Antimicrobial Susceptibility and Clinical Findings of Anaerobic Bacteria

A special issue of Antibiotics (ISSN 2079-6382).

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 27436

Special Issue Editor


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Guest Editor
Department of Microbiology, Hospital Virgen de las Nieves, Avda Fuerzas Armadas, Granada, Spain
Interests: anaerobes; antimicrobials; MALDI-TOF MS; molecular methods
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Special Issue Information

Dear Colleagues,

Anaerobic bacteria are common pathogens in human populations. Anaerobic bacteria may be responsible for severe disease in certain circumstances, such as in blood infections, and may also be present in normally sterile body sites. Antimicrobial susceptibility testing of anaerobic bacteria is performed by only a small number of laboratories. While current recommendations emphasize that testing is only needed for severe infections or for epidemiological studies, a rise in the resistance of anaerobes to some antimicrobial agents may indicate a greater need for this testing. Limited data are available on the resistance of anaerobes worldwide. The objective of this Special Issue is to contribute to knowledge about the percentage of resistance of clinically significant anaerobes in different settings and to determine the key clinical characteristics of these patients. Routine antimicrobial susceptibility testing for anaerobes provides information about the global situation and allows empirical therapies to be selected in accordance with local data on resistant strains.

Dr. Fernando Cobo
Guest Editor

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Keywords

  • Antimicrobials
  • Anaerobes
  • Clinical features
  • MALDI-TOF MS
  • Etest
  • Molecular methods

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Published Papers (9 papers)

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Editorial

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3 pages, 189 KiB  
Editorial
Antimicrobial Susceptibility and Clinical Findings of Anaerobic Bacteria
by Fernando Cobo
Antibiotics 2022, 11(3), 351; https://doi.org/10.3390/antibiotics11030351 - 7 Mar 2022
Cited by 2 | Viewed by 2503
Abstract
Anaerobic microorganisms are the most abundant components of the normal human microbiota; they colonize mucous membranes such as the oral cavity and the gastrointestinal and female genital tracts, and they are common pathogens in human populations [...] Full article

