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Introduction: A COVID-19 outbreak occurred at the end of October 2021 among pilgrims returning from Medjugorje (Bosnia and Herzegovina)., Methodology: Whole genome sequencing (WGS) of SARS-CoV-2, epidemiological data, and phylogenetic analysis were used to reconstruct outbreak dynamics., Results: The results suggest that only in one case, associated with the SARS-CoV-2 sub-lineage AY.9.2, it is possible to trace back the place of contagion to Medjugorje, while the other cases were likely to be acquired in the country of origin., Conclusions: The combined use of phylogenetic data derived from WGS, and epidemiological data allowed us to study epidemic dynamics and to formulate a possible hypothesis on the place of exposure to SARS-CoV-2. The identification of different sub-lineages of the SARS-CoV-2 Delta variant also suggested that different chains of transmission contributed to the outbreak., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2024 Alessandra Lo Presti, Salvatore Rubino, Gabriele Ibba, Luigina Ambrosio, Angela Di Martino, Federica Ferraro, Alessia Rapiti, Francesco Maraglino, Emanuela Maria Frisicale, Giovanni Rezza, Flavia Angioj, Sergio Uzzau, Maria Luciana Contini, Stefania Manca, Ferdinando Coghe, Germano Orrù, Anna Teresa Palamara, Paola Stefanelli, the AOUSS COVID team.)

Mutations in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome continue to threaten the global landscape of the coronavirus disease 2019 (COVID-19) pandemic. The Omicron variant (B.1.1.529) rapidly displaced previous 'variants of concern' (VoC) in 2021 due to its high rate of transmissibility and multitude of mutations. This global influx of infections saturated healthcare systems, overwhelmed testing capacity and case reporting, and increased the COVID-19 death toll. Global health leaders are now being faced with the most transmissible COVID-19 variants yet, the Omicron sublineages BA.4 and BA.5, which contain additional spike protein (S) mutations from previous Omicron and VoC serotypes. With universally observed antibody waning, increasing vaccine-variant mismatch, and resuming international travel, the stage is set for unprecedented levels of breakthrough infections and superspreading events. In this paper, we raise awareness to these novel variants and provide context for the high likelihood of an upcoming wave of infection capable of inflicting significant disease burden on a global scale., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2022 Benjamin Hewins, Christopher Richardson, Salvatore Rubino, Alyson Kelvin, Ali Toloue Ostadgavahi, David J Kelvin.)

Introduction: The novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), etiological agent of coronavirus disease 2019 (COVID-19) was first reported in China in December 2019 and spread worldwide. As of March 6th, 2021, there have been 116,670,105 million confirmed cases globally including 2,592,085 deaths. COVID-19 cases have been reported in 219 countries and territories, creating global panic. Mozambique has witnessed the evolution of COVID-19 epidemic associated with the weakness of health system, mostly in terms of laboratory diagnosis capacity, concerns on compliance to effective public health measures including physical distancing, use of masks in crowded indoor areas, hand hygiene, isolation and quarantine of people., Methodology: The data included in this study were collected from published articles regarding COVID-19 imported cases and severity in Africa, especially in Mozambique. Additionally, official documents of COVID-19 epidemiology from Minister of Health and National Institute of Health of Mozambique from 22nd of March 2020 to 1st of August 2020 were included., Results: The SARS-CoV-2 strains imported mainly from South Africa and European countries might have been playing an important role on COVID-19 epidemic evolution in Mozambique., Conclusions: These circulating strains in the country, might be similar enough to the strains found in other countries, yet the genomic characterization is needed particularly during the phase of borders reopening through understanding the source of infections and guiding the implementation of containment and mitigation measures in the country., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2021 José Sumbana, Alfeu Passanduca, Salvatore Rubino.)

Introduction: To analyze the virus spread among Sassari Hospital staff in the first Covid-19 wave and the impact of the Swab Team, a multidisciplinary task force entitled of nasopharyngeal swab collection and testing., Methodology: Nasopharyngeal swabs from HCWs between March 6 and May 28 2020 are evaluated., Results: 4919 SARS-CoV-2 tests were performed on 3521 operators. Nurses and doctors are the categories at highest risk. After the Swab Team institution, the average number of swabs raised from 47/day to 86/day (p = 0.007). Positive samples decreased from 18.6% to 1.7% (p < 0.0001)., Conclusions: The Swab Team is effective in increasing the cases tested and in reducing the reporting time. Procedure standardization reduces the risk for all the subjects involved (no transmission among swab team members, nor during the sample collection)., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2021 Francesco Bussu, Davide Rizzo, Laura Saderi, Antonio Piras, Laura Maria De Luca, Giacomo De Riu, Luigi Angelo Vaira, Antonello Serra, Paola Altrudo, Domenico Delogu, Ignazio Dettori, Francesco Giuseppe Riu, Flavia Angioj, Laura Firino, Rosalba Govoni, Gabriele Ibba, Vincenzo Lai, Erica Mura, Bianca Paglietti, Claudia Piu, Anna Puggioni, Elena Rimini, Giulia Rocca, Caterina Serra, Sergio Uzzau, Salvatore Rubino, Giovanni Sotgiu.)

