scholarly journals Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr-10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East

2021 ◽  
Vol 12 ◽  
Author(s):  
Yasmine H. Tartor ◽  
Norhan K. Abd El-Aziz ◽  
Rasha M. A. Gharieb ◽  
Hend M. El Damaty ◽  
Shymaa Enany ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Genome Sequencing ◽  
Bovine Milk ◽  
Bovine Mastitis ◽  
Raw Milk ◽  
Whole Genome ◽  
Gram Negative Bacteria ◽  
Gram Negative ◽  
E Coli

Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (n = 350) and subclinical (n = 95) bovine mastitis, and raw unpasteurized milk (n = 125). Klebsiella pneumoniae, Aeromonas hydrophila, Enterobacter cloacae (100% each), Escherichia coli (87.78%), and Proteus mirabilis (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in P. mirabilis (30.30%) and E. coli (3.33%) isolates. Ten isolates (four E. coli, three Klebsiella species and three P. mirabilis) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced E. coli isolates. Three E. coli isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas E. coli ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin mcr-10 and fosfomycin fosA5 resistance genes in a K. pneumoniae (K1) isolate from bovine milk. Sequence analysis of the reconstructed mcr-10 plasmid from WGS of K1 isolate, showed that mcr-10 gene was bracketed by xerC and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including mcr-10-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of K. pneumoniae co-harboring mcr-10 and fosA5 genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.

scholarly journals National Surveillance of Antimicrobial Susceptibility of Bacteremic Gram-Negative Bacteria with Emphasis on Community-Acquired Resistant Isolates: Report from the 2019 Surveillance of Multicenter Antimicrobial Resistance in Taiwan (SMART)

2020 ◽  
Vol 64 (10) ◽  
Author(s):  
Po-Yu Liu ◽  
Yu-Lin Lee ◽  
Min-Chi Lu ◽  
Pei-Lan Shao ◽  
Po-Liang Lu ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Gram Negative Bacteria ◽  
National Surveillance ◽  
Gram Negative ◽  
Content Type ◽  
E Coli ◽  
Carbapenem Resistant

ABSTRACT A multicenter collection of bacteremic isolates of Escherichia coli (n = 423), Klebsiella pneumoniae (n = 372), Pseudomonas aeruginosa (n = 300), and Acinetobacter baumannii complex (n = 199) was analyzed for susceptibility. Xpert Carba-R assay and sequencing for mcr genes were performed for carbapenem- or colistin-resistant isolates. Nineteen (67.8%) carbapenem-resistant K. pneumoniae (n = 28) and one (20%) carbapenem-resistant E. coli (n = 5) isolate harbored blaKPC (n = 17), blaOXA-48 (n = 2), and blaVIM (n = 1) genes.

scholarly journals Virulence Determinants and Plasmid-Mediated Colistin Resistance mcr Genes in Gram-Negative Bacteria Isolated From Bovine Milk

2021 ◽  
Vol 11 ◽  
Author(s):  
Yasmine H. Tartor ◽  
Rasha M. A. Gharieb ◽  
Norhan K. Abd El-Aziz ◽  
Hend M. El Damaty ◽  
Shymaa Enany ◽  
...  
Keyword(s):  
Virulence Genes ◽  
Raw Milk ◽  
Subclinical Mastitis ◽  
Clinical Mastitis ◽  
Gram Negative Bacteria ◽  
Colistin Resistance ◽  
Genetic Characteristics ◽  
Gram Negative ◽  
E Coli ◽  
Resistant Strains

