Microbial physiology in relation to the availability of water

The availability of water is the most important factor for microbial growth on surfaces and this crucial parameter is directly dependent upon the relative humidity (RH). The studies described in this thesis show that, in a (semi-)closed environment, the occurrence of microbial growth will not occur at spots where it is relatively warm. Instead it will be at the cold spots where the local RH is highest. When a surface becomes sufficiently cold the local RH eventually becomes equal to 100% (condensation). This principal also has clinical implications such as in neonatal incubators. This thesis shows that the highest number of microorganisms were indeed located at the coldest spots of its interior. This insight can be used to improve incubator hygiene. The availability of water not only determines which organisms can grow where, but also has a direct effect on their physiology. Experimental setups of a relative-humidity gradient shows that many microorganisms minimize their surface to volume ratio at low RH values by changing their shape, such increase in size, or/and by growing in clusters. Microorganisms furthermore increase their internal osmotic values and adapt their cell wall composition in order to attract or retain water more easily. Other properties, such as antibiotics resistance, are also indirectly altered by these adaptations. Due to all these changes it sometimes seems that one is dealing with different microorganisms when one compares the same microorganism grown at either a high or a low RH.

Concordance between culture, Molecular Culture and Illumina 16S rRNA gene amplicon sequencing of bone and ulcer bed biopsies in people with diabetic foot osteomyelitis

Abstract Background In clinical practice the diagnosis of diabetic foot osteomyelitis (DFO) relies on cultures of bone or ulcer bed (UB) biopsies, of which bone biopsy is reference standard. The slow growth or fastidious nature of some bacteria, hamper expeditious detection and identification. Rapid molecular techniques may solve both issues, but their additional value for everyday practice is unknown. We investigated the concordance between conventional culture, the molecular techniques Molecular Culture (MC), and illumina 16S rRNA gene amplicon (16S) sequencing in people with DFO. Methods In the BeBoP trial, bone and UB biopsies were obtained from people with DFO who visited Amsterdam UMC. These biopsies were analysed using 1) conventional culture, 2)MC, a rapid broad range PCR analysing the 16S-23S ribosomal-interspace-region, and 3) 16S sequencing, and evaluated concordance among these techniques. Results We analysed 20 samples (11 bone and 9 UB) of 18 people. A total of 84 infectious agents were identified, 45 (54%) by all techniques, an additional 22 (26.5%, overall 80.5%) by both MC and 16S, and the remaining 16 species by culture and MC or 16S, or by a single method only. MC and 16S identified anaerobes not detected by culturing in 5 samples, and the presence of bacteria in 7 of 8 culture-negative (6 bone, 2 UB) samples. Conclusion The high level of concordance between MC and 16S and the additional ability of molecular techniques to detect various bacteria not detected by culturing opens up prospects for routine use of fast molecular techniques, in clinical settings including DFO. Trial registration The BeBoP trial is retrospectively registered on 05–03-2019 in Netherlands Trial Register: NL 7582