"this book addresses important themes in the molecular epidemiology of bacterial pathogens ... Another consistent strength of this book is the detailed coverage of antibiotic resistance across the entire spectrum of food and waterborne pathogens ... for clinicians, food or environmental scientists, or public health officials interested in gaining a foundation in the molecular microbiology of this important group of pathogens, this book would provide an excellent foundation. Alternatively, for those with expertise in specific organisms, this book provides an interesting look across the spectrum of food and waterborne bacterial pathogens." from Jason B. Harris (Harvard Medical School, Boston, USA) writing in Clin. Inf. Dis. (2013) read more ...

Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology Edited by: Shah M. Faruque ISBN: 978-1-908230-06-5 Publisher: Caister Academic Press Publication Date: July 2012 Cover: hardback "an excellent foundation" (Clin. Inf. Dis.)

"There are only a few publications on systems biology studies of infectious processes and no summary literature. In this respect, this book is very timely. It presents a comprehensive analysis of all the components and processes of an infectious process, including applied Omic technologies and biochemical analysis, described in the book in detail. The focus is on the adaptation of the pathogen to the host or in the case of the Y. pestis to life in the flea and the response of host cells to infection with Yersinia. A successful and easy-to-understand book, it presents an overview of the latest findings on the biology and control systems of Yersinia ... it is a must for Yersinia researchers and rewarding for all infection specialists." from Petra Dersch (Braunschweig, Germany) writing in Biospectrum (2013) 19: 224. read more ...

Yersinia: Systems Biology and Control Edited by: Elisabeth Carniel and B. Joseph Hinnebusch ISBN: 978-1-908230-05-8 Publisher: Caister Academic Press Publication Date: July 2012 Cover: hardback "a must for Yersinia researchers" (Biospektrum)

"there is a wealth of detailed, up-to-date information on the epidemiology, pathogenesis and molecular biology of these pathogens written by experts in the field. This book would very useful to those studying gastrointestinal bacterial pathogens or food and water microbiology at postgraduate level and as a reference for specialists working in this area." from Kathie Grant (Health Protection Agency, UK) writing in Microbiology Today (2013) read more ...

Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology Edited by: Shah M. Faruque ISBN: 978-1-908230-06-5 Publisher: Caister Academic Press Publication Date: July 2012 Cover: hardback "a wealth of detailed, up-to-date information" (Microbiol. Today)

from Riikka Laukkanen-Ninios and Maria Fredriksson-Ahomaa writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Enteropathogenic yersiniosis is caused due to foodborne infection with Yersinia enterocolitica and Y. pseudotuberculosis. Several virulence factors have been identified that are common to these two pathogens even though Y. pseudotuberculosis is genetically more related to Y. pestis, which is typically transmitted by fleas and not through foods. Diarrhoea and abdominal pain are the most dominant symptoms for Y. enterocolitica and Y. pseudotuberculosis infections. Occasionally, complications such as joint pain and skin rash may occur, typically among adults. Most human cases are caused by Y. enterocolitica. The reported cases are mainly sporadic and outbreaks are uncommon. However, outbreaks of Y. pseudotuberculosis infection, often in school children, have occurred in Finland, Russia and Japan. The most important transmission route is proposed to be via contaminated foods even though these pathogens have seldom been isolated from foods. The low isolation rates are probably due to the low sensitivity of the culture methods. Y. enterocolitica infections have been linked to raw or under-cooked pork and pork products while Y. pseudotuberculosis infections have been linked to raw fresh produce and surface water. Pigs are so far the most important reservoir for human pathogenic Y. enterocolitica. The principal reservoir of Y. pseudotuberculosis is believed to be wild animals, especially rodents and birds. Transmission routes of these pathogens from animals to humans are mostly unknown.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Sangmi Lee, Robin M. Siletzky and Sophia Kathariou writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Listeria monocytogenes is a Gram-positive foodborne pathogen that causes a severe, potentially fatal illness (listeriosis) in animals and humans. The only human pathogen within the genus Listeria, this bacterium is equipped with sophisticated mechanisms to invade mammalian cells and proliferate inracellularly. Population genetics data indicate that some groups of L. monocytogenes are more frequently associated with human listeriosis. However, the ecology and potentially unique characteristics of such groups remain to be elucidated. This review discusses recent advances in the epidemiology of listeriosis and epidemic-associated clonal groups; the characterization of pathogenicity of L. monocytogenes; the evolution of Listeria species and L. monocytogenes; and the increasingly recognized importance of Listeria phages in the ecology of L. monocytogenes in food processing facilities.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from T. Ramamurthy and M. John Albert writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