A major increase of bacterial resistance to colistin, a last-resort treatment for severe infections, was observed globally. Using colistin in livestock rearing is believed to be the ground of mobilized colistin resistance (mcr) gene circulation and is of crucial concern to public health. This study aimed to determine the frequency and virulence characteristics of colistin-resistant Gram-negative bacteria from the milk of mastitic cows and raw unpasteurized milk in Egypt. One hundred and seventeen strains belonging to Enterobacteriaceae (n = 90), Pseudomonas aeruginosa (n = 10), and Aeromonas hydrophila (n = 17) were screened for colistin resistance by antimicrobial susceptibility testing. The genetic characteristics of colistin-resistant strains were investigated for mcr-1–9 genes, phylogenetic groups, and virulence genes. Moreover, we evaluated four commonly used biocides in dairy farms for teat disinfection toward colistin-resistant strains. Multidrug-resistant (MDR) and extensive drug-resistant (XDR) phenotypes were detected in 82.91% (97/117) and 3.42% (4/117) of the isolates, respectively. Of the 117 tested isolates, 61 (52.14%) were colistin resistant (MIC >2 mg/L), distributed as 24/70 (34.29%) from clinical mastitis, 10/11 (90.91%) from subclinical mastitis, and 27/36 (75%) from raw milk. Of these 61 colistin-resistant isolates, 47 (19 from clinical mastitis, 8 from subclinical mastitis, and 20 from raw milk) harbored plasmid-borne mcr genes. The mcr-1 gene was identified in 31.91%, mcr-2 in 29.79%, mcr-3 in 34.04%, and each of mcr-4 and mcr-7 in 2.13% of the colistin-resistant isolates. Among these isolates, 42.55% (20/47) were E. coli, 21.28% (10/47) A. hydrophila, 19.12% (9/47) K. pneumoniae, and 17.02% (8/47) P. aeruginosa. This is the first report of mcr-3 and mcr-7 in P. aeruginosa. Conjugation experiments using the broth-mating technique showed successful transfer of colistin resistance to E. coli J53-recipient strain. Different combinations of virulence genes were observed among colistin-resistant isolates with almost all isolates harboring genes. Hydrogen peroxide has the best efficiency against all bacterial isolates even at a low concentration (10%). In conclusion, the dissemination of mobile colistin resistance mcr gene and its variants between MDR- and XDR-virulent Gram-negative isolates from dairy cattle confirms the spread of mcr genes at all levels; animals, humans, and environmental, and heralds the penetration of the last-resort antimicrobial against MDR bacteria. Consequently, a decision to ban colistin in food animals is urgently required to fight XDR and MDR bacteria.

scholarly journals Genomic surveillance of Escherichia coli and Klebsiella spp. in hospital sink drains and patients

2020 ◽  
Vol 6 (7) ◽  
Author(s):  
Bede Constantinides ◽  
Kevin K. Chau ◽  
T. Phuong Quan ◽  
Gillian Rodger ◽  
Monique I. Andersson ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Type Species ◽  
Whole Genome ◽  
Content Type ◽  
E Coli ◽  
Link Type ◽  
Antimicrobial Resistance Genes

Escherichia coli and Klebsiella spp. are important human pathogens that cause a wide spectrum of clinical disease. In healthcare settings, sinks and other wastewater sites have been shown to be reservoirs of antimicrobial-resistant E. coli and Klebsiella spp., particularly in the context of outbreaks of resistant strains amongst patients. Without focusing exclusively on resistance markers or a clinical outbreak, we demonstrate that many hospital sink drains are abundantly and persistently colonized with diverse populations of E. coli , Klebsiella pneumoniae and Klebsiella oxytoca , including both antimicrobial-resistant and susceptible strains. Using whole-genome sequencing of 439 isolates, we show that environmental bacterial populations are largely structured by ward and sink, with only a handful of lineages, such as E. coli ST635, being widely distributed, suggesting different prevailing ecologies, which may vary as a result of different inputs and selection pressures. Whole-genome sequencing of 46 contemporaneous patient isolates identified one (2 %; 95 % CI 0.05–11 %) E. coli urine infection-associated isolate with high similarity to a prior sink isolate, suggesting that sinks may contribute to up to 10 % of infections caused by these organisms in patients on the ward over the same timeframe. Using metagenomics from 20 sink-timepoints, we show that sinks also harbour many clinically relevant antimicrobial resistance genes including bla CTX-M, bla SHV and mcr, and may act as niches for the exchange and amplification of these genes. Our study reinforces the potential role of sinks in contributing to Enterobacterales infection and antimicrobial resistance in hospital patients, something that could be amenable to intervention. This article contains data hosted by Microreact.

