Supplementary Information
Genomic and transcriptomic analysis of NDM-1 Klebsiella pneumoniae in spaceflight reveal mechanisms underlying environmental adaptability
Jia Li1,4, Fei Liu2, Qi Wang2, Pupu Ge2, Patrick CY Woo3, Jinghua Yan2, Yanli Zhao5, George F Gao2, Cui Hua Liu2, Changting Liu1
1Nanlou Respiratory Diseases Department, Chinese PLA General Hospital, No. 28 Fuxing Road, Haidian District, Beijing 100853, China. 2CAS key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, No. 1 West Beichen Road, Chaoyang District, Beijing 100101, China. 3State Key Laboratory of Emerging Infectious Diseases, Department of Microbiology, The University of Hong Kong, University Pathology Building, Compound Pokfulam Road, Hong Kong, China. 4School of medicine, Nankai University, 94 Weijin Road, Nankai District, Tianjin 300071, China. 5National Center forTuberculosisControl and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbei Road, Changping District, Beijing 102206, China.
Correspondence and requests for materials should be addressed to C.H.L. (email: ) or to C.L. (email: ).
Supplementary Table S1: Drug resistance profiles of the K. pneumoniae strains. All strains including the reference strain ATCC BAA-2146, as well as the D, M, and T strains had identical drug resistance profiles.
(μg/mL)
Penicillins / AMP / ≥32
Antipseudomonal penicillins + beta-lactamase inhibitors / TZP / ≥128
Penicillins + beta-lactamase inhibitors / SAM / ≥32
1st and 2nd generation cephalosporins / CFZ / ≥64
3rd and 4th generation cephalosporins / CRO / ≥64
CAZ / ≥64
FEP / ≥64
Cephamycins / CTT / ≥64
Carbapenems / ETP / ≥8
IMP / ≥16
Monobactams / ATM / ≥64
Fluoroquinolones / CIP / ≥4
LVX / ≥8
Aminoglycosides / GM / ≥16
TOB / ≥16
AMK / ≥64
Folate pathway inhibitors / SXT / ≥320
Nitrofurantoin / FD / ≥512
* Abbreviation of drugs: AMP, Ampicillin; TZP, Piperacillin/Tazobactam; SAM, Ampicillin/Sulbactam; CFZ, Cefazolin; CRO, Ceftriaxone; CAZ, Ceftazidime; FEP, Cefepime; CTT, Cefotetan; ETP, Ertapenem; IMP, Imipenem; ATM, Aztreonam; CIP, Ciprofloxacin; LVX, Levofloxacin; GM, Gentamycin; TOB, Tobramycin; AMK, Amikacin; SXT, Trimethoprim-Sulfamethoxazole; FD, Furadantin.
Supplementary Table S2: Carbon source utilization patterns and chemical sensitivity of the K. pneumoniae strains. “ + ” represents a positive reaction; “ - ” represents a negative reaction.
A1 / Negative Control / - / - / - / -
A10 / Positive Control / + / + / + / +
Carbon source utilization patterns
A2 / Dextrin / - / - / - / -
A3 / D-Maltose / - / - / - / -
A4 / D-Trehalose / - / - / - / -
A5 / D-Cellobiose / - / - / - / -
A6 / Gentiobiose / - / - / - / -
A7 / Sucrose / - / - / - / -
A8 / D-Turanose / - / - / - / -
A9 / Stachyose / - / - / - / -
B1 / D-Raffinose / - / - / - / -
B2 / α-D-Lactose / + / - / - / -
B3 / D-Melibiose / - / - / - / -
B4 / β-Methyl-D-Glucoside / - / - / - / -
B5 / D-Salicin / + / + / + / +
B6 / N-Acetyl-D-Glucosamine / + / + / + / +
B7 / N-Acetyl-β-D-Mannosamine / - / - / - / -