There are five categories of diarrhoeagenic Escherichia coli (DEC) namely enterotoxigenic, enteropathogenic, enterohaemorrhagic, enteroinvasive and enteroaggregative. They have evolved from nonpathogenic commensal strains by acquisition of specific virulence genes through mobile genetic elements. Their pathogenesis differs and they produce distinct clinical syndromes and pathological lesions and have different epidemiological characteristics. The virulence genes are carried on plasmids, bacteriophages, transposons or pathogenicity islands. DEC produce an array of virulence factors which include colonization factors, enterotoxins, cytotoxins, haemolysins, invasins etc. The diseases they produce range from acute watery diarrhea to dysentery to bloody diarrhoea with haemolytic uraemic syndrome. Even though the major burden of the disease is in the developing world, no part of the world is free from them, and EHEC infections are predominant in developed countries. A variety of molecular tools have been developed to study the diversity and transmission of these pathogens. Even though attempts are being made, no ideal vaccine exists against any category of DEC, therefore maintaining appropriate food and water hygiene are the only ways to keep the infections under control. We must also be on guard against the emergence of new pathogenic strains. The recent emergence of a hybrid enteroaggregative-haemorrhagic E. coli with the rare serotype of O104:H4 in Germany that caused high mortality rates is a case in point.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Marie Yeung and Kathryn J. Boor writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

As a natural inhabitant of the marine environment, Vibrio parahaemolyticus is frequently present in seafood, and particularly in oysters. V. parahaemolyticus can multiply rapidly under favorable conditions, but also may exist in a viable but non-culturable state under unfavorable conditions. A small subset of this species can cause human disease, with acute gastroenteritis as the predominant clinical manifestation. Two pore-forming hemolysins, thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH), are recognized as contributors to V. parahaemolyticus pathogenesis. Therefore, many detection methods for pathogenic strains focus on determining the presence of the genes encoding these hemolysins or on detection of beta-hemolysis on Wagatsuma agar (i.e. the Kanagawa Phenomenon). Serotyping and molecular fingerprinting techniques are also used to subtype Vibrio parahaemolyticus isolates. One of the most effective strategies for preventing Vibrio parahaemolyticus infection from consumption of raw or uncooked seafood is to reduce seafood post-harvest storage temperatures to prevent the growth of this species.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Iddya Karunasagar and Anusha Rohit writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Vibrio vulnificus is a normal inhabitant of warm estuarine environments all over the world and may be associated with a wide variety of seafood. In susceptible individuals with underlying liver disease, diabetes or other immunocompromised condition and consuming raw seafood, the organism can cause primary septicaemia with a mortality rate of over 50%. A number of putative virulence factors such as capsule, cytotoxic factors, iron acquisition factors and factors responsible for evading the immune system of the host have been described and multiple factors seem to be involved in causing disease symptoms. The organism can be isolated, identified and enumerated by traditional microbiological methods as well as molecular methods such as polymerase chain reaction (PCR) and real time PCR. Clinical strains can be generally distinguished from most environmental strains by genetic fingerprinting techniques. The organism does not grow at temperatures below 13°C and therefore an important control measure is to cool the seafood to temperatures below this within a few hours of harvest. The organism is sensitive to mild heat, which can be used as a postharvest treatment method to minimise the risk of infection. Relaying shellfish to waters with salinity of >30 ppt has also been found to be an important control measure.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Shah M. Faruque and John J. Mekalanos writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Vibrio cholerae belonging to O1 and O139 seropgroups cause cholera, a life-threatening diarrhoeal disease, which spreads through consumption of water and food contaminated with the pathogen. Other serogroups of V. cholerae are also occasionally associated with mild to moderate enteric infections. Although V. cholerae is a human pathogen, the bacteria are part of the normal aquatic flora in estuarine and brackish waters, and thus are able to persist in the environment outside the human host. The ability of V. cholerae strains to cause disease in humans depends on their virulence gene content, which varies between pathogenic and nonpathogenic strains. Horizontal transfer of critical virulence genes among different V. cholerae strains, as well as microevolution of bacterial genes contribute significantly to the emergence of V. cholerae strains with altered antigenic and pathobiological properties. Seasonal cholera epidemics may selectively enrich genetic variants with unique properties that promote transmission or environmental persistence. The ecosystem comprising V. cholerae, the aquatic environment and the human host offers an understanding of the complex relationship between pathogenesis and the evolution of a typical waterborne bacterial pathogen.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Indrani Karunasagar, Krishna Kumar and G. Balakrish Nair writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Members of the Vibrionaceae family occurring in marine environment are responsible for many of the reported cases of infection worldwide. Among these, Vibrio parahaemolyticus is an important food-borne pathogen transmitted through contaminated seafood. Historically, food poisoning due to V. parahaemolyticus occurred as sporadic cases caused by different serotypes without the clustering of one particular serotype. With the emergence of the pandemic clone belonging to O3:K6 serotype in Kolkata, India, in 1996, the epidemiology of this organism changed abruptly causing large outbreaks and rapid hospitalizations. This new highly virulent strain is now globally disseminated. This review traces the epidemiology of the pandemic strain of V. parahaemolyticus, its emergence, molecular characteristics and clonal dissemination.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Jeanette N. Pham writing in Yersinia: Systems Biology and Control:

