High prevalence of OXA-23 carbapenemase-producing Proteus mirabilis among amoxicillin-clavulanate resistant isolates in France

2021 ◽  
Author(s):  
Amélie Lombes ◽  
Rémy A. Bonnin ◽  
Frédéric Laurent ◽  
Hélène Guet-Revillet ◽  
Emmanuelle Bille ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Proteus Mirabilis ◽  
Inhibition Zone ◽  
Whole Genome ◽  
Multicentric Study ◽  
Inhibition Zone Diameter ◽  
Zone Diameter ◽  
High Prevalence ◽  
Amoxicillin Clavulanate

In this multicentric study performed in 12 French hospitals, we reported that 26.9% (14/52) of the amoxicillin/clavulanate-resistant Proteus mirabilis isolates produced the OXA-23 carbapenemase. We found that inhibition zone diameter less than 11 mm around amoxicillin/clavulanate disc was an accurate screening cut-off to detect these OXA-23 producers. We confirmed by whole genome sequencing that these OXA-23-producers all belonged to the same lineage that has been demonstrated to disseminate OXA-23 or OXA-58 in P. mirabilis .

scholarly journals Multidrug-Resistant Proteus mirabilis Strain with Cointegrate Plasmid

2020 ◽  
Vol 8 (11) ◽  
pp. 1775
Author(s):  
Andrey Shelenkov ◽  
Lyudmila Petrova ◽  
Valeria Fomina ◽  
Mikhail Zamyatin ◽  
Yulia Mikhaylova ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Proteus Mirabilis ◽  
Intestinal Microflora ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Long Read ◽  
Tract Infections ◽  
Eskape Pathogens

Proteus mirabilis is a component of the normal intestinal microflora of humans and animals, but can cause urinary tract infections and even sepsis in hospital settings. In recent years, the number of multidrug-resistant P. mirabilis isolates, including the ones producing extended-spectrum β-lactamases (ESBLs), is increasing worldwide. However, the number of investigations dedicated to this species, especially, whole-genome sequencing, is much lower in comparison to the members of the ESKAPE pathogens group. This study presents a detailed analysis of clinical multidrug-resistant ESBL-producing P. mirabilis isolate using short- and long-read whole-genome sequencing, which allowed us to reveal possible horizontal gene transfer between Klebsiella pneumoniae and P. mirabilis plasmids and to locate the CRISPR-Cas system in the genome together with its probable phage targets, as well as multiple virulence genes. We believe that the data presented will contribute to the understanding of antibiotic resistance acquisition and virulence mechanisms for this important pathogen.

scholarly journals Characterization of SXT/R391 Integrative and Conjugative Elements in Proteus mirabilis Isolates from Food-Producing Animals in China

2016 ◽  
Vol 60 (3) ◽  
pp. 1935-1938 ◽  
Author(s):  
Chang-Wei Lei ◽  
An-Yun Zhang ◽  
Hong-Ning Wang ◽  
Bi-Hui Liu ◽  
Li-Qin Yang ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Resistance Genes ◽  
Proteus Mirabilis ◽  
Whole Genome ◽  
Content Type ◽  
Integrative And Conjugative Elements ◽  
Animal Farms

SXT/R391 integrative and conjugative elements (ICEs) were detected in 8 out of 125Proteus mirabilisisolates from food-producing animals in China. Whole-genome sequencing revealed that seven ICEs were identical to ICEPmiJpn1, carrying the cephalosporinase geneblaCMY-2. Another one, designated ICEPmiChn1, carried five resistance genes. All eight ICEs could be transferred toEscherichia colivia conjugation. The results highlight the idea that animal farms are important reservoir of the SXT/R391 ICE-containingP. mirabilis.

scholarly journals Whole genomic sequencing based genotyping reveals a specific X3 sublineage restricted to Mexico and related with multidrug resistance

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Ana Cristina Jiménez-Ruano ◽  
Carlos Francisco Madrazo-Moya ◽  
Irving Cancino-Muñoz ◽  
Paulina M. Mejía-Ponce ◽  
Cuauhtémoc Licona-Cassani ◽  
...  
Keyword(s):  
Multidrug Resistance ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Multidrug Resistant ◽  
Genomic Sequencing ◽  
Whole Genome ◽  
Drug Resistant ◽  
The Past ◽  
High Prevalence ◽  
Genomic Cluster

AbstractWhole genome sequencing (WGS) has been shown to be superior to traditional procedures of genotyping in tuberculosis (TB), nevertheless, reports of its use in drug resistant TB (DR-TB) isolates circulating in Mexico, are practically unknown. Considering the above the main of this work was to identify and characterize the lineages and genomic transmission clusters present in 67 DR-TB isolates circulating in southeastern Mexico. The results show the presence of three major lineages: L1 (3%), L2 (3%) and L4 (94%), the last one included 16 sublineages. Sublineage 4.1.1.3 (X3) was predominant in 18 (27%) of the isolates, including one genomic cluster, formed by eleven multidrug resistant isolates and sharing the SIT 3278, which seems to be restricted to Mexico. By the use of WGS, it was possible to identify the high prevalence of L4 and a high number of sublineages circulating in the region, also was recognized the presence of a novel X3 sublineage, formed exclusively by multidrug resistant isolates and with restrictive circulation in Mexico for at least the past 17 years.

