Afouda Pamela, Dubourg Grégory, Levasseur Anthony, Fournier Pierre-Edouard, Delerce Jeremy, Mediannikov Oleg, Diene Seydina M, Nahon Daniel, Bourlès Didier, Rolain Jean-Marc, Raoult Didier
Aix Marseille Université, IRD, AP-HM, MEPHI, 13005 Marseille, France.
IHU Méditerranée Infection, 13005 Marseille, France.
Microorganisms. 2020 Oct 3;8(10):1522. doi: 10.3390/microorganisms8101522.
Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., and ). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.
长期以来，通过推断人们一直认为抗生素耐药机制是人类使用抗生素的结果，但事实上，由于此前已从数百万年前的永久冻土样本中检测到抗生素耐药基因，抗生素耐药现象似乎更为古老。由于这些样本保证了古老细菌的生存能力，我们在此提议应用培养组学方法来恢复一个西伯利亚永久冻土样本中的细菌成分，该样本利用原位产生的宇宙成因核素氯36（Cl）测定年代为270万年，以便从进化的角度研究细菌进化的动态。结果，我们培养并测序了28种古老细菌物种的基因组，其中包括一个新物种。为了对永久冻土菌株和现代分离株进行基因组比较，我们选择了其中7个物种（即 和 ）。我们观察到基因组内容存在高度变异性，核心基因组中共享基因的百分比在21.23%至55.59%之间。此外，同一物种的永久冻土菌株和现代菌株之间的单核苷酸多态性（SNP）比较无法根据基因组内容确定古老菌株的年代。每个物种的现代分离株和古老分离株之间的抗生素耐药谱没有显著差异。从永久冻土中回收的所有革兰氏阴性细菌物种在表型上都检测到了对抗生素的获得性耐药，并且检测到了大量编码抗生素耐药性的基因。综上所述，这些发现证实了先前获得的数据，即抗生素耐药性早于人类出现，因为大多数抗菌剂是生物圈中微生物间冲突中使用的天然武器。