Yersinia enterocolitica and Yersinia pseudotuberculosis, the two enteropathogenic species of the genus Yersinia, are poles apart in their natural resistance to β-lactam antibiotics. While Yersinia pseudotuberculosis, as a species, is susceptible to all antibiotics used in the treatment of Gram-negative infections, Y. enterocolitica susceptibility to β-lactam antibiotics varies. Due to the presence of chromosomal β-lactamases, Y. enterocolitica are inherently resistant to ampicillin and cephalothin. The consistent pattern of β-lactam antibiotic susceptibility of each bioserotype and subgroup within a bioserotype is explained by the production or the lack of production of two chromosomally encoded β-lactamases. One is the non inducible broad spectrum enzyme A, a β-lactamase of molecular class A, and the other one is enzyme B, an inducible cephalosporinase of molecular class C. Fluoroquinolones alone or in combination with a third generation cephalosporin are very effective at treating severe infections caused by Y. pseudotuberculosis or Y. enteterocolitica.

Further reading: Yersinia: Systems Biology and Control

from Shah M. Faruque writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Recent studies have provided remarkable insights to our general understanding of the epidemiology, genetics, and ecology of foodborne and waterborne bacterial pathogens. Some of these bacteria have recently been reclassified with updated nomenclature; identification methods have also improved substantially with more extensive use of molecular approaches. The bulk of information generated in different areas of research in these pathogenic organisms have been summarized to provide an over all impression of the progress made. Future directions for research into these organisms have also been discussed with a view to understanding general themes of bacterial pathogens, that cause foodborne and waterborne diseases. In addition, available preventive measures to reduce incidences of disease due to these organisms have been discussed.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Lieneke I. Bouwman and Jos P.M. van Putten writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Campylobacter species are one of the leading causes of bacterial foodborne disease. Campylobacter survives and flourishes in a variety of environmental niches but causes pathology mainly in humans. The pathogenesis of the disease is still poorly understood, and currently only a few Campylobacter virulence determinants have been proposed. Recent studies indicate that Campylobacter displays extensive genome plasticity and a range of environmental adaptation, that likely contribute to the success of the pathogen. In this review, we will discuss the state-of-the-art of the epidemiology, molecular biology, and pathogenesis of Campylobacter infection.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from E. Fidelma Boyd writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

