The problem with the conventional tools used to identify and classify bacteria is that they are just that, conventional, and as such have evolved since the 19th century to identify conventional features and bacterial relationships that are known to exist, have been documented thousands of times and make up a large portion of the body of knowledge of bacterial morphology that has been developed over about 150 years of study. Most of this has been gleaned from light microscopy, the limits of which are well known.
Outside the sphere of influence of the large body of microbiologists, who adhere to a rather rigid view that a coccus is a coccus, a bacillus is a bacillus etc. is a growing, more cutting edge view of the bacterial world where a great many other morphologies and forms exist, even particulate and that these forms, appear to represent defense mechanisms allowing the species to maintain resistance and re-populate in the classic form at an opportune time. The simple fact too, is that those involved in the study of what have become known as atypical bacterial forms, have achieved the highest level of acclaim in their field, yet their work has only slightly rippled the general pool of thinking in that field. Bacteria can take on a bewildering array of shapes, sizes, and forms, either for purposes of reproduction , as evasion tactics or obviously for purposes not understood. Virtually all of the antibiotics of the various families that have come to be relied on and classed as essential medicines in todays pharmacology are derived from naturally occurring substances in the microbial world, usually from molds, which the bacterial species have many years of familiarity with. Bacteria have naturally occurring mechanisms of surviving those substances, mechanisms that have existed in the gene pool for hundreds of thousands of years, They develop resistance as a block, because those genetic traits rise to the surface under the onslaught of a concentration of a chemical they are in fact familiar with historically, not usually because there is a mutation. Mechanisms of resistance are numerous but include such things as the pumping of a chemical out of the cell, cell particulation, the shedding of cell walls, sporulation, biofilm formation, encystment, rapid relocation, formation of electron dense bodies or tissue sequestering and probably so may other mechanisms that it would make your head spin.
When a culture or a serum shows areas of uneven morphology, or a high degree of particulation, the cause could be due to sub microscopic( light microscopy) structures associated with bacterial species but not at the stage of a refined morphology yet. Microscopic tools such as fluorescence , phase or DF have been used in the past to shed some light on such small particles, which defy conventional staining, with some success. Lengthy culturing periods have also been used to more or less extract a strain from it's cloak. In one study by Gerald Domingue et.al. , it took 2 years of constant culturing to achieve a reversion to a classic morphological form, of a mutated Staph. Aureus strain that was synthesizing a human growth hormone like chemical in tumour sites. The culture was obtained from CWD contaminated serum collected from that site.
A couple of wikipedia entries for 2 notables of bacteriology which briefly explains where the field is going in the future. https://en.wikipedia.org/wiki/Gerald_Dominguehttps://en.wikipedia.org/wiki/Lida_Holmes_Mattman