Research

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14 pages, 2935 KiB  
Article
Prevalence and Antimicrobial Resistance of Paeniclostridium sordellii in Hospital Settings
by Hanane Zerrouki, Sid-Ahmed Rebiahi, Yamina Elhabiri, Ahlam Fatmi, Sophie Alexandra Baron, Isabelle Pagnier, Seydina M. Diene and Jean-Marc Rolain
Antibiotics 2022, 11(1), 38; https://doi.org/10.3390/antibiotics11010038 - 29 Dec 2021
Cited by 4 | Viewed by 2687
Abstract
(1) Background: The purpose of this study was to determine the prevalence of clostridia strains in a hospital environment in Algeria and to evaluate their antimicrobial susceptibility to antibiotics and biocides. (2) Methods: Five hundred surface samples were collected from surfaces in the [...] Read more.
(1) Background: The purpose of this study was to determine the prevalence of clostridia strains in a hospital environment in Algeria and to evaluate their antimicrobial susceptibility to antibiotics and biocides. (2) Methods: Five hundred surface samples were collected from surfaces in the intensive care unit and surgical wards in the University Hospital of Tlemcen, Algeria. Bacterial identification was carried out using MALDI-TOF-MS, and then the minimum inhibitory concentrations (MICs) of various antimicrobial agents were determined by the E-test method. P. sordellii toxins were searched by enzymatic and PCR assays. Seven products intended for daily disinfection in the hospitals were tested against Clostridium spp. spore collections. (3) Results: Among 100 isolates, 90 P. sordellii were identified, and all strains were devoid of lethal and hemorrhagic toxin genes. Beta-lactam, linezolid, vancomycin, tigecycline, rifampicin, and chloramphenicol all proved effective against isolated strains. Among all strains tested, the spores of P. sordellii exhibited remarkable resistance to the tested biocides compared to other Clostridium species. The (chlorine-based 0.6%, 30 min), (glutaraldehyde solution 2.5%, 30 min), and (hydrogen peroxide/peracetic acid 3%, 15 min) products achieved the required reduction in spores. (4) Conclusions: Our hospital’s current cleaning and disinfection methods need to be optimized to effectively remove spores from caregivers’ hands, equipment, and surfaces. Full article
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11 pages, 1114 KiB  
Article
Broth Microdilution and Gradient Diffusion Strips vs. Reference Agar Dilution Method: First Evaluation for Clostridiales Species Antimicrobial Susceptibility Testing
by Florian Baquer, Asma Ali Sawan, Michel Auzou, Antoine Grillon, Benoît Jaulhac, Olivier Join-Lambert and Pierre H. Boyer
Antibiotics 2021, 10(8), 975; https://doi.org/10.3390/antibiotics10080975 - 12 Aug 2021
Cited by 5 | Viewed by 3568
Abstract
Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference [...] Read more.
Antimicrobial susceptibility testing of anaerobes is challenging. Because MIC determination is recommended by both CLSI and EUCAST, commercial broth microdilution and diffusion strip tests have been developed. The reliability of broth microdilution methods has not been assessed yet using the agar dilution reference method. In this work, we evaluated two broth microdilution kits (MICRONAUT-S Anaerobes® MIC and Sensititre Anaerobe MIC®) and one gradient diffusion strip method (Liofilchem®) for antimicrobial susceptibility testing of 47 Clostridiales isolates (Clostridium, Clostridioides and Hungatella species) using the agar dilution method as a reference. The evaluation focused on comparing six antimicrobial molecules available in both microdilution kits. Analytical performances were evaluated according to the Food and Drug Administration (FDA) recommendations. Essential agreements (EA) and categorical agreements (CA) varied greatly according to the molecule and the evaluated method. Vancomycin had values of essential and categorical agreements above 90% for the three methods. The CA fulfilled the FDA criteria for three major molecules in the treatment of Gram-positive anaerobic infections (metronidazole, piperacillin/tazobactam and vancomycin). The highest rate of error was observed for clindamycin. Multicenter studies are needed to further validate these results. Full article
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14 pages, 1575 KiB  
Article
Genomic Background and Phylogeny of cfiA-Positive Bacteroides fragilis Strains Resistant to Meropenem-EDTA
by Sylvia Valdezate, Fernando Cobo, Sara Monzón, María J. Medina-Pascual, Ángel Zaballos, Isabel Cuesta, Silvia Pino-Rosa and Pilar Villalón
Antibiotics 2021, 10(3), 304; https://doi.org/10.3390/antibiotics10030304 - 16 Mar 2021
Cited by 7 | Viewed by 2786
Abstract
Background: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfiA-positive) appear as an emergent, evolving clade. Methods: This work examines the genomes, taxonomy, and phylogenetic relationships with respect to other B. fragilis genomes [...] Read more.
Background: Bacteroides fragilis shows high antimicrobial resistance (AMR) rates and possesses numerous AMR mechanisms. Its carbapenem-resistant strains (metallo-β-lactamase cfiA-positive) appear as an emergent, evolving clade. Methods: This work examines the genomes, taxonomy, and phylogenetic relationships with respect to other B. fragilis genomes of two B. fragilis strains (CNM20180471 and CNM20200206) resistant to meropenem+EDTA and other antimicrobial agents. Results: Both strains possessed cfiA genes (cfiA14b and the new cfiA28), along with other AMR mechanisms. The presence of other efflux-pump genes, mexAB/mexJK/mexXY-oprM, acrEF/mdtEF-tolC, and especially cusR, which reduces the entry of carbapenem via the repression of porin OprD, may be related to meropenem–EDTA resistance. None of the detected insertion sequences were located upstream of cfiA. The genomes of these and other B. fragilis strains that clustered together in phylogenetic analyses did not meet the condition of >95% average nucleotide/amino acid identity, or >70% in silico genome-to-genome hybridization similarity, to be deemed members of the same species, although <1% difference in the genomic G+C content was seen with respect to the reference genome B. fragilis NCTC 9343T. Conclusions: Carbapenem-resistant strains may be considered a distinct clonal entity, and their surveillance is recommended given the ease with which they appear to acquire AMR. Full article
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12 pages, 897 KiB  
Article
The Prevalence and Clinical Significance of Anaerobic Bacteria in Major Liver Resection
by Jens Strohäker, Sophia Bareiß, Silvio Nadalin, Alfred Königsrainer, Ruth Ladurner and Anke Meier
Antibiotics 2021, 10(2), 139; https://doi.org/10.3390/antibiotics10020139 - 31 Jan 2021
Cited by 4 | Viewed by 2337
Abstract
(1) Background: Anaerobic infections in hepatobiliary surgery have rarely been addressed. Whereas infectious complications during the perioperative phase of liver resections are common, there are very limited data on the prevalence and clinical role of anaerobes in this context. Given the risk of [...] Read more.
