| Literature DB >> 34189167 |
Emmanuel Lecorche1,2,3, Côme Daniau4, Kevin La1,3, Faiza Mougari2,3, Hanaa Benmansour2,3, Sylvain Kumanski3, Jérôme Robert3,5,6, Sandra Fournier7, Guillaume Lebreton8, Anne Carbonne4, Emmanuelle Cambau1,2,3.
Abstract
BACKGROUND: Postsurgical infections due to Mycobacterium chimaera appeared as a novel nosocomial threat in 2015, with a worldwide outbreak due to contaminated heater-cooler units used in open chest surgery. We report the results of investigations conducted in France including whole-genome sequencing comparison of patient and heater-cooler unit isolates.Entities:
Keywords: heater-cooler units (HCUs); mmpL; molecular epidemiology; nontuberculous mycobacteria (NTM)
Year: 2021 PMID: 34189167 PMCID: PMC8231370 DOI: 10.1093/ofid/ofab192
Source DB: PubMed Journal: Open Forum Infect Dis ISSN: 2328-8957 Impact factor: 3.835
Main Characteristics of the M. chimaera Clinical Isolates
| Characteristic | Patient 1 | Patient 2 | |
|---|---|---|---|
| Isolatea | P1a (I58) | P1b (I57) | P2 (I18) |
| Hospitala | H25 | H25 | H14 |
| SNP difference with strain Zuerich-1 | 5 | 10 | 5 |
| Clarithromycin MIC | 2 | 0.5 | 2 |
| Rifabutin MIC | 2 | 0.25 | 0.5 |
| Ethambutol MIC | 16 | 4 | 16 |
| Isoniazid MIC | >8 | 2 | 2 |
| Moxifloxacin MIC | 4 | 2 | 4 |
| Rifampicin MIC | >8 | 2 | 4 |
| Sulfamethoxazole/trimethoprim MIC | 8/152 | 1/19 | 8/152 |
| Amikacin MIC | 8 | 4 | 16 |
| Linezolid MIC | 32 | 4 | 16 |
| Ciprofloxacin MIC | 16 | 8 | 16 |
| Streptomycin MIC | 16 | 8 | 32 |
| Doxycycline MIC | 16 | >16 | >16 |
| Ethionamide MIC | 20 | 1.2 | 10 |
| Bedaquiline MIC | 0.25 | 0.25 | 0.25 |
MIC (in mg/L) was determined using the commercial microdilution method SLOMYCO Myco Sensititre (Thermo Scientific) following the manufacturer’s recommendations and CLSI guidance for bedaquiline testing [15].
Abbreviations: CLSI, Clinical and Laboratory Standards Institute; MIC, minimum inhibitory concentration; SNP, single nucleotide polymorphism.
aSee details in the Supplementary Table 4 list of isolates.
Figure 1.Overview of studied Mycobacterium chimaera isolates and their origin according to epidemiological investigations. Abbreviations: HCFs, health care facilities; HCU, heater-cooler unit; MAC, Mycobacterium avium complex; WGS, whole-genome sequencing. *Specific identification was not performed systematically for M. chimaera.
Figure 2.Phylogenetic analysis of Mycobacterium chimaera isolates. A, Maximum parsimony tree (logarithmically scaled) built based on the 55 638 SNP positions found through comparison of the 75 genomes that were mapped to the reference genome (*) of M. chimaera ZUERICH-1. The 52 isolates, including Zuerich-1, belonging to group 1 are gathered in a green circle. B, Maximum parsimony tree (logarithmically scaled) built based on the 694 SNP positions found through comparison of the genomes that were mapped to the reference genome of M. chimaera ZUERICH-1. The number of SNP differences with regard to the epidemic strain M. chimaera ZUERICH-1 is indicated inside each circle. Isolates from HCU water samples are labeled in blue, isolates from clinical samples in purple, and isolates from clinical samples related to the outbreak in red. §Two isolates isolated from the same patient. Abbreviations: HCU, heater-cooler unit; SNP, single nucleotide polymorphism.