The spread of new SARS-CoV-2 variants represents a serious threat worldwide, thus rapid and cost-effective methods are required for their identification. Since November 2020, the TaqPath COVID-19 assay (Thermo Fisher Scientific) has been used to identify viral strains of the new lineage B.1.1.7, since it fails to detect the S-gene with the ∆69/70 deletion. Here, we proposed S-gene mutations screening with the Allplex SARS-CoV-2 assay (Seegene), another widely used RT-PCR test that targets Sarbecovirus E, SARS-CoV-2 N, and RdRp/S genes. Accordingly, we evaluated the S gene amplification curve pattern compared to those of the other genes. Exploiting an Allplex assay-generated dataset, we screened 663 RT-PCR digital records, including all SARS-CoV-2 respiratory samples tested in our laboratory with the Allplex assay between January 1st and February 25th, 2021. This approach enabled us to detect 64 samples with peculiar non-sigmoidal amplification curves. Sequencing a selected group of 4 RNA viral genomes demonstrated that those curves were associated with B.1.1.7 variant strains. Our results strongly suggest that B.1.1.7 variant spread has begun in this area at least since January and imply the potential of these analytical methods to track and characterize the spread of B.1.1.7 strains in those areas where Allplex SARS-CoV-2 datasets have been previously recorded., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2021 Gabriele Ibba, Rosangela Sau, Flavia Angioj, Marcello Abbondio, Salvatore Rubino, Sergio Uzzau.)

Mozambique is located on the East Coast of Africa and was one of the last countries affected by COVID-19. The first case was reported on 22 March 2020 and since then the cases have increased gradually as they have in other countries worldwide. Environmental and population characteristics have been analyzed worldwide to understand their possible association with COVID-19. This article seeks to highlight the evolution and the possible contribution of risk factors for COVID-19 severity according to the available data in Mozambique. The available data highlight that COVID-19 severity can be magnified mainly by hypertension, obesity, cancer, asthma, HIV/SIDA and malnutrition conditions, and buffered by age (youthful population). Due to COVID-19 epidemic evolution, particularly in Cabo Delgado, there is the need to increase laboratory diagnosis capacity and monitor compliance of preventive measures. Particular attention should be given to Cabo Delgado, including its isolation from other provinces, to overcome local transmission and the spread of SARS-CoV-2., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2020 Jose Sumbana, Jahit Sacarlal, Salvatore Rubino.)

COVID-19 case fatalities surged during the month of March 2020 in Italy, reaching over 10,000 by 28 March 2020. This number exceeds the number of fatalities in China (3,301) recorded from January to March, even though the number of diagnosed cases was similar (85,000 Italy vs. 80,000 China). Case Fatality Rates (CFR) could be somewhat unreliable because the estimation of total case numbers is limited by several factors, including insufficient testing and limitations in test kits and materials, such as NP swabs and PPE for testers. Sero prevalence of SARS-CoV-2 antibodies may help in more accurate estimations of the total number of cases. Nevertheless, the disparity in the differences in the total number of fatalities between Italy and China suggests investigation into several factors, such as demographics, sociological interactions, availability of medical equipment (ICU beds and PPE), variants in immune proteins (e.g., HLA, IFNs), past immunity to related CoVs, and mutations in SARS-CoV-2, could impact survival of severe COVID-19 illness survival and the number of case fatalities., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2020 Salvatore Rubino, Nikki Kelvin, Jesús F Bermejo-Martin, David Kelvin.)

