Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure

Rehman, Muhammad Attiq; X, Yin; Lepp, Dion; Laing, Chad R.; Ziebell, Kim; Talbot, Guylaine; Topp, Edward; Diarra, Moussa S.

doi:10.3390/vetsci4040057

Cited by 17 publications

(22 citation statements)

References 54 publications

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“…Some studies have shown that ESBL are responsible for producing antibiotic-resistant bacteria strains [11,12]. The spread of the strains is likely to limit the effectiveness of antimicrobials used to treat the patients suffering from pathogen bacteria such as Escherichiacoli and Salmonella [13][14][15][16] These ESBL-producing bacteria often show resistance to several antimicrobials such as third and fourth generation cephalosporins as well as quinolones and aminoglycosides [17][18][19]. Although inhibited by clavulanic acid, ESBL enzymes have the ability to hydrolyze third generation cephalosporins and aztreonam [9].…”

Section: Introductionmentioning

confidence: 99%

Extended spectrum beta-lactamase and ﬂuoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso.

Dembélé

Konaté²,

Traoré

et al. 2020

Preprint

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Background: The emergence and spread of multidrug-resistant gram-negative bacteria (MDR) has become a major public health concern worldwide. This resistance is caused by enzymes-mediated genes (i.e., extended spectrum beta-lactamases) that are common in certain Enterobacterioceae species. However, the distribution of these genes is poorly documented in Burkina Faso. This study aims to determine the prevalence and distribution of the resistant genes coding for broad spectrum beta-lactamases and quinolones in rural Burkina Faso.Methods: Multiplex PCR assays were carried out to detect ESBL-encoding genes, including blaOXA, blaTEM, blaCTX-M, blaSHV. The assays also assessed the presence of quinolone resistance gene namely qnrA, qnrB and qnrS in the quinolone-resistance DEC and Salmonella strains.Results: The Extended-Spectrum Beta-Lactamases (ESBL) resistance phenotype was reported in all the E. coli isolates (5/5). Cross-resistance phenotype to quinolones (CRQ) was shown by one Salmonella strain (1/9) and three E. coli (3/5). Cross-resistance phenotypes to fluoroquinolones (CRFQ) were harboured by one Salmonella (1/9) and carbapenemase phenotypes were detected in two E. coli strains (2/5). Whilst the blaOXA genes were detected in 100% (5/5) of E. coli isolates and in 33.33% (3/9) Salmonella isolates. One strain of E. coli (1/5) harbored the blaCTX-M gene and the qnrB gene simultaneously.Conclusions: This study identified β-lactam (bla) and quinolone resistance (qnr) genes in multidrug-resistant E. coli and Salmonella spp. in rural Burkina Faso. Our finding which highlighted the enterobacteriaceae strains resistance to β-lactams and quinolones are of high interest for adequate management of antimicrobial resistant genes outbreak in Burkina Faso.

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Section: Introductionmentioning

confidence: 99%

Extended spectrum beta-lactamase and ﬂuoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso.

Dembélé

Konaté²,

Traoré

et al. 2020

Preprint

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“…However, we found a bla CMY-2 gene flanked by the IncI1 plasmid marker in one of our isolates. This plasmid-mediated ampC gene was also observed on IncFIB, IncI1, IncA/C, IncF, and IncK/B in E. coli isolates from recreational beaches and private drinking water in Canada (Hopkins et al, 2006;Mulvey et al, 2009;Martin et al, 2012;Rehman et al, 2017). The presence of plasmid Inc groups in the aquatic environment may play a role in maintenance and dissemination of resistance genes between environment, animals and humans.…”

Section: Discussionmentioning

confidence: 76%

“…A maximum likelihood tree was generated based on SNPs alignment (Kaas et al, 2014). SEED Viewer (SEED, 2018) was used to visualize whole genome sequence comparisons of coding sequence identity between reference strains and isolates from this study (Overbeek et al, 2005). …”

