Abstract
Anaerobic bacteria have pivotal roles in the microbiota of humans and they are significant infectious agents involved in many pathological processes, both in immunocompetent and immunocompromised individuals. Their isolation, cultivation and correct identification differs significantly from the workup of aerobic species, although the use of new technologies (e.g., matrix-assisted laser desorption/ionization time-of-flight mass spectrometry, whole genome sequencing) changed anaerobic diagnostics dramatically. In the past, antimicrobial susceptibility of these microorganisms showed predictable patterns and empirical therapy could be safely administered but recently a steady and clear increase in the resistance for several important drugs (β-lactams, clindamycin) has been observed worldwide. For this reason, antimicrobial susceptibility testing of anaerobic isolates for surveillance purposes or otherwise is of paramount importance but the availability of these testing methods is usually limited. In this present review, our aim was to give an overview of the methods currently available for the identification (using phenotypic characteristics, biochemical testing, gas-liquid chromatography, MALDI-TOF MS and WGS) and antimicrobial susceptibility testing (agar dilution, broth microdilution, disk diffusion, gradient tests, automated systems, phenotypic and molecular resistance detection techniques) of anaerobes, when should these methods be used and what are the recent developments in resistance patterns of anaerobic bacteria.
Highlights
Anaerobic bacteria have been implicated in a wide range of infectious processes
The presence of this species was associated with pathogen synergy, it has been described that the presence of B. fragilis and E. coli in mixed intra-abdominal infections enhanced the anti-complement environment of the infection site through bacterial virulence factors [86]
Anaerobic bacteria were traditionally classified into the Clostridium spp. based on the following characteristics: (i) their staining result was Gram-positive (ii) being strict anaerobic (iii) formation of characteristic endospores (iv) inability to reduce sulphates (SO4 2− ) into sulphites (SO3 2− ) [6,7]
Summary
Anaerobic bacteria have been implicated in a wide range of infectious processes. As an integral part of the human microbiome, these microorganisms can be found in different anatomical sites and they can be responsible for a plethora of infections that may be serious or life-threatening [1,2,3,4]. A range of factors are known to increase the likelihood of anaerobic (mixed) infections, most of which are related to either processes that damage the mucous membranes or conditions reducing the oxygen levels of tissues Some of these predisposing factors include diabetes, angiopathies of different origin, malignancies, animal and human bites, wounds contaminated with soil, burns, trauma, surgical interventions (both minor and major), foreign bodies, immunosuppression due to AIDS or drug therapy (corticosteroids, cytotoxic agents), procedures involving fine needle aspiration among others [2,4]. From another point of view, the composition of the microbiota is significant due to inter-species and intra-species horizontal gene transfer (HGT) of various resistance determinants [46,47]
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