18 years ago, in 2002, the world was astonished by the appearance of Severe Acute Respiratory Syndrome (SARS), supported by a zoonotic coronavirus, called SARS-CoV, from the Guangdong Province of southern China. After about 10 years, in 2012, another similar coronavirus triggered the Middle East Respiratory Syndrome (MERS-CoV) in Saudi Arabia. Both caused severe pneumonia killing 774 and 858 people with 8700 cases of confirmed infection for the former, and 2494 for the latter, causing significant economic losses. 8 years later, despite the MERS outbreak remaining in certain parts of the world, at the end of 2019, a new zoonotic coronavirus (SARS-CoV-2) and responsible of coronavirus Disease (COVID-19), arose from Wuhan, Hubei Province, China. It spread rapidly and to date has killed 3,242 persons with more than 81,000 cases of infection in China and causing over 126,000 global cases and 5,414 deaths in 166 other countries around the world, especially Italy. SARS-CoV-2 would seem to have come from a bat, but the intermediate reservoir continues to be unknown. Nonetheless, as for SARS-CoV and MERS CoV, the Spillover effect linked to animal-human promiscuity, human activities including deforestation, illegal bush-trafficking and bushmeat, cannot be excluded. Recently, however, evidence of inter-human only transmission of SARS-CoV-2 has been accumulated and thus, the outbreak seems to be spreading by human-to-human transmission throughout a large part of the world. Herein we will provide with an update on the main features of COVID-19 and suggest possible solutions how to halt the expansion of this novel pandemic., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2020 Carlo Contini, Mariachiara Di Nuzzo, Nicole Barp, Aurora Bonazza, Roberto De Giorgio, Mauro Tognon, Salvatore Rubino.)

As of 28 February 2020, Italy had 888 cases of SARS-CoV-2 infections, with most cases in Northern Italy in the Lombardia and Veneto regions. Travel-related cases were the main source of COVID-19 cases during the early stages of the current epidemic in Italy. The month of February, however, has been dominated by two large clusters of outbreaks in Northern Italy, south of Milan, with mainly local transmission the source of infections. Contact tracing has failed to identify patient zero in one of the outbreaks. As of 28 February 2020, twenty-one cases of COVID-19 have died. Comparison between case fatality rates in China and Italy are identical at 2.3. Additionally, deaths are similar in both countries with fatalities in mostly the elderly with known comorbidities. It will be important to develop point-of-care devices to aid clinicians in stratifying elderly patients as early as possible to determine the potential level of care they will require to improve their chances of survival from COVID-19 disease., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2020 Rossella Porcheddu, Caterina Serra, David Kelvin, Nikki Kelvin, Salvatore Rubino.)

On 31 December 2019 the Wuhan Health Commission reported a cluster of atypical pneumonia cases that was linked to a wet market in the city of Wuhan, China. The first patients began experiencing symptoms of illness in mid-December 2019. Clinical isolates were found to contain a novel coronavirus with similarity to bat coronaviruses. As of 28 January 2020, there are in excess of 4,500 laboratory-confirmed cases, with > 100 known deaths. As with the SARS-CoV, infections in children appear to be rare. Travel-related cases have been confirmed in multiple countries and regions outside mainland China including Germany, France, Thailand, Japan, South Korea, Vietnam, Canada, and the United States, as well as Hong Kong and Taiwan. Domestically in China, the virus has also been noted in several cities and provinces with cases in all but one provinence. While zoonotic transmission appears to be the original source of infections, the most alarming development is that human-to-human transmission is now prevelant. Of particular concern is that many healthcare workers have been infected in the current epidemic. There are several critical clinical questions that need to be resolved, including how efficient is human-to-human transmission? What is the animal reservoir? Is there an intermediate animal reservoir? Do the vaccines generated to the SARS-CoV or MERS-CoV or their proteins offer protection against 2019-nCoV? We offer a research perspective on the next steps for the generation of vaccines. We also present data on the use of in silico docking in gaining insight into 2019-nCoV Spike-receptor binding to aid in therapeutic development. Diagnostic PCR protocols can be found at https://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2020 Robyn Ralph, Jocelyn Lew, Tiansheng Zeng, Magie Francis, Bei Xue, Melissa Roux, Ali Toloue Ostadgavahi, Salvatore Rubino, Mohammed N Al-Ahdal, David J Kelvin, Christopher D Richardson, Jason Kindrachuk, Darryl Falzarano, Alyson Anne Kelvin.)

