Rapid detection of human origin colistin-resistance genes mcr-1, mcr-3, mcr-8, mcr-10 in clinical fecal samples

Characterisation of colistin resistance in Gram-negative microbiota of pregnant women and neonates in Nigeria

A mobile colistin resistance gene mcr was first reported in 2016 in China and has since been found with increasing prevalence across South-East Asia. Here we survey the presence of mcr genes in 4907 rectal swabs from mothers and neonates from three hospital sites across Nigeria; a country with limited availability or history of colistin use clinically. Forty mother and seven neonatal swabs carried mcr genes in a range of bacterial species: 46 Enterobacter spp. and single isolates of; Shigella, E. coli and Klebsiella quasipneumoniae. Ninety percent of the genes were mcr-10 (n = 45) we also found mcr-1 (n = 3) and mcr-9 (n = 1). While the prevalence during this collection (2015-2016) was low, the widespread diversity of mcr-gene type and range of bacterial species in this sentinel population sampling is concerning. It suggests that agricultural colistin use was likely encouraging sustainment of mcr-positive isolates in the community and implementation of medical colistin use will rapidly select and expand resistant isolates.

Genomic characterisation of multi-drug resistant Escherichia coli and Klebsiella pneumoniae co-harbouring mcr-1 and mcr-3 genes on a single plasmid from paediatric clinical cases

OBJECTIVES

Emergence of the plasmid-born mobile colistin resistance (mcr) gene is a growing concern in healthcare. Therefore, this study aimed to genomically characterise multidrug-resistant Escherichia coli and Klebsiella pneumoniae co-harbouring the mcr-1 and mcr-3 genes in young children.

METHODS

E. coli (n = 3) and K. pneumoniae (n = 2) were collected from abdominal secretions and blood, respectively. The isolates were screened using tryptone soy broth with 4 µL/mL polymyxin-B. Growing bacteria were identified using the VITEK-2 system, matrix-assisted laser desorption/ionisation time-of-flight, and 16s RNA sequencing, followed by antibiotic susceptibility testing. Metallo-β-lactamase (MBL) and extended-spectrum β-lactamase (ESBL) production was also detected. Afterwards, strains were subjected to molecular screening targeting mcr variants and ESBL/MBL-encoding genes. Conjugation, pulsed-field gel electrophoresis, Southern hybridisation, multilocus sequence typing, and phylogenic group detection were performed, along with plasmid-genome sequencing and bioinformatics analysis.

RESULTS

E. coli isolates (EC-19-322, 323, and 331) and K. pneumoniae isolates (KP-19-225 and 226) harboured both mcr-1 and mcr-3 genes. These strains were also found to be resistant to more than three classes of antibiotics. The conjugation experiment revealed the presence of mcr-1 and mcr-3 on a single plasmid, and the transmission frequency was 10-2 to 10-3. Both strains were found to be able to produce ESBLs and MBL. E. coli EC-19-322 and 323 were identified as ST131(O25a:H41); SP-19-331, as ST1577 (O16:H30); and K. pneumoniae, as ST231 (K2). All E. coli strains belonged to phylogenetic group B2, and the results of pulsed-field gel electrophoresis supported the multilocus sequence typing findings.

CONCLUSION

This study reported the co-occurrence of mcr-1 and mcr-3 genes on a single plasmid in pathogenic ESBL/MBL-producing E. coli and K. pneumoniae isolated from young children.

Genetic Characterization of an ST5571 Hypervirulent Klebsiella pneumoniae Strain Co-Producing NDM-1, MCR-1, and OXA-10 Causing Bacteremia

Purpose

To investigate the phenotypic and genomic characteristics of the multi-drug resistant and hypervirulent Klebsiella pneumoniae strain recovered from bacteremia.

Methods

Antimicrobial susceptibility testing (AST) was performed by the microdilution method. Antimicrobial resistance genes, virulence-associated genes, multilocus sequence typing (MLST), and plasmid replicon were characterized by next-generation sequencing (NGS) and nanopore sequencing. S1 nuclease-pulsed field gel electrophoresis (S1-PFGE) and Southern blotting were performed to characterize the plasmid profile.