scholarly journals Detection of TEM and CTX-M Genes in Escherichia coli Isolated from Clinical Specimens at Tertiary Care Heart Hospital, Kathmandu, Nepal

Diseases ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 15
Author(s):  
Ram Shankar Prasad Sah ◽  
Binod Dhungel ◽  
Binod Kumar Yadav ◽  
Nabaraj Adhikari ◽  
Upendra Thapa Shrestha ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Clinical Isolates ◽  
Diffusion Method ◽  
Gram Negative Bacteria ◽  
Bacterial Isolates ◽  
Disk Diffusion Method ◽  
Gram Negative ◽  
Clinical Specimens ◽  
E Coli ◽  
Esbl Producers

Background: Antimicrobial resistance (AMR) among Gram-negative pathogens, predominantly ESBL-producing clinical isolates, are increasing worldwide. The main aim of this study was to determine the prevalence of ESBL-producing clinical isolates, their antibiogram, and the frequency of ESBL genes (blaTEM and blaCTX-M) in the clinical samples from patients. Methods: A total of 1065 clinical specimens from patients suspected of heart infections were collected between February and August 2019. Bacterial isolates were identified on colony morphology and biochemical properties. Thus, obtained clinical isolates were screened for antimicrobial susceptibility testing (AST) using modified Kirby–Bauer disk diffusion method, while ESBL producers were identified by using a combination disk diffusion method. ESBL positive isolates were further assessed using conventional polymerase chain reaction (PCR) to detect the ESBL genes blaTEM and blaCTX-M. Results: Out of 1065 clinical specimens, 17.8% (190/1065) showed bacterial growth. Among 190 bacterial isolates, 57.4% (109/190) were Gram-negative bacteria. Among 109 Gram-negative bacteria, 40.3% (44/109) were E. coli, and 30.2% (33/109) were K. pneumoniae. In AST, 57.7% (n = 63) Gram-negative bacterial isolates were resistant to ampicillin and 47.7% (n = 52) were resistant to nalidixic acid. Over half of the isolates (51.3%; 56/109) were multidrug resistant (MDR). Of 44 E. coli, 27.3% (12/44) were ESBL producers. Among ESBL producer E. coli isolates, 58.4% (7/12) tested positive for the blaCTX-M gene and 41.6% (5/12) tested positive for the blaTEM gene. Conclusion: Half of the Gram-negative bacteria in our study were MDR. Routine identification of an infectious agent followed by AST is critical to optimize the treatment and prevent antimicrobial resistance.

scholarly journals Surgical Site Infections with Predominance of Multidrug Resistant in Benin: A Multicenter Study

2020 ◽  
Vol 41 (S1) ◽  
pp. s526-s526
Author(s):  
Carine Laurence YEHOUENOU ◽  
Hector RODRIGUEZ-VILLALOBOS ◽  
Olivia DALLEUR ◽  
Anne SIMON
Keyword(s):  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Antimicrobial Susceptibility ◽  
Surgical Site Infections ◽  
Public Hospitals ◽  
Secondary Outcome ◽  
Gram Negative ◽  
E Coli ◽  
Maldi Tof ◽  
Esbl Producers