Competing Interests: No Conflict of Interest is declared

Background: Cardiac device-related endocarditis has emerged as a serious complication in the era of advanced medical technology. Pacemaker related infections are rare and life-threatening with incidence from 0.06% to 7% and high mortality rate (30-35%). Diagnosis is hard, frequently delayed and could be even missed due to poor clinical findings. The average delay in diagnosis is 5.5 month. We report a case of the late-onset of pacemaker lead endocarditis caused by S. epidermidis successfully treated with open heart surgery., Case Report: Patient with persistent high fever for 11 month and suspicion for infective endocarditis was admitted in Cardiovascular Institute. No clinical signs of endocarditis were observed. TTE revealed large vegetation 30 × 17 mm attached to the atrial electrodes with high embolic potential. This finding was verified by transesophageal echocardiography (TEE), although CT scan did not reveal vegetation. Blood cultures were negative. A sternotomy with cardiopulmonary bypass was performed and electrodes were extracted with large vegetation. Intraoperative finding revealed large thrombus with vegetation around pacemaker leads. Cultures of the electrodes and vegetation revealed Staphylococcus epidermidis. Surgery was followed up with antibiotic treatment for 6 weeks. He has been followed up for the next 2 years, and without complications., Conclusion: The absence of criteria for endocarditis and negative blood cultures should not keep the physician from ruling out lead endocarditis. This complication carries high risk of mortality if left untreated., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2019 Aleksandra Barac, Darko Boljevic, Petar Vukovic, Dejan Kojic, Milovan Bojic, Jelena Micic, Salvatore Rubino, Bianca Paglietti, Aleksandra Nikolic.)

Introduction: In the Europe, the number of tick-borne encephalitis (TBE) has been increased in the last decade, and the number of endemic areas has been also increased and is still growing. In the present case series, we present clinical and socio-epidemiological data of patients with TBE hospitalized in the period of TBE virus epidemic in Serbia., Methodology: A case series was conducted in Serbia in 2017. Patients with confirmed TBE were included in the study. Biochemical and serological analysis of blood and CSF, as well as radiological imaging (CT and MRI) were done., Results: In total, 10 patients with TBE were included in the study. M:F ratio was 1.5:1, while average age was 45.1 years. Half of the patients had severe clinical picture. Endocranial CT scan and MRI did not reveal any abnormality, except in the patient with the most severe CNS infection (meningoencephalomyelitis). Mean value of sedimentation and CRP was slightly elevated (29.6 mm/1hours and 20.1 mg/L, respectively) in 80% of the patients, although elevation was almost negligible. The average number of leucocytes in the cerebrospinal fluid (CSF) was 171×106/L, the mean value of the CSF protein was 1.1g/L. There were no fatal outcomes., Conclusion: Since other CNS infections have similar clinical picture and CSF finding as TBE, serological analysis for TBE should be included in routine diagnostic practice., Competing Interests: No Conflict of Interest is declared, (Copyright (c) 2019 Jasmina Poluga, Aleksandra Barac, Natasa Katanic, Salvatore Rubino, Branko Milosevic, Aleksandar Urosevic, Nikola Mitrovic, Ivana Kelic, Jelena Micic, Goran Stevanovic.)

Competing Interests: No Conflict of Interest is declared

Non-typhoidal Salmonella (NTS) represents a leading cause of food-borne disease worldwide. It is a global public health concern: more than 94 million cases and 115,000 deaths are reported every year, with a disproportionate impact in developing countries. The prevalence of multi-drug-resistant (MDR) Salmonella strains is another major health concern which affects antimicrobial treatment, as many studies report that infections caused by MDR strains are more severe than those caused by susceptible strains. In Algeria, NTS represent one of the primary causes of salmonellosis in both humans and food animal production, especially poultry. Epidemiological surveillance systems and monitoring programs for Salmonella infections are essential requirements to provide data useful for the effective detection and control of Salmonella outbreaks. The present review will supply a perspective on NTS infection, pathogenesis and antimicrobial resistance with a focus on the epidemiology of salmonellosis in Algeria.

Since the onset of the worst epidemic of Ebola virus disease in December 2013, 28,637 cases were reported as confirmed, probable, or suspected. Since the week of 3 January 2016, no more cases have been reported. The total number of deaths have amounted to 11,315 (39.5%). In developed countries, seven cases have been diagnosed: four in the United States, one in Spain, one in the United Kingdom, and one in Italy. On 20 July 2015, Italy was declared Ebola-free. On 9 May 2015, an Italian health worker came back to Italy after a long stay in Sierra Leone working for a non-governmental organization. Forty-eight hours after his arrival, he noticed headache, weakness, muscle pains, and slight fever. The following day, he was safely transported to the Infectious Diseases Unit of University Hospital of Sassari. The patient was hospitalized for 19 hours until an Italian Air Force medical division transferred him to Rome, to the Lazzaro Spallanzani Institute. Nineteen people who had contacts with the patient were monitored daily for 21 days by the Public Health Office of Sassari and none presented any symptoms. So far, neither vaccine nor treatment is available to be proposed on an international scale. Ebola is considered a re-emerging infectious disease which, unlike in the past, has been a worldwide emergency. This case study aimed to establish a discussion about the operative and logistic difficulties to be faced and about the discrepancy arising when protocols clash with the reality of facts.

