Microbial Transmission

The immediate mental representation of the concept of transmission for the public health epidemiologist, clinical microbiologist, or infectious diseases specialist concerns its application to the transmission of pathogenic microorganisms or the transmission of infections. Note that the widely used term “transmissible diseases” is certainly most inappropriate. Disease is the result of particular cross talk between microbe and host and is never transmissible as such. The infective process is what the microbe produces inside a particular host, which is well illustrated in the Latin origin of the word “infection,” derived from inficere (in + facere): “to put in, to dip into, to do an action inside.” Microbes are transmissible, not the infection. In general biology, the most frequent use of “transmission” applies to the transmission of hereditary characters (to the progeny), as in population genetics ( 1 ). To our knowledge, a broad conceptual understanding of transmission has not yet been attempted, although Hugh Dingle has approached the need of expanding the transmission-related concept of migration to different hierarchical levels ( 2 ). In this review, I intend to present the concept of transmission in a broad perspective, as a basic biological and evolutionary process, focusing particularly on the causes (forces and energies) governing transmission, a hitherto neglected field in biological and epidemiological research. For this purpose, it is appropriate to review what we collectively have in mind when considering the concept of transmission.

Antibiotics have saved the lives of countless people suffering from bacterial infections since Alexander Fleming discovered penicillin in 1928 ( 1 ). Nevertheless, this success was accompanied by the emergence of antibiotic resistance (AbR). It is thought that AbR arose originally as a self-protection mechanism of producer organisms ( 2 ). AbR genes rapidly disseminated through the biosphere as a result of the selection pressure established by human application of antibiotics ( 3 ). Resistance mechanisms capable of rendering newly discovered drugs ineffective emerged with astonishing speed, rapidly reaching human pathogens and increasingly invalidating newer antimicrobial therapies ( 4 ). Altogether, >20,000 potential resistance genes of nearly 400 types have been predicted from bacterial genome sequences ( 5 ). The danger created by the ever-increasing number of pathogens resistant to conventional antibiotics is further increased by a significant drop in the development of new antimicrobial compounds ( 6 ). This situation demands solutions to prevent the hundreds of thousands of people dying each year as a result of AbR from becoming millions ( 7 ). Proposed strategies include more-accurate prescription policies and a controlled use and release of antibiotics in animal husbandry and agriculture, restrictions difficult to implement on a global scale ( 3 ).

Horizontal gene transfer (HGT) is a key source of genetic diversity in bacteria ( 1 ), and plasmids are one of the main vehicles driving this process ( 2 ). Plasmids are widely distributed across prokaryotes, and help bacteria adapt to a myriad of different environments, conditions, and stresses ( 3 , 4 ), playing a key role in bacterial ecology and evolution ( 5 – 7 ). The most vivid testimony to the power of plasmids as catalysts for bacterial adaptation is their role in the spread of antibiotic resistance among clinical pathogens ( 8 ), which has emerged as a major health problem over the past decades ( 9 ).

In line with Koch’s postulates, studying virulence typically translates into identifying and characterizing the molecular determinants that underlie colonization of a host by a pathogen and the subsequent appearance of symptoms ( 1 ). In this conceptual framework, the presence of pathogens implies damage to the host whose intensity is proportional to the virulence of the pathogen. This approach is based on the observation that damage is often related to the expression of specific features of the pathogen, i.e., the virulence factors ( 2 ).