(1) Background: Anaerobic infections in hepatobiliary surgery have rarely been addressed. Whereas infectious complications during the perioperative phase of liver resections are common, there are very limited data on the prevalence and clinical role of anaerobes in this context. Given the risk of contaminated bile in liver resections, the goal of our study was to investigate the prevalence and outcome of anaerobic infections in major hepatectomies. (2) Methods: We retrospectively analyzed the charts of 245 consecutive major hepatectomies that were performed at the department of General, Visceral, and Transplantation Surgery of the University Hospital of Tuebingen between July 2017 and August 2020. All microbiological cultures were screened for the prevalence of anaerobic bacteria and the patients’ clinical characteristics and outcomes were evaluated. (3) Results: Of the 245 patients, 13 patients suffered from anaerobic infections. Seven had positive cultures from the biliary tract during the primary procedure, while six had positive culture results from samples obtained during the management of complications. Risk factors for anaerobic infections were preoperative biliary stenting (p = 0.002) and bile leaks (p = 0.009). All of these infections had to be treated by intervention and adjunct antibiotic treatment with broad spectrum antibiotics. (4) Conclusions: Anaerobic infections are rare in liver resections. Certain risk factors trigger the antibiotic coverage of anaerobes. Full article
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11 pages, 877 KiB  
Article
Clinical Presentation and Incidence of Anaerobic Bacteria in Surgically Treated Biliary Tract Infections and Cholecystitis
by Jens Strohäker, Lisa Wiegand, Christian Beltzer, Alfred Königsrainer, Ruth Ladurner and Anke Meier
Antibiotics 2021, 10(1), 71; https://doi.org/10.3390/antibiotics10010071 - 13 Jan 2021
Cited by 6 | Viewed by 2574
Abstract
(1) Background: Cholecystitis and cholangitis are among the most common diseases treated by general surgery. Gallstones lead to inflammation and bacterial infection of the biliary tract. Biliary infections can lead to live threatening bacteremia and liver abscesses. The true role of anaerobes remains [...] Read more.
(1) Background: Cholecystitis and cholangitis are among the most common diseases treated by general surgery. Gallstones lead to inflammation and bacterial infection of the biliary tract. Biliary infections can lead to live threatening bacteremia and liver abscesses. The true role of anaerobes remains unclear. (2) Methods: We retrospectively analyzed bacterial cultures from biliary samples obtained from bile ducts and gallbladders at our tertiary care center. Patient characteristics and clinical outcomes were analyzed. (3) Results: In our database of 1719 patients, 365 patients had microbial testing, of which 42 grew anaerobic bacteria. Anaerobes were more frequently cultured in patients with hepatic abscesses and gallbladder perforation. These patients were older and had more comorbidities than the control group. The overall outcomes of all patients were favorable and the resistance rate to commonly used antibiotics remained low. (4) Conclusions: Anaerobes in biliary tract infections appear to be underdiagnosed and more prevalent in the elderly with advanced disease. Due to low antibiotic resistance, the combination of source control and adjunct anti-infective treatment leads to favorable outcomes. Full article
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9 pages, 434 KiB  
Article
Clinical Findings and Antimicrobial Susceptibility of Anaerobic Bacteria Isolated in Bloodstream Infections
by Fernando Cobo, Jaime Borrego, Esther Gómez, Isabel Casanovas, Elizabeth Calatrava, Carla Foronda and José María Navarro-Marí
Antibiotics 2020, 9(6), 345; https://doi.org/10.3390/antibiotics9060345 - 19 Jun 2020
Cited by 12 | Viewed by 3402
Abstract
The objectives of this study were to report on the antimicrobial susceptibility of 141 clinically significant anaerobic bacteria isolated from bloodstream infections between January 2016 and April 2020 in a tertiary-care hospital in Granada (Spain) and to describe the main clinical features of [...] Read more.
The objectives of this study were to report on the antimicrobial susceptibility of 141 clinically significant anaerobic bacteria isolated from bloodstream infections between January 2016 and April 2020 in a tertiary-care hospital in Granada (Spain) and to describe the main clinical features of the patients. Species identification was performed by MALDI-TOF MS (Bruker Daltonics, Billerica, MA, USA). Antimicrobial susceptibility tests were performed against penicillin, amoxicillin-clavulanic acid, imipenem, moxifloxacin, clindamycin, metronidazole, and piperacillin-tazobactam using the gradient diffusion technique and EUCAST breakpoints, except for moxifloxacin (CLSI breakpoints). The most frequent anaerobes were Bacteroides (43.9%, n = 62), Clostridium (24.1%, n = 34) and Gram-positive anaerobic cocci (GPACs) (15.6%, n = 22). Almost all tested anaerobes were susceptible to imipenem and amoxicillin-clavulanic acid, except for Bacteroides. High overall resistance rates to clindamycin were observed, especially for Gram-positive anaerobic cocci (GPACs) (54.5%) and for Bacteroides spp. (45.1%). Overall, low resistance rates to almost all antibiotics were observed for Clostridium. High resistance rates to penicillin were also observed for Gram-positive anaerobic bacilli (GPABs) (44.4%), as well as to metronidazole (22.2%), although only nine isolates were included. Antimicrobial susceptibility testing for anaerobes should always be performed in severe infections, such as those localized in the bloodstream. The information obtained contributes to selecting empirical treatments according with local data on resistance. Full article
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7 pages, 255 KiB  
Article
Breast Abscesses Caused by Anaerobic Microorganisms: Clinical and Microbiological Characteristics
by Fernando Cobo, Vicente Guillot and José María Navarro-Marí
Antibiotics 2020, 9(6), 341; https://doi.org/10.3390/antibiotics9060341 - 18 Jun 2020
Cited by 13 | Viewed by 4037
Abstract
The objectives of this study were to report the antimicrobial susceptibility of 35 clinically significant anaerobic bacteria isolated from breast abscesses between March 2017 and February 2020 in a tertiary hospital in Granada (Spain) and to describe key clinical features of the patients. [...] Read more.
The objectives of this study were to report the antimicrobial susceptibility of 35 clinically significant anaerobic bacteria isolated from breast abscesses between March 2017 and February 2020 in a tertiary hospital in Granada (Spain) and to describe key clinical features of the patients. Species identification was performed mainly by MALDI-TOF MS. Antimicrobial susceptibility tests were carried out against benzylpenicillin, amoxicillin–clavulanic acid, imipenem, moxifloxacin, clindamycin, metronidazole, and piperacillin–tazobactam using the gradient diffusion technique and European Committee on Antimicrobial Susceptibility Testing EUCAST breakpoints (except for moxifloxacin). The most frequent anaerobes were Finegoldia magna (31.4%; n = 11), Actinomyces spp. (17.1%; n = 6), Propionibacterium spp. (17.1%; n = 6), and Prevotella spp. (14.2%; n = 5). Imipenem, amoxicillin–clavulanic acid, and piperacillin–tazobactam were universally active against all genera tested. High overall resistance rates to clindamycin were observed, especially for Gram-positive anaerobic cocci (56.2%) and Gram-positive anaerobic bacilli (38.4%). High resistance rates to metronidazole were also observed for Gram-positive (76.9%) and Gram-negative anaerobic bacilli (50%). High resistance rates to moxifloxacin were found for Gram-negative anaerobic bacilli (50%) and Gram-positive anaerobic cocci (31.2%). No breast abscess cases of Bacteroides spp. were detected. Routine antimicrobial susceptibility testing for anaerobes in breast abscesses may contribute to allow empirical therapies to be selected in accordance with local data on resistant strains. Full article