B8 / N-Acetyl-D-Galactosamine / - / - / - / -
B9 / N-Acetyl Neuraminic Acid / - / - / - / -
C1 / α-D-Glucose / - / - / - / -
C2 / D-Mannose / - / - / + / -
C3 / D-Fructose / + / + / + / +
C4 / D-Galactose / - / - / - / -
C5 / 3-Methyl Glucose / + / + / + / +
C6 / D-Fucose / + / + / + / +
C7 / L-Fucose / - / - / - / -
C8 / L-Rhamnose / - / - / - / -
C9 / Inosine / - / - / - / -
D1 / D-Sorbitol / - / - / - / -
D2 / D-Mannitol / - / - / - / -
D3 / D-Arabitol / - / - / - / -
D4 / myo-Inositol / - / - / - / -
D5 / Glycerol / - / - / - / -
D6 / D-Glucose-6-PO4 / + / + / + / +
D7 / D-Fructose-6-PO4 / + / + / + / +
D8 / D-Aspartic Acid / - / - / - / -
D9 / D-Serine / - / - / - / -
E1 / Gelatin / - / - / - / -
E2 / Glycyl-L-Proline / + / + / + / +
E3 / L-Alanine / + / + / + / +
E4 / L-Arginine / - / - / - / -
E5 / L-Aspartic Acid / - / - / - / -
E6 / L-Glutamic Acid / + / + / + / +
E7 / L-Histidine / + / + / + / +
E8 / L-Pyroglutamic Acid / - / - / - / -
E9 / L-Serine / - / - / - / -
F1 / Pectin / + / + / + / +
F2 / D-Galacturonic Acid / + / + / + / +
F3 / L-Galactonic Acid Lactone / + / + / + / +
F4 / D-Gluconic Acid / + / + / + / +
F5 / D-Glucuronic Acid / + / + / + / +
F6 / Glucuronamide / + / + / + / +
F7 / Mucic Acid / + / + / + / +
F8 / Quinic Acid / + / + / + / +
F9 / D-Saccharic Acid / + / + / + / +
G1 / p-Hydroxy-Phenylacetic Acid / + / + / + / +
G2 / Methyl Pyruvate / - / - / - / -
G3 / D-Lactic Acid Methyl Ester / - / - / - / -
G4 / L-Lactic Acid / + / + / + / +
G5 / Citric Acid / + / + / + / +
G6 / α-Keto-Glutaric Acid / - / - / - / -
G7 / D-Malic Acid / - / - / - / -
G8 / L-Malic Acid / - / - / - / -
G9 / Bromo-Succinic Acid / - / - / - / -
H1 / Tween 40 / - / - / - / -
H2 / γ-Amino-Butryric Acid / - / - / - / -
H3 / α-Hydroxy-Butyric Acid / - / - / - / -
H4 / β-Hydroxy-D,L-Butyric Acid / - / - / - / -
H5 / α-Keto-Butyric Acid / - / - / - / -
H6 / Acetoacetic Acid / - / - / - / -
H7 / Propionic Acid / - / - / - / -
H8 / Acetic Acid / - / - / - / -
H9 / Formic Acid / - / - / - / -
Chemical sensitivity
A11 / pH 6 / + / + / + / +
A12 / pH 5 / + / + / + / +
B10 / 1% NaCl / + / + / + / +
B11 / 4% NaCl / + / + / + / +
B12 / 8% NaCl / + / + / + / +
C10 / 1% Sodium Lactate / + / + / + / +
C11 / Fusidic Acid / + / + / + / +
C12 / D-Serine / + / + / + / +
D10 / Troleandomycin / + / + / + / +
D11 / Rifamycin SV / + / + / + / +
D12 / Minocycline / + / + / + / +
E10 / Lincomycin / + / + / + / +
E11 / Guanidine HCl / + / + / + / +
E12 / Niaproof 4 / + / + / + / +
F10 / Vancomycin / + / + / + / +
F11 / Tetrazolium Violet / + / + / + / +
F12 / Tetrazolium Blue / + / + / + / +
G10 / Nalidixic Acid / + / + / + / +
G11 / Lithium Chloride / + / + / + / +
G12 / Potassium Tellurite / + / + / + / +
H10 / Aztreonam / + / + / + / +
H11 / Sodium Butyrate / + / + / + / +
H12 / Sodium Bromate / - / - / - / -
Supplementary Table S3: Summary of all SNPs and Indels identified in D, M, and T strains. Synonymous SNPs were excluded.
