriological Analytical Manual and phenotypic antimicrobial susceptibility test was performed by the disk diffusion method. Of the 200 examined meats and their related samples, 38% were positive for E. coli. Notably, E. coli was highest in raw beef (80%) and lowest in RTE pork (0%). The 45 E. coli isolates were resistant ≥ 50% to amoxicillin, trimethoprim and tetracycline. They were susceptible to azithromycin (87.1%), chloramphenicol (81.3%), imipenem (74.8%), gentamicin (72.0%) and ciprofloxacin (69.5%). A relatively high intermediate resistance of 33.0% was observed for ceftriaxone. E. coli from raw meats, RTE meats, hands of meat sellers and working tools showed some differences and similarities in their phenotypic antimicrobial resistance patterns. Half (51.1%) of the E. coli isolates exhibited multidrug resistance. The E. coli isolates showed twenty-two different resistant patterns, with a multiple antibiotic resistance index of 0.0 to 0.7. The resistant pattern amoxicillin (A, n = 6 isolates) and amoxicillin-trimethoprim (A-TM, n = 6 isolates) were the most common. This study documents that raw meats, RTE meats and their related samples in Ghana are potential sources of antimicrobial-resistant E. coli and pose a risk for the transfer of resistant bacteria to the food chain, environment and humans.

Download Full-text

Antimicrobial susceptibility and diarrheagenic diagnosis of Escherichia coli and Salmonella enterica isolated from feral pigeons (Columba livia) captured in Fortaleza, Brazil

Pesquisa Veterinária Brasileira ◽

10.1590/1678-5150-pvb-5633 ◽

2018 ◽

Vol 38 (11) ◽

pp. 2150-2154 ◽

Cited By ~ 2

Author(s):

Ruben V. Horn ◽

Windleyanne G.A. Bezerra ◽

Elisângela S. Lopes ◽

Régis S.C. Teixeira ◽

Isaac N.G. Silva ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Clavulanic Acid ◽

Antimicrobial Susceptibility ◽

Salmonella Enterica ◽

Columba Livia ◽

Susceptibility Test ◽

Antimicrobial Susceptibility Test ◽

E Coli ◽

Feral Pigeons

ABSTRACT: This study aimed to isolate Escherichia coli and Salmonella enterica from captured feral pigeons in Fortaleza, Brazil, and, in addition to evaluate the antimicrobial susceptibility profiles and diagnose diarrheagenic E. coli strains. Pigeons were captured in four public locations in Fortaleza with three techniques. Individual cloacal swab samples were collected and submitted to bacterial isolation, biochemical identification and antimicrobial susceptibility test. Disk diffusion technique was used with twelve antibiotics. E. coli strains were submitted to DNA extraction followed by PCR to diagnose five diarrheagenic pathotypes. A total of 124 birds were captured. One bird was positive for Salmonella enterica (0.81%) and 121 (97.58%) were positive for E. coli. Among these, 110 isolates were submitted to antimicrobial susceptibility test and 28.18% (31/110) presented resistance to at least one antibiotic. Resistance to azithromycin was the most frequent (21.82%), followed by tetracycline (10.91%) and sulfamethoxazole with trimethoprim (8.9%). Multidrug resistance, calculated as a resistance to at least 3 antimicrobial classes, was identified in 3.64% (4/110) of strains. The maximum number of antimicrobial classes to which one strain was resistant was seven. Results demonstrated nine different resistance profiles and the most frequent was tetracycline and sulfamethoxazole with trimethoprim (4 strains), followed by chloramphenicol, azithromycin, tetracycline and sulfamethoxazole with trimethoprim (3 strains). Amoxicillin with clavulanic acid and tobramycin presented lowest levels of antimicrobial resistance, to which none of the tested strains were resistant. A single strain was positive for the eltB gene, which is a diagnostic tool to identify the Enterotoxigenic E. coli (ETEC) pathotype. None of the other investigated genes (stx1, stx2, estA, eaeA, ipaH, aatA and aaiC) were identified. The single isolate of S. enterica was a rough strain of Salmonella enterica subsp. enterica, but serotype identification was not possible. However, this isolate presented resistance to amoxicillin, amoxicillin with clavulanic acid, tetracycline and sulfamethoxazole with trimethoprim. Therefore, captured feral pigeons of Fortaleza presented a low prevalence of S. enterica and diarrheagenic E. coli. Considering the investigated pathogens, our results suggest a good health status and a low public health risk. However, important antimicrobial resistance profiles were identified.

Download Full-text

Incidence and Antimicrobial Susceptibility of Escherichia coli and Klebsiella pneumoniae with Extended-Spectrum β-Lactamases in Community- and Hospital-Associated Intra-Abdominal Infections in Europe: Results of the 2008 Study for Monitoring Antimicrobial Resistance Trends (SMART)

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00265-10 ◽

2010 ◽

Vol 54 (7) ◽

pp. 3043-3046 ◽

Cited By ~ 58

Author(s):

Stephen P. Hawser ◽

Samuel K. Bouchillon ◽

Daryl J. Hoban ◽

Robert E. Badal ◽

Rafael Cantón ◽

...

Keyword(s):

Escherichia Coli ◽

Antimicrobial Resistance ◽

Klebsiella Pneumoniae ◽

Antimicrobial Susceptibility ◽

Beta Lactamase ◽

Extended Spectrum Beta Lactamase ◽

E Coli ◽

Extended Spectrum ◽

Abdominal Infections

ABSTRACT From 2002 to 2008, there was a significant increase in extended-spectrum beta-lactamase (ESBL)-positive Escherichia coli isolates in European intra-abdominal infections, from 4.3% in 2002 to 11.8% in 2008 (P < 0.001), but not for ESBL-positive Klebsiella pneumoniae isolates (16.4% to 17.9% [P > 0.05]). Hospital-associated isolates were more common than community-associated isolates, at 14.0% versus 6.5%, respectively, for E. coli (P < 0.001) and 20.9% versus 5.3%, respectively, for K. pneumoniae (P < 0.01). Carbapenems were consistently the most active drugs tested.

Download Full-text