scholarly journals Contamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso

PLoS ONE ◽  
2021 ◽  
Vol 16 (6) ◽  
pp. e0253312
Author(s):  
Marguerite E. M. Nikiema ◽  
Maria Pardos de la Gandara ◽  
Kiswensida A. M. Compaore ◽  
Absétou Ky Ba ◽  
Karna D. Soro ◽  
...  
Keyword(s):  
Burkina Faso ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Public Health Problem ◽  
Multidrug Resistant ◽  
Whole Genome ◽  
Global Public Health ◽  
Gastrointestinal Infections ◽  
Street Food ◽  
High Prevalence

Background Gastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation. Methods Between June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants. Results The prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade). Conclusion This study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern.

scholarly journals Whole Genome Sequencing Links Mycobacterium bovis From Cattle, Cheese and Humans in Baja California, Mexico

2021 ◽  
Vol 8 ◽  
Author(s):  
Alejandro Perera Ortiz ◽  
Claudia Perea ◽  
Enrique Davalos ◽  
Estela Flores Velázquez ◽  
Karen Salazar González ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Mycobacterium Bovis ◽  
Baja California ◽  
Whole Genome ◽  
Direct Pcr ◽  
Tissue Samples ◽  
High Prevalence

Mycobacterium bovis causes tuberculosis (TB) in cattle, which in turn can transmit the pathogen to humans. Tuberculosis in dairy cattle is of particular concern where the consumption of raw milk and dairy products is customary. Baja California (BCA), Mexico, presents high prevalence of TB in both cattle and humans, making it important to investigate the molecular epidemiology of the disease in the region. A long-term study was undertaken to fully characterize the diversity of M. bovis genotypes circulating in dairy cattle, cheese and humans in BCA by whole-genome sequencing (WGS). During a 2-year period, 412 granulomatous tissue samples were collected from local abattoirs and 314 cheese samples were purchased from local stores and vendors in BCA and sent to the laboratory for mycobacterial culture, histology, direct PCR and WGS. For tissue samples M. bovis was recovered from 86.8%, direct PCR detected 90% and histology confirmed 85.9% as mycobacteriosis-compatible. For cheese, M. bovis was recovered from 2.5% and direct PCR detected 6% of the samples. There was good agreement between diagnostic tests. Subsequently, a total of 345 whole-genome SNP sequences were obtained. Phylogenetic analysis grouped these isolates into 10 major clades. SNP analysis revealed putative transmission clusters where the pairwise SNP distance between isolates from different dairies was ≤3 SNP. Also, human and/or cheese isolates were within 8.45 (range 0–17) and 5.8 SNP (range 0–15), respectively, from cattle isolates. Finally, a comparison between the genotypes obtained in this study and those reported previously suggests that the genetic diversity of M. bovis in BCA is well-characterized, and can be used to determine if BCA is the likely source of M. bovis in humans and cattle in routine epidemiologic investigations and future studies. In conclusion, WGS provided evidence of ongoing local transmission of M. bovis among the dairies in this high-TB burden region of BCA, as well as show close relationships between isolates recovered from humans, cheese, and cattle. This confirms the need for a coordinated One Health approach in addressing the elimination of TB in animals and humans. Overall, the study contributes to the knowledge of the molecular epidemiology of M. bovis in BCA, providing insight into the pathogen's dynamics in a high prevalence setting.

scholarly journals Fluoroquinolone Resistance among Clonal Complex 1 Group BStreptococcusStrains

2016 ◽  
Vol 2016 ◽  
pp. 1-5 ◽  
Author(s):  
Alefiya Neemuchwala ◽  
Sarah Teatero ◽  
Samir N. Patel ◽  
Nahuel Fittipaldi
Keyword(s):  
North America ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clonal Complex ◽  
Opportunistic Pathogen ◽  
Fluoroquinolone Resistance ◽  
Whole Genome ◽  
High Prevalence ◽  
Invasive Diseases ◽  
Group B

Fluoroquinolone resistance in group BStreptococcusis increasingly being reported worldwide. Here, we correlated fluoroquinolone resistance with mutations ingyrA,gyrB,parC, andparEgenes, identified by mining whole-genome sequencing (WGS) data of 190 clonal complex 1 group BStreptococcusstrains recovered from patients with invasive diseases in North America. We report a high prevalence of fluoroquinolone resistance (12%) among GBS strains in our collection. Our approach is the first step towards accurate prediction of fluoroquinolone resistance from WGS data in this opportunistic pathogen.

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