C120809T / Kpn2146_0117 / small subunit ribosomal RNA / C181T
A125412G / Kpn2146_0120 / large subunit ribosomal RNA / A2817G
T125420C / Kpn2146_0120 / large subunit ribosomal RNA / T2825C
T1023679C / Kpn2146_0993 / tRNA-Ala / T610C
T1340237C / Kpn2146_1328 / Hypothetical protein / T952C / C318R / Non-synonymous
G1341908A / Kpn2146_1328 / Hypothetical protein / G2623A / A875T / Non-synonymous
T1344930C / Kpn2146_1332 / Reverse transcriptase / T1267C / Y423H / Non-synonymous
C1499679T / Kpn2146_1478 / TonB-dependent receptor Outer membrane receptor for ferric enterobactin and colicins B D / C415T / G139S / Non-synonymous
T1522183C / Kpn2146_1498 / Ribose ABC transport system ATP-binding protein, RbsA / T380C / V127A / Non-synonymous
G1539668C / Kpn2146_1513 / D-3-phosphoglycerate dehydrogenase / G20C / R7P / Non-synonymous
T2039008C / Kpn2146_2013/
Kpn2146_2014 / Periplasmic thiol: disulfide interchange protein, DsbA/RtT RNA / T-61C / Intergenic regions
C2041701T / Kpn2146_2018 / Transcriptional regulator LysR family / C550Y / P184S / Non-synonymous
G2042488A / Kpn2146_2018/
Kpn2146_2019 / Transcriptional regulator LysR family/RtT RNA / G-28A / Intergenic regions
G2042492T / Kpn2146_2018/
Kpn2146_2019 / Transcriptional regulator LysR family/RtT RNA / G-24T / Intergenic regions
T2383666C / Kpn2146_2394 / Hypothetical protein / T2465C / I822T / Non-synonymous
T2403013C / Kpn2146_2411
Kpn2146_2412 / Hypothetical protein/Hypothetical protein / T-22C / Intergenic regions
T2403507C / Kpn2146_2412 / Hypothetical protein / T473C / V158A / Non-synonymous
C2403540A / Kpn2146_2412 / Hypothetical protein / C506A / T169K / Non-synonymous
G2546676A / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-526A / Intergenic regions
G2546698T / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-504T / Intergenic regions
G2546785T / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-417T / Intergenic regions
T2546875G / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / T-327G / Intergenic regions
C2546964A / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / C-238A / Intergenic regions
G2610928T / Kpn2146_2617 / Hypothetical protein / G112T / L38I / Non-synonymous
G2611469A / Kpn2146_2618 / 2-hydroxy-3-oxopropionate reductase / G485A / A162V / Non-synonymous
G2612995C / Kpn2146_2619/
Kpn2146_2620 / DeoR family transcriptional regulator probably involved in glycerate glycolaldehyde metabolism/Ambler Class A beta lactamase SHV-11 / G-1C / Intergenic regions
G2613880A / Kpn2146_2620/
Kpn2146_2621 / Ambler Class A beta lactamase SHV-11/Hypothetical protein / G-274A / Intergenic regions
T3252757A / Kpn2146_3273/
Kpn2146_3274 / RtT RNA/tRNA-Tyr(GTA) / T-39A / Intergenic regions
C3252759T / Kpn2146_3273/
Kpn2146_3274 / RtT RNA/tRNA-Tyr(GTA) / C-37T / Intergenic regions
A4944210G / Kpn2146_5014 / large subunit ribosomal RNA / A2546G
G4946124A / Kpn2146_5015 / small subunit ribosomal RNA / G1400A
A5143211C / Kpn2146_5218 / Protein yhjK / A1354C / S452A / Non-synonymous
C5323238G / Kpn2146_5387/
Kpn2146_5388 / Transcriptional regulator RutR of pyrimidine catabolism (TetR family)/Putative acetyltransferase / C-289G / Intergenic regions
T5323259A / Kpn2146_5387/
Kpn2146_5388 / Transcriptional regulator RutR of pyrimidine catabolism (TetR family)/Putative acetyltransferase / T-368A / Intergenic regions
Supplementary Table S4: SNPs and Indels shared by D, M, and T strains. Synonymous SNPs were excluded.