The acquisition of new phenotypes by bacteria is largely driven by horizontal gene transfer (HGT), a process that is ubiquitous among bacteria and universally present among enteric pathogens. The common vectors of HGT in enteric pathogens include phages, pathogenicity islands and plasmids, all genetic elements that can encode virulence factors essential for host colonization and infection. In this review, Salmonella enterica, Escherichia coli, Vibrio cholerae and V. parahaemolyticus are discussed in terms of their virulence genes encoded within mobile and integrative genetic elements and their role in the mechanism of pathogenesis.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from E. Diane Williamson and Petra C.F. Oyston writing in Yersinia: Systems Biology and Control:

In this review we review the progress to date on the development of acellular vaccines to protect against plague; we examine the pathogenicity of the causative organism and how an understanding of this has led to the identification of these new vaccine candidates. The approaches available to demonstrate the potential benefit arising from the use of such candidate vaccines in a human population, where vaccine efficacy in man cannot be determined directly, are discussed. The concept of deriving immune correlates of protective efficacy in authentic animal models of the human disease and then identifying surrogate markers of protection for application to clinical trials is discussed, together with an assessment of the prospects ultimately for eventual vaccine licensure. We explore the potential impact of candidate vaccines on disease occurrence, particularly the likelihood of achieving defined sub-unit vaccines which provide prophylaxis against pneumonic plague, since this represents a new capability against the most hazardous form of the disease.

Further reading: Yersinia: Systems Biology and Control

from Zongmin Du and Ruifu Yang writing in Yersinia: Systems Biology and Control:

Yersinia pestis, the etiological agent of plague, is highly virulent and has acquired an ability to transmit among hosts via fleabite. The high bacterial load in the blood meal from terminal septicemic rodents makes the fleabite transmission route feasible. Molecular mechanisms underlying the high virulence and the unique transmission strategy of Y. pestis have not been clearly elucidated till now. Host transcriptomic responses to Y. pestis in host immune cells or in infected tissues have provided valuable insights into the pathogenic mechanisms adopted by this pathogen. It is now established by detailed histopathology analysis and transcriptional profiling studies on infected animal tissues that the immune response is delayed in both bubonic and pneumonic plague animal models, and neutrophil infiltration and proinflammatory cytokine production occur only after the infection progresses into a systemic septicemic stage. This chapter reviews the recent progress in studies on the host transcriptional responses to Y. pestis infection and prospects the future trends that will lead us to go further in probing into the pathogenicity of this pathogen.

Further reading: Yersinia: Systems Biology and Control

from Shah M. Faruque writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Foodborne and waterborne bacterial pathogens are a major cause of mortality in developing countries and cause significant morbidity in developed nations. Some countries carry a disproportionately heavy burden of these infectious diseases due to inadequate resources to provide sanitation and hygienic facilities, and safe water. The most important bacterial pathogens transmitted through contaminated water and food include species or strains of Salmonellae, Vibrio (e.g., V. cholerae, V. parahemolyticus, V. vulnificus); Shigella (S. dysnteriae, S. flexneri, S. sonnie, S. boydii); Escherichia coli, Yersinia, Staphylococcus and Campylobacter. The pathogenic mechanisms of these bacteria involve synergistic actions of multiple virulence factors produced by the pathogen after infecting the host. Besides carrying sets of virulence genes which are often horizontally transferred between strains, many of these bacteria may also carry precise genetic programs that allow them to adapt and survive in water leading to enhanced transmission or prolonged persistence in the aquatic environment. Understanding the epidemiology, pathogenesis and evolution of these pathogens can contribute significantly to control foodborne and waterborne diseases.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Christian E. Demeure writing in Yersinia: Systems Biology and Control:

