The recA operon: A novel stress response gene cluster in Bacteroides fragilis

A mouse model of occult intestinal colonization demonstrating antibiotic-induced outgrowth of carbapenem-resistant Enterobacteriaceae

BACKGROUND

The human intestinal microbiome is a complex community that contributes to host health and disease. In addition to normal microbiota, pathogens like carbapenem-resistant Enterobacteriaceae may be asymptomatically present. When these bacteria are present at very low levels, they are often undetectable in hospital surveillance cultures, known as occult or subclinical colonization. Through the receipt of antibiotics, these subclinical pathogens can increase to sufficiently high levels to become detectable, in a process called outgrowth. However, little is known about the interaction between gut microbiota and Enterobacteriaceae during occult colonization and outgrowth.

RESULTS

We developed a clinically relevant mouse model for studying occult colonization. Conventional wild-type mice without antibiotic pre-treatment were exposed to Klebsiella pneumoniae but rapidly tested negative for colonization. This occult colonization was found to perturb the microbiome as detected by both 16S rRNA amplicon and shotgun metagenomic sequencing. Outgrowth of occult K. pneumoniae was induced either by a four-antibiotic cocktail or by individual receipt of ampicillin, vancomycin, or azithromycin, which all reduced overall microbial diversity. Notably, vancomycin was shown to trigger K. pneumoniae outgrowth in only a subset of exposed animals (outgrowth-susceptible). To identify factors that underlie outgrowth susceptibility, we analyzed microbiome-encoded gene functions and were able to classify outgrowth-susceptible microbiomes using pathways associated with mRNA stability. Lastly, an evolutionary approach illuminated the importance of xylose metabolism in K. pneumoniae colonization, supporting xylose abundance as a second susceptibility indicator. We showed that our model is generalizable to other pathogens, including carbapenem-resistant Escherichia coli and Enterobacter cloacae.

CONCLUSIONS

Our modeling of occult colonization and outgrowth could help the development of strategies to mitigate the risk of subsequent infection and transmission in medical facilities and the wider community. This study suggests that microbiota mRNA and small-molecule metabolites may be used to predict outgrowth-susceptibility. Video Abstract.

Tightly controlled response to oxidative stress; an important factor in the tolerance of Bacteroides fragilis

The exposure of Bacteroides fragilis to highly oxygenated tissues induces an oxidative stress due to a shift from the reduced condition of the gastrointestinal tract to an aerobic environment of host tissues. The potent and effective responses to reactive oxygen species (ROS) make the B. fragilis tolerant to atmospheric oxygen for several days. The response to oxidative stress in B. fragilis is a complicated event that is induced and regulated by different agents. In this review, we will focus on the B. fragilis response to oxidative stress and present an overview of the regulators of responses to oxidative stress in this bacterium.

Gut Bacteroides species in health and disease

The functional diversity of the mammalian intestinal microbiome far exceeds that of the host organism, and microbial genes contribute substantially to the well-being of the host. However, beneficial gut organisms can also be pathogenic when present in the gut or other locations in the body. Among dominant beneficial bacteria are several species of Bacteroides, which metabolize polysaccharides and oligosaccharides, providing nutrition and vitamins to the host and other intestinal microbial residents. These topics and the specific organismal and molecular interactions that are known to be responsible for the beneficial and detrimental effects of Bacteroides species in humans comprise the focus of this review. The complexity of these interactions will be revealed.

The central role of the SOS DNA repair system in antibiotics resistance: A new target for a new infectious treatment strategy

Bacteria have a considerable ability and potential to acquire resistance against antimicrobial agents by acting diverse mechanisms such as target modification or overexpression, multidrug transporter systems, and acquisition of drug hydrolyzing enzymes. Studying the mechanisms of bacterial cell physiology is mandatory for the development of novel strategies to control the antimicrobial resistance phenomenon, as well as for the control of infections in clinics. The SOS response is a cellular DNA repair mechanism that has an essential role in the bacterial biologic process involved in resistance to antibiotics. The activation of the SOS network increases the resistance and tolerance of bacteria to stress and, as a consequence, to antimicrobial agents. Therefore, SOS can be an applicable target for the discovery of new antimicrobial drugs. In the present review, we focus on the central role of SOS response in bacterial resistance mechanisms and its potential as a new target for control of resistant pathogens.

Mechanisms of Bacteroides fragilis resistance to metronidazole

Metronidazole-resistant Bacteroides fragilis (B. fragilis) have been reported worldwide. Several mechanisms contribute to B. fragilis resistance to metronidazole. In some cases, the mechanisms of metronidazole resistance are unknown. Understanding the mechanisms of resistance is important for therapy, the design of new alternative drugs, and control of resistant strains. In this study, a comprehensive review of the B. fragilis resistance mechanisms to metronidazole was prepared. The rate of metronidazole-resistant B. fragilis has been reported as ranging from 0.5% to 7.8% in many surveys. According to CLSI, isolates with MICs ≥32 μg/mL are considered to be metronidazole-resistant. In the majority of cases, metronidazole resistance in B. fragilis is coupled with the existence of nim genes. Metronidazole resistance could be induced in nim-negative strains by exposure to sub-MIC levels of metronidazole. There are multi-drug efflux pumps in B. fragilis which can pump out a variety of substrates such as metronidazole. The recA overexpression and deficiency of feoAB are other reported metronidazole resistance mechanisms in this bacterium.

Antimicrobial susceptibility of Bacteroides fragilis group organisms in Hong Kong by the tentative EUCAST disc diffusion method

This study used a recently developed EUCAST disc diffusion method to measure the susceptibility of 741 B. fragilis group isolates to six antibiotics. Isolates nonsusceptible to imipenem and metronidazole by the disc method were further investigated by E-test. Species identification was obtained by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), PCR assays and 16S rRNA sequencing. The most common species were B. fragilis (n = 424, including 81 division II and 343 division I isolates), B. thetaiotaomicron (n = 111), B. ovatus (n = 53) and B. vulgatus (n = 46). Overall, metronidazole following by imipenem and amoxicillin-clavulanate are the most active agents with over 90% of all the isolates being susceptible at the tentative disc breakpoints. Susceptibility rates for moxifloxacin (69.5%), piperacillin-tazobactam (58.2%) and clindamycin (37.2%) were much lower. Metronidazole is the only agent active against >90% of B. fragilis, non-fragilis Bacteroides and Parabacteroides isolates. With the exception of B. fragilis division II, imipenem was active against 88.0%-98.3% of isolates of the other species. Susceptibility rates for clindamycin (14.4%-54.3%) and moxifloxacin (33.3%-80.6%) were low across all species and many isolates had no inhibition zone around the discs. E-test testing confirmed 8.2% (61/741) and 1.6% (12/741) isolates as nonsusceptible to imipenem and metronidazole, respectively with B. fragilis and B. thetaoiotaomicron accounting for a large share of the observed resistance to both agents. Two imipenem-resistant and one metronidazole-resistant B. dorei were misidentified as B. vulgatus by MALDI-TOF MS. These data highlights the importance anaerobic susceptibility testing in clinical laboratories to guide therapy.