**2. Chlamydia: the organism**

The phylum of Chlamydiae has obligate intracellular, Gram-negative bacteria. They consist of the following four groups (Simkania, Waddila, Chlamydiaceae and Parachlamydia family) with five added Candidatus families (Parilichlamydiaceae, Clavichlamydiaceae, Rhabdochlamydiaceae, Criblamydiaceae, and Piscichlamydiaceae) [1]. Literature search tells us that chlamydia like caused diseases in the eye have occurred in ancient Egyptian papyri (1555–1553 BC) and Chinese writings (2700 BC). The associates of Albert Neisser, von Prowazek and Halberstaedter, noticed inclusions within the cytoplasm of cells in the scrapings of conjunctiva, from patients with trachoma in 1907. Chlamydiae was isolated by Levinthal, Cole and Lillie between 1929 and 1930 while they were studying psittacosis. It was described as a virus by Bedson an Bland in 1932 [2]. Earlier chlamydiae were considered to be protozoa in 1997 as chlamydia-like microorganisms were first found in single-celled, free-living environmental acanthamoebae [3]. Then as they passed through filters of 0.45 μm diameter and had a biphasic intracellular development cycle, they were thought of as viruses. However, as it had- both RNA and DNA, the ability to synthesize nucleic acids, proteins and lipids, the susceptibility to antibiotics; hence they were concluded as bacteria. However, as they are obligate intracellular pathogens, they are cultivated only within living cells, unlike free living bacteria [2].

At present there are 16 species put forward in the *Chlamydiaceae* family, which infect a broad range of hosts and different anatomical sites. Out of which humans are primarily infected by *C. trachomatis* and *C. pneumoniae*, with *C. psittaci* having proven zoonotic potential in humans [4].

*C. trachomatis* remains an elusive human infecting species constantly under focus. It consists of four ocular serovars A, B, Ba, and C that cause endemic trachoma, with at least eight serovars, D to K, that cause infections of the genital tract. In addition three L serovars are also included that cause lymphogranuloma venerum. Genome sequencing helped in knowing this enigmatic organism more. An early study on genomic phylogeny described the "trachoma clade" in which *C. trachomatis* is divided into two distinct clades of LGV and the ocular and genital tract isolates [5]. This clade has two lineages (T1 and T2). Clade T1 includes more common urogenital isolates, whereas T2 contains rarer urogenital isolates and ocular strains, that makes this cluster, making one suspect that these ocular isolates could have emerged from a urogenital ancestor. It is suspected that chlamydiae spread further from a urogenital niche to infect the eye, resulting in trachoma [6]. This notion evolves from the ability of urogenital isolates to utilize indole and synthesize tryptophan that is abundant in the vagina due to it's microbiome, but ocular strains lack this ability. Hence, urogenital strains can flourish both in the eye and genital tract, whereas ocular strains fail to thrive in the genital tract [7]. Myths like, *C. trachomatis* is a parasite as it derives energy from the eukaryotic host cell have been quashed with the help of genome sequencing with the discovery of all the required genes for the biosynthesis of ATP [8].

Over the years Chlamydiacae family evolved to give rise to new variants, serovars and species and humans have discovered new species as well while studying this organism over the years. The process of Lateral gene transfer (LGT) influences bacterial ecology and pathogenesis of diseases, evolution of Chlamydia and the propagation of antibiotic resistance across different species. Also known as Horizontal gene transfer, it involves genetic material (DNA) transfer between the cells followed by it's integration into the recipient cell's genome. Mutation is not the only adaptive strategy of *C. trachomatis* to evolve. High recombination rates among the strains seen using phylogenetic analysis of genomes, tell us otherwise. The overall average recombination rate seen has been around 26% (5–32%) [9]. The phenomenon of intrastrain recombination among *C. trachomatis* was first reported

*Chlamydia: The Secret Enemy from the Past to Present, and Future DOI: http://dx.doi.org/10.5772/intechopen.110902*

in literature, in the 1990s. It was based on gene-specific sequence analysis of gene *ompA*, that is responsible for synthesis of major outer membrane protein (MOMP). A wide range of such regions with high recombination rates are present in *C. trachomatis* and *C. pneumonia* like *ompA*, *tarp* (the translocated actin-recruiting phosphoprotein encoding gene)*,* the polymorphic membrane protein-encoding genes (*pmps*), and *incA*, as well as the plasticity zone (PZ). Studies show that recombination events keep occurring across the complete genome leading to evolution of *C. trachomatis* as well as other chlamydial species such as *C. pneumoniae*, *C. suis and C. psittaci*. Cross-species and intraspecies genetic transfer vary. Intraspecies LGT maintains wild-type genomes within the cell, that otherwise might be considered stressful and mutagenic [10]. Whereas interspecies recombination leads to replication termination. It is now possible to genetically modify the organism, as evident in knockout mutants where the genes that are involved in LGT are inactivated [11].

The more we write about it and understand this organism, more is the number of doors we see that take us forward to amazement.