The reemergence of plague in the world, the appearance of antibiotic-resistant strains and the risk that genetically modified Y. pestis could serve as a bioterrorist weapon have fostered a renewed interest for vaccination. Currently, researchers mainly follow two distinct vaccinal strategies: one is the development of acellular sub-unit vaccines based on two recombinant targets (F1 and V), and the other is the development of improved live vaccines. Live plague vaccines have been previously largely used in humans and their efficiency against bubonic plague is not disputed. Rather, critics pointed to a limited duration of protection, an unverified protection against pneumonic plague, instability of vaccine seed strain characteristics and the fact that vaccination could induce severe local and systemic reactions. New live vaccine candidates should combine both the known advantages of replicating vaccines: humoral and cell-mediated immune responses, robustness against mutant microorganisms, easiness of mass production and use, limited cost, etc. whilst providing guarantees in terms of security, stability and efficiency against pneumonic plague. They are based not only on attenuated Y. pestis strains, but also on other Yersiniae and live vectors (Salmonella, viruses) expressing Y. pestis antigens. Vaccines against enteropathogenic Yersiniae are also developed.

Further reading: Yersinia: Systems Biology and Control

from Indrani Karunasagar, Patit Paban Bhowmick and Deekshit Vijaya Kumar writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Foodborne and waterborne infections due to Salmonella species are a major concern worldwide. Several virulence genes have been identified in Salmonella and located in clusters called Salmonella Pathogenicity Island (SPI). There are 17 Pathogenicity Islands of Salmonella reported to date. Salmonella possess two distinct type three secretion system (T3SS) encoded by genes present in two different SPI viz. SPI-1 and SPI-2 that play an important role in adhesion, invasion and survival in the host cells. It has been also reported that a variety of Salmonella phenotypes associated with bioluminescence, biofilm formation, conjugation, motility, competence, and antibiotic production, are regulated in response to signaling molecules of quorum-sensing systems. The development of resistance to various antibiotics (particularly in Asian countries) including extended-spectrum cephalosporins worldwide is a cause of concern. Some variants of Salmonella have developed multidrug-resistance as an integral part of the genetic material of the organism, and are therefore likely to retain their drug-resistance genes even when antimicrobial drugs are no longer used. The role of plasmids, bacteriophages, transposons and integrons in the transfer of resistance genes is discussed.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from G. P. Pazhani and T. Ramamurthy writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Shigella species are often associated with diarrhoea/dysentery among children in developing countries of Asia-African regions and also cause foodborne infections in developed countries. During infection, this pathogen secretes a number of effectors via the type III secretion system. Recently, Shigella-infected cases have increased considerably in Asia, but the death rate decreased substantially due to nutritional and clinical interventions. Antimicrobials reduce the episodes of shigellosis. However, multiple antibiotic resistance in shigellae have increased over the years due to improper use of antimicrobials in the treatment of diarrhoea. Several mechanisms such as plasmids and other mobile genetic elements are involved in the transmission of resistance in shigellae. Due to poor efficacy of many of the existing Shigella vaccines, none has been licensed for use in endemic areas. This chapter reviews our current understanding of mechanism involved in the pathogenesis of Shigella, antimicrobial resistance and also its epidemiological importance and clinical management of shigellosis.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Rebecca J. Eisen and Kenneth L. Gage, writing in Yersinia: Systems Biology and Control:

Plague is a severe, primarily flea-borne, rodent-associated zoonosis caused by Yersinia pestis. The majority of human infections are associated with epizootic periods that are defined by rapid transmission in rodent populations. In this chapter, we highlight how modeling has been used to integrate field- and laboratory-derived data to provide insights into identifying when and where epizootics are most likely to occur, how Y. pestis is maintained during periods of apparent quiescence, what triggers a transition to the epizootic phase, and the forces that drive plague epizootics. Understanding these dynamics is critically important for targeting limited public health resources for surveillance, prevention and control, informing wildlife management decisions, and anticipating future disease trends in relation to changing climatic and land use patterns.