The bacterial species Salmonella enterica comprises Gram-negative pathogenic microorganisms that cause infections in humans and livestock. S. enterica is subdivided into six subspecies, with subspecies I responsible for infections in warm-blooded vertebrates, including mammals and birds ( 1 , 2 ). To date, >2,500 serovars have been reported in subspecies I. Some of these serovars are host adapted, whereas others infect a broad range of hosts. Host-adapted serovars cause systemic infections that result in typhoid (paratyphoid) fever and bacteremia. Among these serovars are Typhi, Paratyphi A, Paratyphi C (humans), Cholerasuis (swine), Dublin (cow), and Gallinarum (fowl). Nontyphoidal serovars normally cause self-limiting gastroenteritis, although the severity of the infection varies depending on the immune defense status of the host and/or a unique genetic makeup that may render the clone highly invasive. An example is the recently characterized invasive serovar Typhimurium isolates that cause systemic disease in HIV-infected individuals of sub-Saharan African countries ( 3 , 4 ) and Latin America ( 5 ). Importantly, high transmissibility has been reported for all serovars, especially in those areas in which hygiene conditions in water and food are poor. The ability of all S. enterica serovars to cause persistent asymptomatic infections, especially following infection by host-adapted serovars, imposes more difficulties on control of transmission ( 6 , 7 ). This capacity to persist in the host without causing pathology has attracted physicians and microbiologists for more than a century, given its undoubtable negative impact on pathogen eradication. The reader is directed to the pioneering book The Carrier Problem in Infectious Diseases by Ledingham and Arkwright, which in 1912 exhaustively compiled all existing information about cases of asymptomatic carriers and their impact on pathogen transmission ( 8 ). These authors focused on six diseases known at that time to have high transmission rates, including typhoid and paratyphoid fever, diphtheria, epidemic cerebrospinal meningitis, dysentery, and cholera ( 8 ). Studies performed in mouse asymptomatic chronic infection models using the serovar Typhimurium have identified pathogen genes required to persist in the animal for long periods of time (weeks to a few months) ( 9 , 10 ). These studies also showed that serovar Typhimurium evolves during a chronic infection in the host and that this condition selects for adaptive mutations ( 9 ). This is an intense and fascinating area of research that will certainly aid to combat Salmonella transmissibility among individuals. We also refer to the chapter in this book by Wolf-Dietrich Hardt and colleagues, which addresses within-host evolution in Salmonella and the transmission of the virulent genotype in populations differentially affected by antibiotic treatments.

Antibiotics are compounds that inhibit (bacteriostatic drugs) or kill (bactericidal drugs) bacteria by a specific interaction with a specific target in the bacterial cell, and they are arguably the most important medical intervention introduced by humans. Ever since antibiotics were introduced on large scale in the late 1940s to treat human bacterial infectious diseases, there has been a steady selection and increase in the frequency of antibiotic-resistant bacteria, generating a very problematic situation ( 1 – 3 ). Resistance evolution is a complex process that is driven by the interaction between a number of biotic and abiotic factors. Fundamental factors underlying this dynamic are the rates of emergence and persistence of resistant bacterial clones; time and space gradients of antibiotics and other xenobiotics; and transmission rates within human populations and between humans and various other sources, including animals, the environment, food, etc. Furthermore, with the realization that antibiotic resistance has become a serious medical problem, human attempts to reduce transmission of infectious bacteria in general, and resistant ones in particular, by hygienic measures, vaccination, reduced antibiotic pressures, etc., has also influenced this dynamic.

The evolution of living beings is a complex process, with a large degree of serendipity, in which the offspring displace the ancestors. Indeed, what we find in the current multicellular world, and more specifically in the animal world, are the last members of an evolutionary process; all other members in the same branch of the phylogenetic tree have disappeared. In this regard, most multicellular organisms can be considered as newcomers on Earth, which have appeared quite recently in evolutionary terms. Although there are still some progenitors that stand after the evolution of their siblings, the most common scenario for multicellular organisms is that ancestors disappear once the evolved progeny displace them (see the evolution of Homo sapiens). This type of recent evolution followed by extinction is not so frequent in the case of bacterial species, although it may have happened on some occasions (see the example of Yersinia described below). Indeed, the origin of different pathogens has been tracked to more than 100 million years ago, long before the human being (or an ancestor) was present on Earth ( 1 ). Despite this extremely long evolutionary time, which should have allowed for large diversification with the loss of ancestors, bacterial core genomes are remarkably stable. It could be expected that the allelic variants of bacterial genes should cover nearly the entire potential spectrum of synonymous mutations and even those nonsynonymous mutations without substantial associated fitness costs. However, today we can use multilocus sequence typing for distinguishing among different clones in bacterial populations, under the assumption that, at least for several of the core genome genes, fixation of mutations is not a frequent event ( 2 ). It then seems that, unless there is a major change in habitat, mutation-driven evolution is not the most important process in the speciation of bacteria in general, and in particular in the case of bacterial pathogens. A major force in such evolution, however, would be the acquisition of genetic elements ( 3 – 5 ), what has been dubbed evolution in quantum leaps ( 6 ). These acquired genes constitute the accessory genome of an organism and the pangenome of a given species ( 7 ).