C120809T / Kpn2146_0117 / small subunit ribosomal RNA / C181T
A125412G / Kpn2146_0120 / large subunit ribosomal RNA / A2817G
T125420C / Kpn2146_0120 / large subunit ribosomal RNA / T2825C
T1023679C / Kpn2146_0993 / tRNA-Ala / T610C
T1340237C / Kpn2146_1328 / Hypothetical protein / T952C / C318R / Non-synonymous
G1341908A / Kpn2146_1328 / Hypothetical protein / G2623A / A875T / Non-synonymous
T1344930C / Kpn2146_1332 / Reverse transcriptase / T1267C / Y423H / Non-synonymous
C1499679T / Kpn2146_1478 / TonB-dependent receptor Outer membrane receptor for ferric enterobactin and colicins B D / C415T / G139S / Non-synonymous
T1522183C / Kpn2146_1498 / Ribose ABC transport system ATP-binding protein, RbsA / T380C / V127A / Non-synonymous
T2039008C / Kpn2146_2013/
Kpn2146_2014 / Periplasmic thiol: disulfide interchange protein, DsbA/RtT RNA / T-61C / Intergenic regions
C2041701T / Kpn2146_2018 / Transcriptional regulator LysR family / C550Y / P184S / Non-synonymous
G2042488A / Kpn2146_2018/
Kpn2146_2019 / Transcriptional regulator LysR family/RtT RNA / G-28A / Intergenic regions
G2042492T / Kpn2146_2018/
Kpn2146_2019 / Transcriptional regulator LysR family/RtT RNA / G-24T / Intergenic regions
T2383666C / Kpn2146_2394 / Hypothetical protein / T2465C / I822T / Non-synonymous
T2403013C / Kpn2146_2411
Kpn2146_2412 / Hypothetical protein/Hypothetical protein / T-22C / Intergenic regions
T2403507C / Kpn2146_2412 / Hypothetical protein / T473C / V158A / Non-synonymous
C2403540A / Kpn2146_2412 / Hypothetical protein / C506A / T169K / Non-synonymous
G2546676A / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-526A / Intergenic regions
G2546698T / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-504T / Intergenic regions
G2546785T / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / G-417T / Intergenic regions
C2546964A / Kpn2146_2552/
Kpn2146_2553 / 4-carboxymuconolactone decarboxylase/Hypothetical protein / C-238A / Intergenic regions
G2611469A / Kpn2146_2618 / 2-hydroxy-3-oxopropionate reductase / G485A / A162V / Non-synonymous
A4944210G / Kpn2146_5014 / large subunit ribosomal RNA / A2546G
A5143211C / Kpn2146_5218 / Protein yhjK / A1354C / S452A / Non-synonymous
T5323259A / Kpn2146_5387/
Kpn2146_5388 / Transcriptional regulator RutR of pyrimidine catabolism (TetR family)/Putative acetyltransferase / T-368A / Intergenic regions
Supplementary Table S5: Antibiotics resistance-associated genes detected in K. pneumoniae ATCC BAA-2146.
Antipseudomonal penicillins + beta-lactamase inhibitors , penicillins + beta-lactamase inhibitors, 1st and 2nd generation cephalosporins, 3rd and 4th generation cephalosporins, cephamycins / blaCTX-M-1 / +
blaCTX-M-2 / -
blaCTX-M-3 / +
blaCTX-M-8 / -
blaCTX-M-9 / -
blaCTX-M-14 / -
blaCTX-M-15 / -
blaCTX-M-10 / +
blaCTX-M-25 / -
blaCTX-M-55 / -
blaSHV-1 / +
blaSHV-2 / -
blaSHV-11 / -
blaSHV-85 / -
blaTEM-1 / +
blaTEM-186 / -
blaCMY-2 / +
blaDHA-1 / -
blaFOX / -
Carbapenems / blaKPC-2 / -
blaNDM-1 / +
blaIMP / -
blaVIM / -
blaOXA-48 / -
Folate pathway inhibitors / dhfr / -
Fluoroquinolones / qnrA / -
qnrB / +
qnrC / -
qnrD / -
qnrS / -
aac(6’)-Ib-cr / +
qepA / -
gyrA mutations T247A(Ser83Ile) / +
parC mutations / -
Aminoglycosides / aacA4 / +
aacC1 / -
aacC2 / +
aadA1 / +
aadB / -
aphA6 / -
armA / -
rmtB / -
Supplementary Table S6: Differentially expressed genes in T strain vs. D strain.