Further reading: Yersinia: Systems Biology and Control

from Marc Galimand and Patrice Courvalin writing in Yersinia: Systems Biology and Control:

For many years, Yersinia pestis was considered as uniformly susceptible to antimicrobial agents that are active against Gram-negative bacteria. In 1995, the first two multidrug-resistant strains of Y. pestis were identified in Madagascar and shown to contain self-transmissible plasmids, pIP1202 conferring resistance to all antimicrobial agents recommended for plague treatment and prophylaxis and pIP1203 to a smaller array of drugs. Both plasmids could be transferred by conjugation from the source Y. pestis strains to other Y. pestis and Escherichia coli. Plasmid pIP1203 could be transferred from E. coli to Y. pestis in the midgut of co-infected rat fleas, common vectors of plague. Comparative analysis of the DNA sequence of pIP1202 revealed a shared IncA/C plasmid backbone with multidrug resistant plasmids from Salmonella enterica and Yersinia ruckeri suggesting recent acquisition from a common ancestor. In addition, similar IncA/C backbones were detected in numerous multidrug resistant enterobacterial pathogens isolated from retail meat products in the United States as well as in multidrug resistant plasmids from aquatic environments. This bacterial reservoir of mobile resistance determinants, probably widespread globally, has the potential to disseminate to bacterial pathogens, including Y. pestis, and therefore represents a significant public health concern.

Further reading: Yersinia: Systems Biology and Control

from Kaisar Ali Talukder and Ishrat Jahan Azmi writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

Shigellosis, also known as acute bacillary dysentery, produces inflammatory reactions and ulceration on the intestinal epithelium followed by bloody or mucoid diarrhoea. Shigellosis is caused by any one of the four species or groups of Shigella, namely, S. dysenteriae, S. flexneri, S. boydii, and S. sonnei. At least 54 serotypes or subtypes of Shigella are currently recognized, of which S. dysenteriae has 16 serotypes, S. flexneri has 17 serotypes and subserotypes, S. boydii has 20 and S. sonnei has a single serotype. Shigellosis can occur in sporadic, epidemic and pandemic forms. To develop an effective vaccine it is important to monitor the prevalent serotypes and their changes around the world because immunity to Shigella is serotype specific. The genetic variability between serotypes and emergence of atypical strains accentuates the problems to the development of an effective vaccine. In view of the emergence of new strains with altered characteristics than the ones established globally for many years, there is also a need for revising the nomenclature for the three groups of Shigella: flexneri, boydii and dysenteriae. This chapter discusses the recent serotyping scheme of Shigella with special focus on the emergence of new variants and the necessity to make an updated scheme. Furthermore, the epidemiology, phenotypic and molecular characteristics, population genetics and clinical impact of these variants have been described.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Rembert Pieper and Scott N. Peterson writing in Yersinia: Systems Biology and Control:

In the last few years, proteomic analyses of Y. pestis have been focused on the identification of proteins derived from in vitro cultures that sought to mimic important aspects of in vivo environments and have provided valuable insight into dynamic abundance profiles of numerous proteins and their subcellular localizations, comparing growth conditions relevant in the context of the flea vector/mammalian host life cycle. A proteomic analysis of Y. pestis under iron starvation conditions revealed marked changes in the utilization of pathways related to energy metabolism, stress response and Fe-S cluster assembly. Virulence-associated factors were often found to be highly expressed only under specific environmental conditions. This included T3SS subunits (such as LcrV and YopD), Pla protease, the phospholipase D2 Ymt, the outer membrane (OM) receptor for iron/yersiniabactin, the β-barrel OM adhesion protein Ail and the capsular F1 antigen. Some of these proteins were also major antigens (Caf1, LcrV, YopD and YopE) although the human immune response appears to target a larger variety of Y. pestis proteins than the aforementioned virulence factors.