Food is considered one of the main environmental drivers shaping the human microbiota across the life span. Microorganisms vehiculated by food can be related to a variety of scenarios, including those benefiting health (e.g., stimulation of host antibodies, release of chemicals to stimulate the health of the overall system, or inhibition of pathogen development), those causing minimal change within the equilibrium of the host microbial community, and those that are pathogenic or have been associated with gut-host dysbiosis ( 1 – 3 ). Recently there has been an increase in knowledge on gut bacterial genera and species commonly affected by diet, as well as evidence suggesting that the intestinal microbiome plays an important role in modulating the risk of several chronic diseases (e.g., inflammatory bowel disease, obesity, type 2 diabetes, cardiovascular disease, and cancer) ( 1 – 3 ). Nevertheless, comprehensive information about the types of diet that transmit bacteria implicated in those diseases, as well as environmental and host factors favoring their colonization, remains scarce. Notwithstanding, food as a transmission mode for microorganisms reaching humans is extensively characterized for different pathogenic bacteria, the environment, animals, and humans being their main reservoirs ( Fig. 1 ) and the fecal-oral route their main transmission route ( 4 – 6 ). A triad including a contaminated food item, a susceptible human host, and bacterial pathogens able to survive and multiply in specific environmental conditions must be present for the occurrence of a foodborne disease. Nevertheless, transmission of typical foodborne pathogens can also occur more rarely by alternative transmission modes, as by direct contact of humans with infected animals or between humans ( 7 ).

Arthropods are a phylum of invertebrate animals with an exoskeleton, including >1 million species and accounting for >80% of all known living animal species ( 1 ).

Oliver Wendell Holmes was the first to describe the direct transmission of possible infective (“pestilent”) agents to puerperal women through the physician’s contaminated hands ( 1 ). In 1855, he published a book entitled Puerperal Fever, as a Private Pestilence in the United States ( 2 ). Nevertheless, the worldwide recognition of this relevant observation was classically attributed to Ignaz Philipp Semmelweis, who published a scientifically based demonstration of the role of hand disinfection in his thesis titled “The Etiology, the Concept and the Prophylaxis of Childbed Fever,” developing seminal observations carried out in the year 1847 ( 3 ). Both authors implicated, for first time, the role of human hands contaminated with “cadaverous particles” in the deadly transmission process. Their legacy persists today, with considerable influence on current medicine, in which hand hygiene remains a liturgy in surgical procedures and is also a general measure with a pivotal role in the prevention and control of communicable diseases ( 4 , 5 ).

The use of antimicrobial agents has resulted in the subsequent development of resistance by bacteria to such agents, with increased transmission of several significant antimicrobial-resistant pathogenic microorganisms within the health care system ( 1 ; see also https://www.cdc.gov/drugresistance/pdf/ar-threats-2013-508.pdf and http://www.jpiamr.eu/document-library/strategicresearchagenda). These bacteria include methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococcus (VRE), extended-spectrum β-lactamase (ESBL)-producing Gram-negative bacteria, and carbapenemase-producing Gram-negative enteric bacteria (CPE). The transmission of these antimicrobial-resistant organisms (AROs) has the potential to negatively impact patient morbidity and mortality ( 2 ).

The introduction of DNA fingerprinting tools for the analysis of Mycobacterium tuberculosis (MTB) isolates has transformed the way we control the transmission of this pathogen. As with any other infection transmitted via aerosolized particles harboring infective bacteria, obtaining accurate data on the index case and subsequent contacts involved in a transmission chain is challenging.

