Scarce detection of mobile erm genes associated with tetQ in Bacteroides and Parabacteroides from Costa Rica

Parabacteroides distasonis: intriguing aerotolerant gut anaerobe with emerging antimicrobial resistance and pathogenic and probiotic roles in human health

Parabacteroides distasonis is the type strain for the genus Parabacteroides, a group of gram-negative anaerobic bacteria that commonly colonize the gastrointestinal tract of numerous species. First isolated in the 1930s from a clinical specimen as Bacteroides distasonis, the strain was re-classified to form the new genus Parabacteroides in 2006. Currently, the genus consists of 15 species, 10 of which are listed as 'validly named' (P. acidifaciens, P. chartae, P. chinchillae, P. chongii, P. distasonis, P. faecis, P. goldsteinii, P. gordonii, P. johnsonii, and P. merdae) and 5 'not validly named' (P. bouchesdurhonensis, P. massiliensis, P. pacaensis, P. provencensis, and P. timonensis) by the List of Prokaryotic names with Standing in Nomenclature. The Parabacteroides genus has been associated with reports of both beneficial and pathogenic effects in human health. Herein, we review the literature on the history, ecology, diseases, antimicrobial resistance, and genetics of this bacterium, illustrating the effects of P. distasonis on human and animal health.

Anaerobic resistance: should we be worried?

PURPOSE OF REVIEW

Anaerobic bacteria are implicated in a broad range of infections and can cause significant morbidity and mortality. As such, development of antimicrobial resistance (AMR) increases the risk of worse clinical outcomes and death.

RECENT FINDINGS

Anaerobe AMR is highly variable according to region and species included in the survey. The overall trend is to increasing resistance, particularly in Europe and Asia, and in the Bacteroides fragilis group and Clostridium sp. Conversely, with the decline in RT027, resistance in Clostridiodes difficile is decreasing. Resistance to moxifloxacin and clindamycin has reached 30-50%, whereas prevalence of metronidazole and carbapenem resistance is generally low. Infections due to multidrug anaerobes have been increasingly reported, with clinical studies demonstrating adverse clinical outcomes, including higher mortality, with anaerobic resistance or inappropriate therapy. The role of antimicrobial stewardship in the setting of increasing anaerobe resistance is yet to be fully elucidated.

SUMMARY

These findings highlight the importance of continuous surveillance in monitoring emerging trends in anaerobe AMR. Mean inhibitory concentrations should be reported due to variable susceptibility breakpoints and for detection of isolates with reduced susceptibility. At a local level, the clinical microbiology laboratory has a key role in identifying and undertaking susceptibility testing to inform individual patient management, develop local antibiograms and liaise with antimicrobial stewardship teams. A greater understanding of the clinical impact of anaerobic resistance and the role of antimicrobial stewardship in preventing resistance is required.

Predominance and high antibiotic resistance of the emerging Clostridium difficile genotypes NAPCR1 and NAP9 in a Costa Rican hospital over a 2-year period without outbreaks

Clostridium difficile is the major causative agent of nosocomial antibiotic-associated diarrhea. In a 2009 outbreak of C. difficile-associated diarrhea that was recorded in a major Costa Rican hospital, the hypervirulent NAP1 strain (45%) predominated together with a local genotype variant (NAP_CR1, 31%). Both strains were fluoroquinolone-resistant and the NAP_CR1 genotype, in addition, was resistant to clindamycin and rifampicin. We now report on the genotypes and antibiotic susceptibilities of 68 C. difficile isolates from a major Costa Rican hospital over a 2-year period without outbreaks. In contrast to our previous findings, no NAP1 strains were detected, and for the first time in a Costa Rican hospital, a significant fraction of the isolates were NAP9 strains (n=14, 21%). The local NAP_CR1 genotype remained prevalent (n=18, 26%) and coexisted with 14 strains (21%) of classic hospital NAP types (NAP2, NAP4, and NAP6), eight new genotypes (12%), four environmental strains classified as NAP10 or NAP11 (6%), three strains without NAP designation (4%) and seven non-toxigenic strains (10%). All 68 strains were resistant to ciprofloxacin, 88% were resistant to clindamycin and 50% were resistant to moxifloxacin and rifampicin. Metronidazole and vancomycin susceptibilities were universal. The NAP_CR1 and NAP9 strains, which have been associated with more severe clinical infections, were more resistant to antibiotics than the other strains. Altogether, our results confirm that the epidemiology of C. difficile infection is dynamic and that A⁻B⁺ strains from the NAP9 type are on the rise not only in the developed world. Moreover, our results reveal that the local NAP_CR1 strains still circulate in the country without causing outbreaks but with equally high antibiotic-resistance rates and levels.