Further reading: Yersinia: Systems Biology and Control

from Mahbubur Rahman writing in Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology:

The genus Salmonella has three species namely Salmonella enterica, Salmonella bongori and Salmonella subterranean. The type species S. enterica is further classified into six subspecies: enterica (subsp. I), arizonae (subsp. IIIa), diarizonae (subsp. IIIb), houtenae (subsp. IV), indica (subsp. VI), and salamae (subsp. II). Salmonella strains belong to over 50 serogroups based on the O antigen, and to over 2500 serovars (each having a unique combination of somatic O, flagellar H1 and H2 antigens). Most of these serovars (1,531) belong to Salmonella subsp., enterica, and cause more than 99% of the diseases in humans including gastroenteritis and enteric fever (typhoid). Genome sequencing and comparative genomic analysis of 28 S. enterica serovars identified similarity of core regions of the genomes, together with evidence of recombination and rearrangement, genomic degradation, pseudogenes and clonal diversity both within and among the serovars. Genomic comparisons of host-restricted (S. Typhi, S. Paratyphi and S. Gallinarum) and host-adapted (S. Typhimurium and S. Enteridis) S. enterica serovars indicate that genomic degradation is a common evolutionary mechanism for host adaptation and increased pathogenicity of Salmonella. Drug resistances in Salmonella is mainly due to Salmonella genomic island 1 (an integrative mobile element) carrying various antibiotic resistance gene clusters, and to conjugative R plasmids which confer resistance to many antibiotics including extended-spectrum cephalosporins. Continuous genetic re-assortment in Salmonella leading to increased virulence and the emergence of resistance to multiple drugs are of significant public health concern.

Further reading: Foodborne and Waterborne Bacterial Pathogens: Epidemiology, Evolution and Molecular Biology

from Truls Nesbakken writing in Yersinia: Systems Biology and Control:

Yersinia enterocolitica is a zoonotic bacterium that has its main reservoir within the domestic pig population. Accordingly, interventions in the meat chain are essential for protection of consumers against infection with pathogenic Y. enterocolitica. Occurrence of Y. enterocoliticaY. enterocolitica is less frequent in mixed breeding-finishing herds than in fattening herds. Accordingly, purchase of animals from other herds, with an unknown carrier state of Y. enterocolitica, should be avoided. Slaughter hygiene, including enclosure of the anus into a plastic bag after rectum-loosening, and hygienic handling of the head and the plucks during slaughter and dressing is crucial to avoid carcass contamination. Modified atmosphere packaging of meat emphasizes the importance of temperature control during storage at refrigeration temperature. Avoidance of cross-contamination in the kitchen is particularly necessary because Y. enterocolitica is able to propagate at refrigeration temperature. It is important not to drink from raw water supplies that are liable to contamination by animals, and to ensure that drinking water supplies are treated effectively so that Y. enterocolitica are inactivated or eliminated. Some of the preventive measures listed for Y. enterocolitica are also valid for Y. pseudotuberculosis, in particular measures listed regarding vegetables, water, personal and kitchen hygiene and animal contact.

Further reading: Yersinia: Systems Biology and Control

from Jean-Marc Duplantier writing in Yersinia: Systems Biology and Control:

Surveillance focuses primarily on human cases, then on vectors and reservoirs, but it is important not to neglect the bacteria (virulence and resistance to antimicrobial agents). Absence of human cases does not mean that plague does not continue to circulate in rodents. Recent re-emergences show the importance of monitoring historic foci considered as extinct. There is a need for surveillance in shantytowns, mines, refugee camps, etc., even far from known foci. It is essential to improve the declaration of human cases. Specific identification of reservoirs is necessary as their sensitivity or resistance to plague varies. Rodent surveillance should be based mainly by estimating their abundance, flea indexes and Yersinia pestis prevalence. Specific identification of fleas is also essential as the different species have not the same transmission efficiency and the same level of resistance to insecticides. Pest control must focus as a priority on the fleas, but it is imperative to combine rodent and flea control. It is preferable to use anticoagulant rodenticides and dust formulations of the insecticides and to focus their application in burrows or bait boxes. As surveillance is costly, determining indicators easy to collect is essential and modeling of long-time series proved that it is possible.