Background: Surgical site infections remain common and widespread; they contribute to increasing antimicrobial resistance among the etiological agents. Antimicrobial resistance is the ability of a microorganism like bacteria to stop an antimicrobial from working against it. This study was conducted to determine the spectrum of bacterial isolates from surgical site infections and their susceptibility patterns. A secondary outcome was to compare bacterial identification by a local lab and a European one. Methods: This descriptive cross-sectional study was conducted between January and August 2019 in 6 public hospitals in Benin. Pus specimens were processed using standard microbiological procedures, and identification was performed using the analytical profile index (API). Antimicrobial susceptibility testing was performed in Benin following the modified Kirby-Bauer disk-diffusion technique and was confirmed in Belgium by MALDI-TOF mass spectrometry. A second antimicrobial susceptibility test was performed using BD Phoenix automated microbiology system (Becton Dickinson). Clinical data of enrolled patients were obtained from hospital records. Results: The mean age of patients was 32 ± 11 years (range, 18–76). The median time for surgical site infections was 9 postoperative days. Of the 229 patients from whom wound swabs were collected, 195 (85.15%) showed positive aerobic bacterial growth. In total, 164 pathogenic bacteria were isolated, including 41 gram-positive organisms (25%), 78 gram-negative fermentative bacteria (47.5%), and 45 gram-negative nonfermentative bacteria (27.5%). We observed 3 discrepancies between API technique and MALDI-TOF. Two Klebsiella pneumoniae and 1 Pseudomonas spp (API) versus, respectively, Klebsiella varicola and Pseudomonas mendocina (MALDI-TOF). The most prevalent bacterial species were E. coli (31%), followed by S. aureus (25%), Pseudomonas aeruginosa (18%), and Klebsiella pneumoniae (11%). Of the 41 S. aureus, 26 (63,41%) were methicillin-resistant Staphylococcus aureus (MRSA), and 3 of these were carrying both MRSA and induced clindamycin resistance (ICR). Extended-spectrum β-lactamase (ESBL)–producing Enterobacteriaceae were observed in 60 of 78 isolates tested (77%). All of 2 Morganella morgannii and 89% of K. pneumoniae were ESBL producers. Conclusions: Among S. aureus, 2 of 3 were MRSA, whereas almost K. pneumoniae and E. coli were ESBL producers. Three strains are pan–drug resistant in nonfermentative bacteria, and no isolate was susceptible to all antibiotics. These findings are of high interest for better management of patients and control of antimicrobial resistance in Benin.Funding: This study was supported by Académie de Recherche pour l’Enseignement Supérieur (ARES).Disclosures: None

scholarly journals Whole-Genome Sequencing for Molecular Characterization of Carbapenem-Resistant Enterobacteriaceae Causing Lower Urinary Tract Infection among Pediatric Patients

Antibiotics ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 972
Author(s):  
Hassan Al Mana ◽  
Sathyavathi Sundararaju ◽  
Clement K. M. Tsui ◽  
Andres Perez-Lopez ◽  
Hadi Yassine ◽  
...  
Keyword(s):  
Urinary Tract ◽  
Antimicrobial Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Bacterial Species ◽  
Whole Genome ◽  
E Coli ◽  
Carbapenem Resistant ◽  
Tract Infections ◽  
Carbapenem Resistant Enterobacteriaceae

Antibiotic resistance is a growing public health problem globally, incurring health and cost burdens. The occurrence of antibiotic-resistant bacterial infections has increased significantly over the years. Gram-negative bacteria display the broadest resistance range, with bacterial species expressing extended-spectrum β-lactamases (ESBLs), AmpC, and carbapenemases. All carbapenem-resistant Enterobacteriaceae (CRE) isolates from pediatric urinary tract infections (UTIs) between October 2015 and November 2019 (n = 30). All isolates underwent antimicrobial resistance phenotypic testing using the Phoenix NMIC/ID-5 panel, and carbapenemase production was confirmed using the NG-Test CARBA 5 assay. Whole-genome sequencing was performed on the CREs. The sequence type was identified using the Achtman multi-locus sequence typing scheme, and antimicrobial resistance markers were identified using ResFinder and the CARD database. The most common pathogens causing CRE UTIs were E. coli (63.3%) and K. pneumoniae (30%). The most common carbapenemases produced were OXA-48-like enzymes (46.6%) and NDM enzymes (40%). Additionally, one E. coli harbored IMP-26, and two K. pneumoniae possessed mutations in ompK37 and/or ompK36. Lastly, one E. coli had a mutation in the marA porin and efflux pump regulator. The findings highlight the difference in CRE epidemiology in the pediatric population compared to Qatar’s adult population, where NDM carbapenemases are more common.