Zika virus (ZIKV) is an emerging arbovirus of the Flaviviridae family and is related to dengue, Chikungunya, West Nile, yellow fever, and Japanese encephalitis viruses. ZIKV was first discovered in Uganda in 1947. Different species of mosquito from the Aedes genus, mainly A. aegypti and A. albopictus are the vectors responsible for ZIKV infection in humans. It is also reported that ZIKV is transmitted congenitally, sexually, and through blood donation. Until recently, ZIKV outbreaks were sporadic and self-limiting. The first large epidemic was reported from Yap Island in 2007 followed by an outbreak of Zika fever in French Polynesia in 2013. Brazil is the epicenter of the current ZIKV epidemic which is rapidly spreading across the Americas. ZIKV infection remained relatively less studied in view of its low case numbers, and low clinical impact relative to other arboviruses. However, all this is set to change with its rapid spread in the Western hemisphere and suspected complications particularly microcephaly in newborn babies with ZIKV infected mothers. ZIKV is expected to substantially add to both short-term and long-term economic burden of the effected countries. Due to the large number of people travelling across the borders and some reported cases of transmission of ZIKV via contaminated blood, screening and identification of asymptomatic infected individuals are important.

We have developed a mobile App called ZIKATracker (zikatracker.net) to voluntarily be used to report ZIKV cases on a public or private level. As the Zika virus (ZIKV) infection zones are rapidly expanding across South, Central, and North America, and reports have emerged linking ZIKV infection with developmental defects and neurological sequelae, reporting the movement and sequelae of ZIKV is essential. ZIKATracker is a multi-lingual App (English, French, Spanish, and Portuguese) freely available to anyone worldwide wishing to report a suspected or confirmed case of Zika virus and related symptoms. Knowledge gained from the use of this App will help direct the implementation of mosquito control measures in needed areas, bring aid to those affected by the Zika virus, and understand the movement and sequelae of ZIKV as it spreads through communities and across continents.

Increasing antimicrobial resistance to key antibiotics in Helicobacter pylori has become a main cause of treatment failures in many countries, including Vietnam. For this reason it is advisable to perform antimicrobial sensitivity tests to provide more focused regimens for H. pylori eradication. However, this approach is generally unavailable for H. pylori in Vietnam and the selection of treatment regimens is mainly based on the trend of antibiotic use in the population, resistance development in the region, and history of H. pylori eradication of patients. The aim of this review is to examine the current situation of antimicrobial resistance in Vietnam and suggest management strategies for treatment selection.

Introduction: The objective of this study was to evaluate the involvement of the ompR gene in the acid adaptation and thermal resistance of S. Enteritidis SE86, responsible agent of more than 95 % of investigated food-borne diseases, throughout the last decade in Southern Brazil. In this study, we constructed a mutant strain of S. Enteritidis SE86 (ΔompR) that was attenuated by a knockout technique. The OmpR protein expression was determined in a tagged (3XFLAG) strain of S. Enteritidis SE86., Methodology: The mutant strains were cultivated separately in nutrient broth and nutrient broth supplemented with 1% glucose (NBG) to induce acid adapted cells. The organisms were exposed to different temperature such as 37 ºC, 52 ºC, and 60ºC. The survival of the SE86 wild type (WT) and attenuated strain was determined by bacterial count, and the tagged protein (ompR::3XFLAG cat::FLAG) was detected by SDS-PAGE and immunoblotting with anti-FLAG antibodies., Results: Results showed that when exposed at 52ºC, the acid-adapted SE86 WT cells were completely inactivated after 300 minutes; however, non-adapted cells (WT and ΔompR) and acid-adapted ΔompR demonstrated higher thermal sensitivity, since they were completely inactivated in 240 minutes. At 60ºC, the acid-adapted SE86 ΔompR also demonstrated higher sensitivity that SE86 WT, being totally inactivated after 15 minutes, while the WT cells were inactivated in 20 minutes., Conclusion: The acid adapted cells showed increased expression of OmpR when exposed to 52 ºC and 60ºC, this confirmed the requirement of acid adaptation  for S. Enteritidis SE86 to resist elevated temperatures.