SNP Analyses Determined From the Genomic Comparison of Clinical Isolates From Patients P1 and P2 and of Environmental Isolates Related to the P2 Case
| Isolates | Positiona | Nucleotide Modification | Gene Characterization | Codon | Mutation Effect |
|---|---|---|---|---|---|
| Comparison of clinical isolates from the P1 and P2 cases | |||||
| P1a, P1b, P2 | 2 587 843 | T->C | Glycosyltransferase | CAC->CGC | H->R |
| P1a, P1b, P2 | 3 709 626 | G->A | Type III polyketide synthase | GCG->GTG | A->V |
| P1a, P1b, P2 | 4 520 250 | T->A | Signal peptidase I | GAA->GAT | E->D |
| P1a, P1b, P2 | 4 919 479 | A->G | Helix-turn-helix transcriptional regulator | TCC->CCC | S->P |
| P1a, P1b | 2 67 758 | C->A | Hypothetical protein | GAC->TAC | D->Y |
| P1b | 2 22 733 | T->C | Decaprenyl-phosphate phosphoribosyltransferase | TTC->CTC | Synonymous |
| P1b | 1 256 515 | G->T | IS481 family transposase | AGC->ATC | S->I |
| P1b | 1 256 515b | G->T | NAD(P)-dependent oxidoreductase | AGC->AGA | S->R |
| P1b | 1 509 107 | C->G | LuxR family transcriptional regulator | CGC->GGC | R->G |
| P1b | 4 708 684 | G->A | RND family transporter (mmpL5) | TGG->TGA | W->UGA |
| P1b | 5 517 224 | T->A | Porphobilinogen synthase | ATG->TTG | M->L |
| P2 | 2 436 71 | T->C | Arabinosyltransferase | ATG->GTG | M->V |
| Comparison of environmental isolates related to the P2 case | |||||
| I36, I35 | 5 234 848 | A->G | FAD-dependent oxidoreductase | CAC->CGC | H->R |
| I36, I35 | 5 947 828 | C->A | NAD(P)/FAD-dependent oxidoreductase | GAC->AAC | D->K |
| I35 | 3 350 727 | A->T | PPE family protein | CTG->CAG | L->Q |
| I30, I34 | 1 367 077 | T->C | Hypothetical protein | GTG->GCG | V->A |
| I30, I34 | 2 057 124 | C->A | Valine-tRNA ligase | CCC->CCA | Synonymous |
| I30, I34 | 5 952 067 | G->C | Cytochrome P450 | CAC->CAG | H->Q |
| I30, I34 | 5 952 114 | G->T | NIPSNAP family protein | CTC->CTA | Synonymous |
| I30, I34 | 6 159 327 | G->A | Hypothetical protein | CGC->CAC | R->H |
| I30 | 539 741 | C->A | SpoIIE family protein phosphatase | CGT->CTG | R->L |
| I30 | 576 340 | C->T | Type II secretion system F family protein | CTG->TAG | L->stop |
| I30 | 4 243 378 | C->G | Hypothetical protein | GGG->GGC | Synonymous |
| I34 | 1 204 266 | G->T | LuxR family transcriptional regulator | GCC->GCA | Synonymous |
| I34 | 1 562 307 | G->A | Alpha/beta hydrolase | CAG->CAA | Synonymous |
| I34 | 2 093 313 | C->T | PE-PPE domain–containing protein | GCG->GCA | Synonymous |
| I34 | 2 447 021 | T->C | DNA primase | ATC>ACC | I->T |
| I34 | 2 842 316 | C->A | MCE family protein | CTG>CTT | Synonymous |
| I34 | 4 179 540 | T->C | Hypothetical protein | ACA>ACG | Synonymous |
| I34 | 4 243 378 | C->G | Hypothetical protein | GGG>GGC | Synonymous |
| I34 | 5 019 553 | G->A | Unknown function | CCC>CCT | Synonymous |
aSNPs were generated with regards to the sequence of the epidemic strain Mycobacterium chimaera ZUERICH-1 (NCBI reference sequence NZ_CP015272.1).
bThe SNP at the 1256515 position affected 2 genes, 1 forward and the other in reverse.
Figure 3.Phylogenetic analysis of Mycobacterium chimaera isolates related to P2. Maximum parsimony tree (logarithmically scaled) built based on the 21 106 SNP positions mapped to the genome of M. chimaera ZUERICH-1 found through comparison of the 11 isolates related to patient P2. The number of SNP differences compared with patient P2’s isolate is indicated inside each circle. Isolates from HCU water samples are labeled in blue, and isolates from clinical samples related to the outbreak are labeled in red. Abbreviations: HCU, heater-cooler unit; SNP, single nucleotide polymorphism.