scholarly journals Genomic Analysis of a Pan-Resistant Isolate ofKlebsiella pneumoniae, United States 2016

mBio ◽  
2018 ◽  
Vol 9 (2) ◽  
Author(s):  
Tom J. B. de Man ◽  
Joseph D. Lutgring ◽  
David R. Lonsway ◽  
Karen F. Anderson ◽  
Julia A. Kiehlbauch ◽  
...  
Keyword(s):  
Public Health ◽  
United States ◽  
Antimicrobial Resistance ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
The United States ◽  
Whole Genome ◽  
Beta Lactams ◽  
Content Type

ABSTRACTAntimicrobial resistance is a threat to public health globally and leads to an estimated 23,000 deaths annually in the United States alone. Here, we report the genomic characterization of an unusualKlebsiella pneumoniae, nonsusceptible to all 26 antibiotics tested, that was isolated from a U.S. patient. The isolate harbored four known beta-lactamase genes, including plasmid-mediatedblaNDM-1andblaCMY-6, as well as chromosomalblaCTX-M-15andblaSHV-28, which accounted for resistance to all beta-lactams tested. In addition, sequence analysis identified mechanisms that could explain all other reported nonsusceptibility results, including nonsusceptibility to colistin, tigecycline, and chloramphenicol. Two plasmids, IncA/C2 and IncFIB, were closely related to mobile elements described previously and isolated from Gram-negative bacteria from China, Nepal, India, the United States, and Kenya, suggesting possible origins of the isolate and plasmids. This is one of the firstK. pneumoniaeisolates in the United States to have been reported to the Centers for Disease Control and Prevention (CDC) as nonsusceptible to all drugs tested, including all beta-lactams, colistin, and tigecycline.IMPORTANCEAntimicrobial resistance is a major public health threat worldwide. Bacteria that are nonsusceptible or resistant to all antimicrobials available are of major concern to patients and the public because of lack of treatment options and potential for spread. AKlebsiella pneumoniaestrain that was nonsusceptible to all tested antibiotics was isolated from a U.S. patient. Mechanisms that could explain all observed phenotypic antimicrobial resistance phenotypes, including resistance to colistin and beta-lactams, were identified through whole-genome sequencing. The large variety of resistance determinants identified demonstrates the usefulness of whole-genome sequencing for detecting these genes in an outbreak response. Sequencing of isolates with rare and unusual phenotypes can provide information on how these extremely resistant isolates develop, including whether resistance is acquired on mobile elements or accumulated through chromosomal mutations. Moreover, this provides further insight into not only detecting these highly resistant organisms but also preventing their spread.

scholarly journals Polyclonal dissemination of NDM-1- and NDM-9-producing Escherichia coli and Klebsiella pneumoniae in French Polynesia

2021 ◽  
Author(s):  
Saoussen Oueslati ◽  
Cécile Emeraud ◽  
Victor Grosperrin ◽  
Marc Levy ◽  
Garance Cotellon ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Potential Risk ◽  
French Polynesia ◽  
Foreign Country ◽  
Whole Genome ◽  
Sequencing Analysis ◽  
E Coli

The whole genome sequencing analysis revealed a polyclonal dissemination of NDM-1 and NDM-9 variants in E. coli (n=20) and K. pneumoniae (n=2) in Tahiti since 2015 via interspecies transfer of three different blaNDM-carrying plasmids (IncR, IncHI2 and IncF) and patient-to-patient cross-transmissions. It highlights the potential risk of importation of NDM producers in France where French Polynesia is not considered stricto senso as a foreign country from which repatriated patients have to be screened.

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