Introduction: HIV infection is considered a risk factor for severe outcomes of influenza A(H1N1)v infection. However, data on immune response against influenza A(H1N1)v virus in HIV-infected patients are lacking., Methodology: Data from seven HIV-positive and 14 HIV-negative patients infected with A(H1N1)v and from 23 HIV-positive and six HIV-negative asymptomatic controls were analyzed to evaluate the clinical picture, A(H1N1)v viral shedding, and the immune response against the virus., Results: Patients displayed mainly upper respiratory tract diseases (57.1%), while pneumonia was diagnosed only in HIV-negative patients (23.8% of subjects, of which 4.8% required intensive care unit admission). At day seven, 29% of HIV-infected patients were still positive for A(H1N1)v by RT-PCR on nasopharyngeal swabs. Interestingly, a persistence of CXCL10 secretion at high level and lower IL-6 levels was observed in HIV-positive subjects. The geometric mean haemagglutination inhibition titer (HI-GMT) and anti-influenza IgM levels were lower in HIV-positive individuals while anti-influenza IgG levels remained similar in the two groups., Conclusions: The immune impairment due to HIV infection could affect A(H1N1)v clearance and could lead to a lower antibody response and a persistent secretion of CXCL10 at high levels. However, the lower IL-6 secretion and treatment with highly active antiretroviral therapy (HAART) could result in a milder clinical picture.

Introduction: The etiological association of Helicobacter pylori with gastric ulcer (GU), gastric cancer (GC), and duodenal ulcer (DU) is well-known. Understanding the epidemiology of H. pylori facilitates the estimation of disease burden in a certain population. This study presents the diversity of H. pylori genotypes and their association with different clinical outcomes among dyspeptic patients in Pakistan over a period of four years., Methodology: Gastric biopsy samples from a total of 450 dyspeptic individualswere subjected to PCR, genotypingand histology., Results: A total of 201 (45%) cases were found positive for H. pylori. The detection rate was high in GU (91%), DU (86%) and GC (83%) cases compared with those cases who had intact gastric mucosa (18%). Histology revealed the presence of infection in 68% of cases of mild/chronic nonspecific gastritis with others belonging to the GU sequel. cagA gene carriage was observed in 104 (51%) cases or mostly from DU, GU and GC groups, of which 97 were Western type strains while 3 were East-Asian type strains that are rarely observed in South Asia. vacA allelic variant s1am1 was most commonly observed, followed by s1am2, and s1bm1, with direct correlation in diseased cases (gastritis, GU, DU and GC). Prevalent genotypic combinations were s1am1/cagA- in gastritis and s1am1/cagA+ in DU, GU, and GC., Conclusions: Our study indicates the predominant circulation of Western type cagA and vacAs1am1 type H. pylori strains in Pakistan.

The publication of studies using next generation sequencing to analyse large numbers of bacterial isolates from global epidemics is transforming microbiology, epidemiology and public health. The emergence of multidrug resistant Salmonella Typhimurium ST313 is one example. While the epidemiology in Africa appears to be human-to-human spread and the association with invasive disease almost absolute, more needs to be done to exclude the possibility of animal reservoirs and to transfer the ability to track all Salmonella infections to the laboratories in the front line. In this mini-review we summarise what is currently known about non-typhoidal Salmonella in sub-Saharan Africa and discuss some of the issues which remain.

Introduction: Wild migratory birds are global distributors of pathogens. Sardinia, Italy, is the second largest Island in the Mediterranean and is a land bridge between Europe and Africa., Methodology: We designed a surveillance protocol to investigate wild migratory birds for presence, frequency, and type of avian influenza viruses. We collected over 4,000 avian samples and compared three sampling methods, fecal, cloacal, and tracheal, to determine the most productive for virus identification. To determine frequency of infection, RNA was extracted and RT-PCRs for avian influenza virus genes were run. Positive samples were cultivated for live virus, sub typed and sequenced., Results: Forty-four samples were positive for influenza nucleoprotein gene. We identified two previously unidentified H3 subtype strains and found cloacae to have the highest rate of virus identification and fecal sampling to provide quality RNA and repeatable results for determination of virus presence., Conclusion: Our investigation provides information on the frequency of Mediterranean avian influenza viruses, and validates the initiation of an avian influenza surveillance protocol.  Taken together with global avian influenza findings, these results give insight into infectious disease distributions which is important for viral pandemic monitoring and design of preventative measures.

Although viruses that belong to the coronavirus family are known since the 1930s, they only gained public health attention when they were discovered to be the causative agent of the severe acute respiratory syndrome (SARS) outbreak in China in 2002-2003. On 22 September 2012, the Ministry of Health (MOH) in Saudi Arabia announced the detection of what was described as a "rare pattern" of coronavirus respiratory infection in three individuals, two Saudi citizens and one person from the Gulf Region. Neither Saudi citizen survived the infection. Molecular analysis of the isolates showed that the virus belongs to the genus beta-coronavirus. It is not known if the new isolates are circulating in the population or has recently diverged. The emergence of these novel isolates that resulted in fatal human infection ascertains that health authorities all over the world must be vigilant for the possibility of new global pandemics due to novel viral infection.