Tuberculosis (TB) is the biggest killer of humanity. TB has killed more human beings than any other infectious disease in history, with an estimated loss of over a billion lives in the past 200 years ( 1 ). Despite effective treatment, in the WHO 2016 there were an estimated 10.4 million new TB cases and 1.8 million deaths attributed to the disease worldwide, surpassing those caused by AIDS ( 2 ). Still more worrying is the rising transmission of multidrug-resistant TB (MDR-TB), caused by mycobacteria that are resistant to treatment with at least two of the most powerful first-line anti-TB drugs, isoniazid and rifampin ( 2 ). Nearly half a million new MDR-TB cases are estimated every year, which together with increasing globalization makes TB an alarming global health problem ( 2 ). Loss of compliance with the current treatments for TB raises the frightening idea of a return to the pre-antibiotic era, when 50% of TB patients died in the absence of an effective treatment. Dissemination of multi- and extremely drug-resistant Mycobacterium tuberculosis strains has adverse implications for TB control in the 21st century.

Ebolaviruses are the causative agents responsible for several outbreaks of hemorrhagic fever. Ebolavirus is a genus within the family Filoviridae. The genus Ebolavirus contains five species: Zaire ebolavirus (EBOV), Sudan ebolavirus (SUDV), Reston ebolavirus (RESTV), Täi Forest ebolavirus (TAFV), and Bundibugyo ebolavirus (BDBV) ( 1 , 2 ). Ebolaviruses were identified for the first time during two major outbreaks of hemorrhagic fever disease, which took place almost at the same time in Yambuku, Democratic Republic of the Congo (DRC, previously Zaire), and Nzara, Sudan, in 1976 ( 3 , 4 ), and were demonstrated to be caused respectively by the agents now known as EBOV and SUDV. More than 500 cases were reported in those outbreaks, with a striking mortality rate of 88% in Zaire and of 53% in Sudan. The origin of the name Ebola corresponds to a river in nearby Yambuku, DRC, the first location known to be affected by EBOV ( 5 ). Within the Filoviridae there is also the genus Marburgvirus, with its unique species, Marburg marburgvirus (MARV), which shares many epidemiological and pathogenic aspects with EBOV. MARV was actually the first filovirus discovered, in 1967 during an outbreak in Germany and Belgrade, Serbia, that resulted in the infection of several laboratory technicians who were manipulating tissues from African monkeys ( 6 ). At that time, structures with thread-like morphology were visualized by electron microscopy in organs of infected individuals, and the term filovirus was coined ( 7 ) to describe these agents. All ebolaviruses except RESTV have been described in Africa and are highly pathogenic for humans: EBOV and SUDV in 1976, TAFV in 1994, and BDBV in 2007. RESTV comes from Asia (Philippines), and for unknown reasons it is unique in not causing disease in humans, an observation based on a number of documented zoonotic infections, since RESTV can asymptomatically infect swine and eventually be transmitted to humans ( 8 , 9 ). Intriguingly, despite being nonpathogenic for humans and swine, RESTV is capable of being highly lethal in nonhuman primates (NHPs) ( 9 – 15 ). Recently a third genus of filovirus, Cuevavirus, has been described infecting cave bats in northern Spain. The single agent within Cuevavirus, named Lloviu virus, has not been replicated in culture although it has been fully characterized by sequencing analysis. Its pathogenic potential for humans is unknown ( 16 , 17 ).

Transmissibility is the defining attribute of infectious diseases, and it has profound consequences for their epidemiology. In contrast to noncommunicable diseases, the risk of an individual contracting an infectious disease increases with the number of infected and infectious individuals present in the population. This is positive feedback, and it makes the epidemiology of infectious diseases considerably more complex and often hard to understand intuitively. For example, reducing the per capita transmission rate is expected to decrease the size of an epidemic, but it is difficult to estimate by how much; because of the positive feedback, there is not a proportional (or linear) relationship between epidemic size and transmission rate. Less obvious still is the expectation that decreasing transmission rate may increase rather than decrease the duration of an outbreak ( 1 ).

The problem of antibiotic resistance in hospital bacteria and the human community has been recognized by various organizations ( 1 – 3 ) as one of the greatest challenges to public health, which calls into question the maintenance and progress of modern medicine ( 4 , 5 ). This alarm is based on the inability to treat and prevent infections caused by microorganisms that are resistant to all therapeutic alternatives available. In recent years, there have been some unexpected circumstances that have acted synergistically and have worsened the problem, namely, (i) a general failure to discover new antimicrobials; (ii) the exponential development of antibiotic resistance in overcrowded countries with serious health deficits and the global spread of multiresistant bacteria; (iii) the invasion by resistant bacteria of ecosystems (surface water and sewage, soil, animals, and food) and, particularly, the invasion of human intestinal microbiota; and (iv) a pollution environment with high concentrations of antibiotics, metals, and biocides that favor the selection of multiresistant bacteria and their persistence. An estimated 25,000 people die each year in Europe and the United States from antibiotic resistance ( 5 ).