Results

The hypervirulent colistin- and carbapenem-resistant K. pneumoniae strain DY2009 was identified as ST5571, co-carrying mcr-1, bla NDM-1, and bla OXA-10. In silico analysis found that it was K2 serotype. AST results revealed that DY2009 was resistant to carbapenems, cephalosporins, ciprofloxacin, chloramphenicol, and colistin but remained susceptible to aztreonam, gentamicin, amikacin, and tigecycline. Through the whole-genome analysis, a variety of virulence determinants were identified, including rmpA. Plasmid analysis confirmed that the mcr-1 and bla NDM-1 gene harbored a ~33 kb IncX4 plasmid and a ~44 kb IncX3 plasmid. In contrast, bla OXA-10 was encoded by chromosome.

Conclusion

To the best of our knowledge, we first report the clinical hypervirulent K. pneumoniae isolate co-producing MCR-1, NDM-1, and OXA-10 causing bacteremia. We found that mcr-1 and bla NDM-1 genes were located on two self-conjugative epidemic plasmids, contributing to the widespread MCR-1 and NDM-1 in China. The results of this work improve our understanding of the genetic background of colistin- and carbapenem-resistant K. pneumoniae isolate from bacteremia and the resistance mechanisms. Our findings highlight the urgent need for infection control of such strain to prevent it from becoming an extensive-drug resistant clone.

Emergence of Colistin Resistance Gene mcr-10 in Enterobacterales Isolates Recovered from Fecal Samples of Chickens, Slaughterhouse Workers, and a Nearby Resident

The wide spread of plasmid-borne mobilized colistin resistance (mcr) genes from animals to humans broadly challenges the clinical use of polymyxins. Here, we evaluated the incidence of a recently reported mcr variant, mcr-10, in animals and humans in the same area. Our results revealed the presence of novel mcr-10-carrying plasmids in two Klebsiella pneumoniae isolates from chickens, one Escherichia coli isolate from slaughterhouse workers, and a chromosome-borne mcr-10 gene in Enterobacter kobei from a healthy resident in the same region. It is worth mentioning that the multidrug-resistant ST11 K. pneumoniae isolates coharboring mcr-10 and mcr-8 genes in two separate plasmids not only were resistant to polymyxins (MIC = 8 mg/L) but also showed reduced susceptibility to tigecycline (MIC ≥ 2 mg/L) due to the tet(A) mutation or the tmexCD1-toprJ1 gene cluster. The structure xerC-mcr10-insCinsD-like was found in genetic environments of both the plasmid and chromosome carrying mcr-10. We compared genomic epidemiological characteristics of mcr-10-harboring bacteria available in 941,449 genomes in the NCBI database (including strains of K. pneumoniae, E. coli, and E. kobei) with isolates in this study. The results indicated a sporadic distribution of mcr-10 all around the world and in a variety of sources, including humans, environments, and animals, which confirms that mcr-10 has spread among various hosts and warrants close monitoring and further future studies. IMPORTANCE We discovered mcr-10-harboring isolates in the "one health" approach and reported for the first time multidrug-resistant clinically threatening ST11 K. pneumoniae isolates coharboring mcr-10 and mcr-8 genes that are resistant to polymyxins and show reduced susceptibility to tigecycline. The exhaustive screening of 941,449 bacterial genomes in the GenBank database discovered a sporadic distribution of mcr-10-harboring isolates all around the world in a variety of sources, especially humans, which warrants close monitoring and a particular concern in clinical settings.

Ferrate (VI) Oxidation Is an Effective and Safe Way to Degrade Residual Colistin - a Last Resort Antibiotic - in Wastewater

The rise of novel mcr mobile resistance genes seriously threatens the use of colistin as a last resort antibiotic for treatment of multidrug-resistant Gram-negative bacterial infections in humans. Large quantities of colistin are released annually into the environment through animal feces. This leads to environmental toxicity and promotes horizontal transmission of the mcr gene in aqueous environments. We examined colistin degradation catalyzed by the presence of strong oxidant Fe (VI). We found almost complete colistin degradation (>95%) by Fe (VI) at initial colistin levels of 30 μM at a molar ratio of Fe (VI): colistin of 30 using an initial pH 7.0 at 25°C for 60 min. The presence of humic acid did not alter the degradation rate and had no significant impact on the removal of colistin by Fe (VI). Quantitative microbiological assays of Fe (VI)-treated colistin solutions using Escherichia coli, Staphylococcus aureus, and Bacillus subtilis indicated that the residual antibacterial activity was effectively eliminated by Fe (VI) oxidation. Luminescent bacteria toxicity tests using Vibrio fischeri indicated that both colistin and its degradation products in water were of low toxicity and the products showed decreased toxicity compared to the parent drug. Therefore, Fe (VI) oxidation is a highly effective and environment-friendly strategy to degrade colistin in water.