Wastewater-based surveillance in Italy leading to the first detection of mcr-10-positive Klebsiella quasipneumoniae

Formenti, Nicoletta; Guarneri, Flavia; Bertasio, Cristina; Parisio, Giovanni; Romeo, Claudia; Scali, Federico; Birbes, Laura; Boniotti, M. B.; Diegoli, Giuseppe; Candela, Loredana; Romeo, Gianluca Antonio; Pasquali, Paolo; Alborali, Giovanni Loris

doi:10.1186/s13756-022-01194-9

Cited by 5 publications

(9 citation statements)

References 24 publications

(42 reference statements)

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“…Most mcr-10-harbouring isolates reported in previous studies were susceptible to colistin [17][18][19][20], but we demonstrated that mcr-10-harbouring K. pneumoniae showed decreased susceptibility to colistin in BHIB. mcr-9 expression in colistin-resistant Enterobacterales was regulated by the two-component system QseBC [15], but colistin-resistant Enterobacterales harbouring mcr-10 had no two-component system like QseBC.…”

Section: Discussioncontrasting

confidence: 57%

“…Thus far, mcr-10-harbouring isolates have been detected in Cronobacter sakazakii, Enterobacter spp., E. coli and Klebsiella spp. from humans, the environment, companion animals and livestock in several countries, including Australia, Canada, PR China, Egypt, Italy, Japan, the Netherlands, Sierra Leone, Switzerland, the UK and Vietnam [17][18][19][20]. These mcr-10-harbouring isolates possessed no carbapenemase-encoding gene.…”

Section: Discussionmentioning

confidence: 99%

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Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

Tada,

Oshiro,

Watanabe

et al. 2023

Journal of Medical Microbiology

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Background. The spread of Enterobacteriaceae coproducing carbapenemases, 16S rRNA methylase and mobile colistin resistance proteins (MCRs) has become a serious public health problem worldwide. This study describes two clinical isolates of Klebsiella pneumoniae coharbouring bla IMP-1, armA and mcr-10. Methods. Two clinical isolates of K. pneumoniae resistant to carbapenems and aminoglycosides were obtained from two patients at a hospital in Myanmar. Their minimum inhibitory concentrations (MICs) were determined by broth microdilution methods. The whole-genome sequences were determined by MiSeq and MinION methods. Drug-resistant factors and their genomic environments were determined. Results. The two K. pneumoniae isolates showed MICs of ≥4 and ≥1024 µg ml−1 for carbapenems and aminoglycosides, respectively. Two K. pneumonaie harbouring mcr-10 were susceptible to colistin, with MICs of ≤0.015 µg ml−1 using cation-adjusted Mueller–Hinton broth, but those for colistin were significantly higher (0.5 and 4 µg ml−1) using brain heart infusion medium. Whole-genome analysis revealed that these isolates coharboured bla NDM-1, armA and mcr-10. These two isolates showed low MICs of 0.25 µg ml−1 for colistin. Genome analysis revealed that both bla NDM-1 and armA were located on IncFIIs plasmids of similar size (81 kb). The mcr-10 was located on IncM2 plasmids of sizes 220 or 313 kb in each isolate. These two isolates did not possess a qseBC gene encoding a two-component system, which is thought to regulate the expression of mcr genes. Conclusion. This is the first report of isolates of K. pneumoniae coharbouring bla NDM-1, armA and mcr-10 obtained in Myanmar.

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Section: Discussioncontrasting

confidence: 57%

Section: Discussionmentioning

confidence: 99%

Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

Tada,

Oshiro,

Watanabe

et al. 2023

Journal of Medical Microbiology

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“…Two multiplex PCRs were set up using the QIAGEN Multiplex PCR Plus Kit for mcr genes from 1 to 5 and from 6 to 10 [ 50 ]. For the first nine mcr, we used primers described in [ 50 , 51 ], while for mcr -10 primers design was based on the first submitted gene sequence [ 52 ], as described in [ 16 ]. PCR reactions were composed as follows: mcr 1–5 genes: 6.75 µL of RNase-free water, 12.5 µL of Multiplex PCR master mix (2×), 2.5 µL of Coral Dye and 1.25 µL of primer mix 10× (0.2 µL of each primer) mcr 6–10 genes: 6.75 µL of RNase-free water, 12.5 µL of Multiplex PCR master mix (2×), 2.5 µL of Coral Dye and 1.25 µL of primer mix 10× (0.2 µL of each primer).…”