Further reading: Yersinia: Systems Biology and Control

from Maria Fredriksson-Ahomaa writing in Yersinia: Systems Biology and Control:

Yersiniosis caused by Y. enterocolitica and Y. pseudotuberculosis is primarily acquired via contaminated food or water. However, several difficulties have been associated with isolating pathogenic Yersinia strains from food and environmental samples. The detection rates of enteropathogenic yersiniae in animal reservoirs, foods and in the environment have been shown to be clearly higher by PCR than by culturing. In epidemiological studies, subtyping of Y. enterocolitica and Y. pseudotuberculosis strains is necessary to identify infection sources and transmission routes. A number of different DNA-based methods have been used in molecular typing of enteropathogenic Yersinia spp. Pulsed-field gel electrophoresis (PFGE) is so far the most frequently used typing method for Y. enterocolitica and Y. pseudotuberculosis because it is one of the most powerful tools to subtype these two pathogens. Pigs have shown to be the main reservoir of human pathogenic Y. enterocolitica strains because of the high prevalence of these strains in the tonsils and the high similarity of pig strains to human strains. However, the transmission routes from pigs to humans, especially to young children, are still unknown. Contaminated fresh produce and drinking water have been demonstrated as important sources of human Y. pseudotuberculosis infections but yet the transmission routes have remained unclear.

Further reading: Yersinia: Systems Biology and Control

from B. Joseph Hinnebusch, Florent Sebbane, and Viveka Vadyvaloo writing in Yersinia: Systems Biology and Control:

DNA microarray technology enables a comprehensive, systems biology approach to investigate the microbial gene expression program associated with adaptation to different environments. Monitoring the whole-genome transcriptional response of pathogens within infected tissues has rarely been achieved, but has been possible with Yersinia pestis. The transcriptional profiles of Y. pestis in infective fleas and in the lymph node of rats during bubonic plague were compared to identify important adaptational responses associated with successful colonization of the flea, transmission, and the establishment of disease in the mammal. The differential patterns of gene expression indicate metabolic reprogramming, response to different stresses, and specific induction of virulence and transmission factors as Y. pestis alternates between its two hosts.

Further reading: Yersinia: Systems Biology and Control

from Reinhard Hoffmann, Ekaterina Lenk, and Jürgen Heesemann writing in Yersinia: Systems Biology and Control:

The infection of the host is a complex biological process which prompted infection biologists to pursue reductionist approaches to unravel molecular events of pathogen-host interaction. DNA microarray provides us with a systems biology approach to gain a more holistic picture. Transcriptional profiling of host cell-pathogen interactions results in vast data sets which have to be carefully analyzed by considering the pathogen on a clonal level, the particular cell type (cell lines or primary cells) and the infection model. Here we summarize and discuss the available transcriptional profiling data obtained from Yersinia enterocolitica infection models in relation to the general gene expression program of host cells to microbial infection.

Further reading: Yersinia: Systems Biology and Control

from Ali Navid and Eivind Almaas writing in Yersinia: Systems Biology and Control:

Bubonic plague is one of the deadliest diseases known to man. Unfortunately, despite all of our medical advances, we still do not have a working vaccine against this disease. Worse yet, discovery of anti-microbial resistant strains of Yersinia pestis, the causative agent of plague, could soon render our current therapeutic means ineffective. Unique characteristics of bacterial metabolism constitute one of the primary sets of targets for drug design. Accordingly, metabolism of Y. pestis has been one of the most studied aspects of its physiology.

Further reading: Yersinia: Systems Biology and Control

from Michael Marceau and Michel Simonet writing in Yersinia: Systems Biology and Control:

Yersinia pseudotuberculosis is a septicemic pathogen for rodents and many other animals. However, in certain immunosuppressive conditions, it may also invade the human bloodstream and little is known about the physiological events that take place once the microorganism has entered this compartment. DNA arrays are powerful tools for comparing wide and complex RNA population samples and, therefore, are appropriate to gain insight into the metabolic pathways and virulence factors expressed by the bacterium in this situation. Using such a technology, we compared the overall gene transcription patterns (the transcriptome) of Y. pseudotuberculosis cultured in either human plasma or Luria-Bertani medium. In this chapter, we will try to decipher, and sometimes speculate a little bit, on the physiological events behind the most salient transcriptional regulatory events detected in our experiments, with the intention of making the story as less descriptive as possible. Discordances between our data and those obtained in identical conditions with Y. pestis will be discussed when necessary.

Further reading: Yersinia: Systems Biology and Control