In recent decades, microbiologists have discovered an astounding disparity of prokaryotic life. Our field has identified the most anciently divergent prokaryotic lineages, and we have found them to be utterly different in every aspect of their being: their cell architecture, biochemistry, physiology, genome content, and how they make a living. Our understanding of the prokaryotes’ phylogenetic diversity began in large part with Carl Woese’s tree of all life, based on the universal 16S rRNA gene ( 1 ). His universal tree yielded the surprising result that the not-yet-named archaea and bacteria, already known to be extremely different in cell structure, represented the deepest divisions of life. Subsequent surveys of 16S diversity, using cultivation-free methods, led to discovery of vast numbers of uncultivated prokaryotic taxa, at all levels from species to phyla, in even the most familiar of habitats ( 2 ). While cultivation has yielded discovery of ∼30 bacterial phyla, cultivation-free methods focusing on 16S have expanded the number of bacterial phyla to nearly 100 ( 3 ). Moreover, we can extrapolate that among rare, presently uncultivable organisms, we will eventually discover ∼1,300 phyla ( 4 )! Most recently, single-cell genomic approaches have yielded much greater resolution for prokaryotic phylogeny and have revealed a totally unexpected superphylum at the base of the bacteria tree. This group is predominated by phyla with limited metabolic capabilities and a shared stubbornness against cultivation ( 5 ). These are all exciting forays into estimating the vastness and organization of prokaryotic diversity, but these purely phylogenetic approaches fail to portray the profound distinctness among the most anciently divergent prokaryotes.

It has been proposed that an organism and its microbes form an assemblage called a holobiont ( 1 , 2 ). The human body and human genome along with gut microbes and their genomes can be seen as a dynamic holobiont system ( 3 – 5 ), i.e., a superorganism amalgamating microbial and human attributes ( 6 ). In this multipartite holobiont, the host genome provides the primary genome, while microbial genes constitute the “second human genome,” which is in fact a prokaryotic pangenome ( 3 , 7 , 8 ). Whether the holobionts are units of selection is actively debated ( 9 – 11 ), yet other aspects of their biology are less controversial, and holobionts are becoming a major object of study in biology. Among these uncontroversial features lies the observation that, by definition, a holobiont is home to several different modes of genetic transmission. In nuclear transmission, the genetic material is inherited from one individual (in parthenogenesis, for example) or, most of the time, from two individuals, whereas in organelle transmission (of mitochondria, for example), the material is mostly inherited from the mother, in animals ( 12 ). Both types of transmission result directly from the reproduction of the host. This stands in contrast to transmission of the microbiota, that is, the acquisition (or loss) of microbes between host generations. In mammals, at birth, the microbiota is inherited from the mother, but this is not always the case for other animal groups, where it could also be inherited from the environment ( 12 , 13 ). During the life of the individual, the microbiota may even evolve, depending on different factors, which are currently not well characterized (e.g., host constraints, diet, environment, and transmission between different hosts) ( 14 ). The transmission of microbiomes differs in turn from the transmission of microbiotas, since it is no longer (or at least not only) microbes that are exchanged, acquired, or lost, but genes themselves. These genes may be carried by microbes, but also by viruses, plasmids, or other classes of mobile genetic elements (MGEs). For example, transmissions in the gut microbiome are in part due to horizontal gene transfer (HGT) ( 4 , 15 , 16 ) because of the high cell density in microorganisms, and mediated by viruses—especially temperate prophages ( 17 , 18 )—integrases, recombinases ( 19 ), and conjugative transposons ( 20 ). Finally, the transmission of microbes from the environment to the host has not been systematically taken into account ( 11 ). As with any transmission, microbial transmission can be transient or permanent ( Fig. 1 ).