Other

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5 pages, 404 KiB  
Case Report
First Case of Bacteraemia Due to Carbapenem-Resistant Bacteroides faecis
by Charlotte Kaeuffer, Tiffany Ruge, Laure Diancourt, Benoît Romain, Yvon Ruch, Benoît Jaulhac and Pierre H. Boyer
Antibiotics 2021, 10(3), 319; https://doi.org/10.3390/antibiotics10030319 - 19 Mar 2021
Cited by 8 | Viewed by 2309
Abstract
Multidrug resistant (MDR) bacteria are increasingly observed in nosocomial and community-acquired settings. Anaerobes are no exception to this rule, but there are fewer reports of MDR in the scientific literature on anaerobes than there are for other bacteria. In this short case report, [...] Read more.
Multidrug resistant (MDR) bacteria are increasingly observed in nosocomial and community-acquired settings. Anaerobes are no exception to this rule, but there are fewer reports of MDR in the scientific literature on anaerobes than there are for other bacteria. In this short case report, we describe the first case of bacteraemia caused by a multidrug-resistant Bacteroides faecis, which produces a carbapenemase encoded by the blaCfiA gene. This bacteraemia followed a digestive surgery operation. Surprisingly, these findings did not lead to a change in antibiotic therapy, probably because the patient’s clinical state had improved. Nevertheless this report calls for better knowledge of anaerobic bacteria and for a systematic antimicrobial stewardship procedure following bacteraemia. Full article
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