Section: Methodsmentioning

confidence: 99%

Antimicrobial‐Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms

Taggar

Rehman

et al. 2018

J of Env Quality

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Untreated surface waters can be contaminated with a variety of bacteria, including Escherichia coli, some of which can be pathogenic for both humans and animals. Therefore, such waters need to be treated before their use in dairy operations to mitigate risks to dairy cow health and milk safety. To understand the molecular ecology of E. coli, this study aimed to assess antimicrobial resistance (AMR) in E. coli recovered from untreated surface water sources of dairy farms. Untreated surface water samples (n = 240) from 15 dairy farms were collected and processed to isolate E. coli. A total of 234 E. coli isolates were obtained and further characterized for their serotypes and antimicrobial susceptibility. Of the 234 isolates, 71.4% were pan‐susceptible, 23.5% were resistant to one or two antimicrobial classes, and 5.1% were resistant to three or more antimicrobial classes. Whole genome sequence analysis of 11 selected multidrug‐resistant isolates revealed AMR genes including blaCMY‐2 and blaCTX‐M‐1 that confer resistance to the critically important extended‐spectrum cephalosporins, as well as a variety of plasmids (mainly of the IncF replicon type) and class 1 integrons. Phylogenetic and comparative genome analysis revealed a genetic relationship between some of the sequenced E. coli and Shiga toxin‐producing E. coli O157:H7 (STEC), which warrants further investigation. This study shows that untreated surface water sources contain antimicrobial‐resistant E. coli, which may serve as a reservoir of AMR that could be disseminated through horizontal gene transfer. This is another reason why effective water treatment before usage should be routinely done on dairy farm operations. Core Ideas Surface water is a valuable input for livestock production. Untreated surface water can be a source of antimicrobial‐resistant bacteria. Multidrug‐resistant E. coli strains may facilitate spread of antimicrobial resistance (AMR). Whole genome sequencing provides insight into the molecular ecology of E. coli from surface water. This highlights the need to implement efficient water treatment units for dairy farms.

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“…Infections caused by extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae have been linked to their dissemination through both food and the environment [1][2][3]. ESBL-producing bacteria, including E. coli are frequently resistant to multiple antimicrobials including 3rd and 4th generation cephalosporins in addition to quinolones and aminoglycosides [1,2,4]. These bacteria have been designated priority group 1 pathogens for the development of alternative antimicrobial therapies by the World Health Organization [5] as they can cause serious urinary tract [6,7] and bloodstream [8][9][10] infections, occasionally resulting in mortalities [11].…”

Section: Introductionmentioning

confidence: 99%

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

Adator

Walker²,

Narváez‐Bravo

et al. 2020

Microorganisms

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Antimicrobial resistance (AMR) has important implications for the continued use of antibiotics to control infectious diseases in both beef cattle and humans. AMR along the One Health continuum of the beef production system is largely unknown. Here, whole genomes of presumptive extended-spectrum β-lactamase E. coli (ESBL-EC) from cattle feces (n = 40), feedlot catch basins (n = 42), surrounding streams (n = 21), a beef processing plant (n = 4), municipal sewage (n = 30), and clinical patients (n = 25) are described. ESBL-EC were isolated from ceftriaxone selective plates and subcultured on ampicillin selective plates. Agreement of genotype-phenotype prediction of AMR ranged from 93.2% for ampicillin to 100% for neomycin, trimethoprim/sulfamethoxazole, and enrofloxacin resistance. Overall, β-lactam (100%; blaEC, blaTEM-1, blaSHV, blaOXA, blaCTX-M-), tetracycline (90.1%; tet(A), tet(B)) and folate synthesis (sul2) antimicrobial resistance genes (ARGs) were most prevalent. The ARGs tet(C), tet(M), tet(32), blaCTX-M-1, blaCTX-M-14, blaOXA-1, dfrA18, dfrA19, catB3, and catB4 were exclusive to human sources, while blaTEM-150, blaSHV-11–12, dfrA12, cmlA1, and cmlA5 were exclusive to beef cattle sources. Frequently encountered virulence factors across all sources included adhesion and type II and III secretion systems, while IncFIB(AP001918) and IncFII plasmids were also common. Specificity and prevalence of ARGs between cattle-sourced and human-sourced presumptive ESBL-EC likely reflect differences in antimicrobial use in cattle and humans. Comparative genomics revealed phylogenetically distinct clusters for isolates from human vs. cattle sources, implying that human infections caused by ESBL-EC in this region might not originate from beef production sources.

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Genomic Analysis of Third Generation Cephalosporin Resistant Escherichia coli from Dairy Cow Manure

Cited by 17 publications

References 54 publications

Extended spectrum beta-lactamase and ﬂuoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso.

Extended spectrum beta-lactamase and ﬂuoroquinolone resistance genes among Escherichia coli and Salmonella isolates from children with diarrhea, Burkina Faso.

Antimicrobial‐Resistant E. coli from Surface Waters in Southwest Ontario Dairy Farms

Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase Producing Escherichia coli along Segments of the One Health Continuum

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