Identification and antimicrobial susceptibility of obligate anaerobic bacteria from clinical samples of animal origin

The etiology of veterinary infectious diseases has been the focus of considerable research, yet relatively little is known about the causative agents of anaerobic infections. Susceptibility studies have documented the emergence of antimicrobial resistance and indicate distinct differences in resistance patterns related to veterinary hospitals, geographic regions, and antibiotic-prescribing regimens. The aim of the present study was to identify the obligate anaerobic bacteria from veterinary clinical samples and to determinate the in vitro susceptibility to eight antimicrobials and their resistance-associated genes. 81 clinical specimens obtained from food-producing animals, pets and wild animals were examined to determine the relative prevalence of obligate anaerobic bacteria, and the species represented. Bacteroides spp, Prevotella spp and Clostridium spp represented approximately 80% of all anaerobic isolates. Resistance to metronidazole, clindamycin, tetracycline and fluoroquinolones was found in strains isolated from food-producing animals. Ciprofloxacin, enrofloxacin and cephalotin showed the highest resistance in all isolates. In 17%, 4% and 14% of tetracycline-resistant isolates, the resistance genes tetL, tetM and tetW were respectively amplified by PCR whereas in 4% of clindamycin-resistant strains the ermG gene was detected. 26% of the isolates were positive for cepA, while only 6% harbored the cfxA (resistance-conferring genes to beta-lactams). In this study, the obligate anaerobic bacteria from Costa Rica showed a high degree of resistance to most antimicrobials tested. Nevertheless, in the majority of cases this resistance was not related to the resistance acquired genes usually described in anaerobes. It is important to address and regulate the use of antimicrobials in the agricultural industry and the empirical therapy in anaerobic bacterial infections in veterinary medicine, especially since antibiotics and resistant bacteria can persist in the environment.

Regulation of CTnDOT conjugative transfer is a complex and highly coordinated series of events

CTnDOT is a 65-kb conjugative transposon that is found in Bacteroides spp., which are one of the more abundant members within the lower human gastrointestinal tract. CTnDOT encodes resistance to the antibiotics erythromycin and tetracycline (Tc). An interesting feature of CTnDOT is that exposure to low levels of Tc induces a cascade of events that ultimately results in CTnDOT conjugative transfer. However, Tc is apparently not a switch that activates transfer but rather a signal that appears to override a series of negative regulators that inhibit premature excision and transfer of CTnDOT. In this minireview, we summarize over 20 years of research that focused on elucidating the highly coordinated regulation of excision, mobilization, and transfer of CTnDOT.

IMPORTANCE

Bacteroides spp. are abundant commensals in the human colon, but they are also considered opportunistic pathogens, as they can cause life-threatening infections if they should escape the colon. Bacteroides spp. are the most common cause of anaerobic infections and are rather difficult to treat due to the prevalence of antibiotic resistance within this genus. Today over 80% of Bacteroides are resistant to tetracycline (Tc), and a study looking at both clinical and community isolates demonstrated that this resistance was specifically due to the conjugative transposon CTnDOT.