Section: Methodsmentioning

confidence: 99%

“…We performed both short-read (on Miniseq, Illumina, San Diego, CA, USA) and long-read sequencing (on MinION, Oxford Nanopore Technologies, Oxford, UK). Genomic DNA extraction, Illumina libraries and sequencing runs on the MiniSeq platform were performed as previously described [ 16 ]. The DNA library for MinION was prepared using the Rapid Barcoding kit (SQK-RBK004) following the manufacturer’s instructions ( , accessed on 2 March 2023).…”

Section: Methodsmentioning

confidence: 99%

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First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm

et al. 2023

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The emergence of colistin resistance raises growing concerns because of its use as a last-resort antimicrobial for the treatment of severe gram-negative bacterial infections in humans. Plasmid-borne mobile colistin resistance genes (mcr) are particularly worrisome due to their high propensity to spread. An mcr-9-positive Escherichia coli was isolated from a piglet in Italy, representing the first isolation of this gene from an E. coli of animal origin in the country. Whole genome sequencing (WGS) revealed that mcr-9 was borne by an IncHI2 plasmid carrying several other resistance genes. The strain was indeed phenotypically resistant to six different antimicrobial classes, including 3rd and 4th generation cephalosporins. Despite the presence of mcr-9, the isolate was susceptible to colistin, probably because of a genetic background unfavourable to mcr-9 expression. The lack of colistin resistance, coupled with the fact that the farm of origin had not used colistin in years, suggests that mcr-9 in such a multidrug-resistant strain can be maintained thanks to the co-selection of neighbouring resistance genes, following usage of different antimicrobials. Our findings highlight how a comprehensive approach, integrating phenotypical testing, targeted PCR, WGS-based techniques, and information on antimicrobial usage is crucial to shed light on antimicrobial resistance.

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Seasonal Patterns in Mobile Colistin Resistance Gene Variants in Wastewater Bioaerosols and Liquid Sludge

Isanovic,

Correa Velez,

Viner

et al. 2024

ACS EST Water

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To address the growing threat of global antimicrobial resistance, a one-health approach is needed to understand the complex socioecological cycling of antibiotic resistance genes. In this study, a metagenomics approach using DNA shotgun sequencing, metagenome assembly, and antibiotic resistance gene (ARG) annotation was used to examine seasonal patterns in the abundance of mobile colistin resistance (mcr) gene variants in bioaerosols and liquid sludge in three wastewater treatment plants (WWTPs). ARGs represented 0.2−0.8 and 0.1−0.2% of the bioaerosol and liquid sludge metagenomes, respectively, while mcr genes represented 0−0.3 and 0−0.5% of the identified ARGs in bioaerosol and liquid sludge metagenomes. Seven of the ten known mcr variants were detected in wastewater bioaerosol and liquid samples, with mcr-5 and mcr-8 being the most prevalent across all seasons and sites. Additional functional and taxonomic annotation of mcr-containing metagenomic contigs showed that mcr genes were often located on contigs with other co-occurring ARGs and mobile genetic elements and may be harbored by opportunistic human pathogens and other bacterial taxa not previously associated with mcr genes. Atmospheric dispersion modeling showed that mcr-containing bioaerosols can be transported kilometers away from the WWTPs, resulting in the possible dissemination of these ARGs into surrounding environments and communities.

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Wastewater-based surveillance in Italy leading to the first detection of mcr-10-positive Klebsiella quasipneumoniae

Cited by 5 publications

References 24 publications

Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

Klebsiella pneumoniae co-harbouring bla NDM-1 , armA and mcr-10 isolated from blood samples in Myanmar

First Detection of mcr-9 in a Multidrug-Resistant Escherichia coli of Animal Origin in Italy Is Not Related to Colistin Usage on a Pig Farm

Seasonal Patterns in Mobile Colistin Resistance Gene Variants in Wastewater Bioaerosols and Liquid Sludge

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