Introduction: We developed and evaluated a multiplex-PCR method for rapid detection of the most common Salmonella serovars in both developed and developing countries. Additionally, the stability of the premixed reagents at high room temperature was studied., Methodology: Fifty-two Salmonella strains belonging to the collections of the University of Sassari, Italy, and to the University of the Basque Country, Spain, and a collection of a hundred blinded strains, were used to evaluate the multiplex-PCR. Primers targeting genes STY1599 and fliC were selected, and the method was evaluated both intra and inter-laboratories., Results: The inter-laboratory reproducibility was 95.92%, with a kappa index of 0.757 that indicates a substantial agreement and a high accuracy (80.81%). The sensitivity, specificity, accuracy and precision indexes for the Salmonella genus and S. Typhi targets were maximum, although the targets for Paratyphi A, Typhimurium and Enteritidis showed less accuracy. During a seven-week period, hot-start multiplex-PCR runs were performed with reagents mixed with wax to test their stability at 30ºC, and no significant variation in the patterns of amplification was observed., Conclusions: An improved multiplex-PCR for rapid detection of the most common serovars of Salmonella operable in both developed and developing countries has been designed and tested intra and inter-laboratories. Following a careful optimization protocol will not only allow the confirmation of any suspicious colony by the amplification of the Salmonella genus target, but also the preliminary adscription to the prevalent serovars. Premixed reagents with wax facilitate the throughput and stability of reagents at high room temperatures.

At the beginning of May an outbreak of bloody diarrhoea and haemolytic uraemic syndrome (HUS) began in Germany. During the succeeding months following the initial outbreak in Germany, thousands of infections occurred resulting in 877 cases of haemolytic uraemic syndrome (HUS) with 32 deaths and 3,043 cases of enterohaemorrhagic Escherichia coli (EHEC) with 16 deaths.

Introduction: Hepatitis C virus (HCV), which is a major cause of liver diseases worldwide, undergoes genetic variation during the course of infection. The aim of this study was to examine sequence variations within the HVR1 region of HCV genotype 4 in infected Saudi patients treated with a combination therapy of interferon-α and ribavirin., Methodology: cDNA of the HVR1 region of HVC-4 from one responder and one non-responder patients was generated, cloned and sequenced. Ten clones were randomly selected and analyzed for changes in nucleotide and amino acid sequences before the start of treatment, and subsequently three and six months after the start of the therapy course., Results: Based on nucleotide and amino acid sequence variations, the HVR1 region is highly sequence variable. In both the responder and the non-responder patients, amino acid sequence variations were observed and a clear distinction between patients was evident. The amino acid changes after the treatment course were different in the responder compared to the non-responder subject. Five amino acids (residues 364 to 367, 381 and 409) were unique in the non-responder patient., Conclusion: Considerable amino acid variations were observed in the HVR1 region in both responder and non-responder patients. These findings could have implications for the development of an HCV vaccine as well as treatment protocols for HCV infections.

Introduction: Salmonella pathogenicity islands (SPIs) are regions scattered along the bacterial chromosome, with an acknowledged pivotal role during gastrointestinal and systemic infection. The distribution of SPIs has been investigated in reference strains. However, there is a lack of studies on their presence and/or assortment within the genomes of Salmonella enterica (S. enterica) serovars that circulate in different geographical regions. Therefore, in this study, we aimed to determine the presence of genes of the pathogenicity islands 1 to 5 (SPI-1 to 5), in Salmonella clinical isolates from Colombian patients with systemic and enteric outcomes., Methodology: A total of 125 strains of S. enterica belonging to different serovars were isolated from various clinical samples. Strains were identified and screened for the presence of various genes located in pathogenicity islands. The genes tested were selected according to the attributed pathogenic function and detected by PCR for the SPI-1 hilA and invA; for SPI-2 spiC and ttrC; for SPI-3 misL and mgtC; for SPI-4 orfL and SPI-4R; and for SPI-5 pipD and sopB., Results: Salmonella pathogenicity islands 1 to 5 were detected in isolates from patients with systemic and gastrointestinal infection. All the systemic isolates possessed all the genes tested; in contrast, 16 isolates from stool samples lacked one or more sequences encoded by the SPI-3 and SPI-4 (p < 0.000001)., Conclusions: These results describe the heterogeneous distribution of SPIs-encoded sequences within the genomes of Colombian clinical isolates, and reveal important differences among systemic and stool sample isolates.

Typhoid fever is endemic in the Mediterranean North African countries (Morocco, Algeria, Tunisia, Libya, and Egypt) with an estimated incidence of 10-100 cases per 100,000 persons. Outbreaks caused by Salmonella enterica serovar Typhi are common and mainly due to the consumption of untreated or sewage-contaminated water. Salmonella enterica Paratyphi B is more commonly involved in nosocomial cases of enteric fever in North Africa than expected and leads to high mortality rates among infants with congenital anomalies. Prevalence among travellers returning from this region is low, with an estimate of less than one per 100,000. Although multidrug resistant strains of Salmonella Typhi and Paratyphi are prevalent in this region, the re-emergence of chloramphenicol- and ampicillin-susceptible strains has been observed. In order to better understand the epidemiology of enteric fever in the Mediterranean North African region, population-based studies are needed. These will assist the health authorities in the region in preventing and controlling this important disease.

Background: Salmonellosis remains one of the most frequent food-borne diseases worldwide, especially in developing countries. The emergence of antimicrobial resistance in Salmonella isolates from food can potentially compromise the treatment of these infections. This investigation was conducted for the first time in Morocco both to detect the occurrence of Salmonella in foods as well as to determine the antibiotic resistance profile of the Salmonella isolates., Methodology: In total, 11,516 food samples collected from 2002 to 2005 were investigated. Isolated Salmonella were characterized by serotyping and susceptibilities were determined for 15 antimicrobial drugs using the disc diffusion assay., Results: The overall percentage of Salmonella prevalence (n=105) was 0.91% with rates of 71% for slaughterhouses and 9% for seafood. Sixteen different serotypes were identified among 104 Salmonella enterica isolates including serotypes Infantis (n=25), Bredeney (n=13), Blokley (n=11), Typhimurium (n=9), Mbandaka (n=8), Branderup II (n=7), and Kiambu (n=6); 1 isolate of Salmonella enterica belonged to subspecies II salamae. Twenty-nine percent of isolates (n=30/105) were resistant to at least one antimicrobial. Resistance to tetracycline was the most common finding (21%), followed by resistance to ampicillin (13%), amoxicillin+clavulanic acid (9%), streptomycin (7%), chloramphenicol (4%) and nalidixic acid (3,8%). None of the isolates was resistant to 3rd-cephalosporin and fluoroquinolones (i.e. ciprofloxacin). Multidrug resistance (MDR) was seen in 9.5% of the isolates, mainly in S.. Typhimurium DT104 with R-type ACSSuT and S. Hadar., Conclusions: Despite a low frequency of Salmonella isolation, S. Typhimurium DT104 was identified in the first step of the food chain. The study points out the need control antibiotic resistance in Salmonella isolated from food in Morocco to avoid the spread of MDR.

Background: Enteric fever caused by Salmonella enterica serovar Typhi has not been adequately explored in Jordan., Methodology: In this study we investigated antibiotic resistance patterns and resistance determinants coupled with fingerprint methods of forty-eight isolates of S. Typhi obtained from 113 patients with suspected enteric fever admitted at six governmental hospitals in different directorates in Jordan. Twenty-four isolates were from an outbreak of typhoid fever that occurred between October 2004 and January 2005, and another twenty-four were from sporadic cases from 2005., Results: All isolates of S. Typhi were resistant to streptomycin. A multidrug resistant (MDR) pattern of ampicillin, chloramphenicol, co-trimoxazole with tetracycline and streptomycin (R-type ACCoTS) was found in 58% of the epidemic strains causing the outbreak and in 98% of the strains from sporadic cases. MDR isolates harbored a single IncHI1 plasmid containing a class 1 integron (dfrA7). Plasmid conjugation studies demonstrated a genetic transfer of resistance (ACCoT). S. Typhi isolates were all sensitive to fluoroquinolones and cefotaxime, the alternative drugs recommended for treatment of typhoid fever. The genomic analysis using PFGE showed: a) the outbreak was caused by an introduced circulating clone with/without an MDR plasmid, and b) isolates from the sporadic cases from 2005 are the same MDR clone that persisted and spread in the country., Conclusion: The emergence of MDR S. Typhi strains is a majorn important public health issue in Jordan. This study should guide selection of effective antibiotic therapy for the treatment of typhoid and monitoring of the spread of MDR of S. Typhi.