Surveillance In Italy Research Articles

ArboItaly: Leveraging open data for enhanced arbovirus surveillance in Italy.

ArboItaly: Leveraging open data for enhanced arbovirus surveillance in Italy.

Web search volume as a near-real-time complementary surveillance tool of tick-borne encephalitis (TBE) in Italy

The Internet is an important gateway for accessing health-related information, and data generated through web queries have been increasingly used as a complementary source for monitoring and forecasting of infectious diseases and they may partially address the issue of underreporting. In this study, we assessed whether tick-borne encephalitis (TBE)-related Internet search volume may be useful as a complementary tool for TBE surveillance in Italy. Monthly Google Trends (GT) data for TBE-related information were extracted for the period between January 2017 and September 2022, corresponding to the available time series of TBE notifications in Italy. Time series modeling was performed by applying seasonal autoregressive integrated moving average (SARIMA) models with or without GT data. The search terms relative to tick bites reflected best the observed temporal distribution of TBE cases, showing a correlation coefficient of 0.81 (95 % CI: 0.71–0.88). Particularly, both the reported number of TBE cases and GT searches occurred mainly during the summer. The peak of disease notifications coincided with that of Google searches in 4 of 6 years. Once calibrated, SARIMA models with or without GT data were applied to a validation set. Retrospective forecast made by the model with GT data was associated with a lower prediction error and accurately predicted the peak timing. By contrast, the traditional SARIMA model underestimated the actual number of TBE notifications by 65 %. Timeliness, easy availability, low cost and transparency make monitoring of the TBE-related Internet search queries a promising addition to the traditional methods of TBE surveillance in Italy.

Isolation and Characterisation of Human-Derived blaKPC-3-Producing Salmonella enterica Serovar Rissen in 2018.

In this study, we describe a Salmonella enterica serovar (S.) Rissen strain with a reduced susceptibility to meropenem, isolated from a urinary infection in an 89-year-old woman in 2018 during activity surveillance in Italy (Enter-Net Italia). The genomic characteristics, pathogenicity, and antimicrobial resistance mechanisms were investigated via a genomic approach. Antimicrobial susceptibility testing revealed a "susceptible, increased exposure" phenotype to meropenem in the S. Rissen strain (4_29_19). Whole-genome sequencing (WGS) was performed using both the NovaSeq 6000 S4 PE150 XP platform (Illumina, San Diego, CA, USA) and MinION (Oxford Nanopore). The S. Rissen 4_29_19 strain harboured two plasmids: a pKpQIL-like plasmid carrying the blaKPC-3 resistance gene in a Tn4401a transposon (pKPC_4_29_19), and a ColE-like plasmid (p4_4_29_19) without resistance genes, highly prevalent among Enterobacterales. Comparative analysis revealed that the pKPC_4_29_19 plasmid was highly related to the pKpQIL reference plasmid (GU595196), with 57% coverage and 99.96% identity, but lacking a region of about 30 kb, involving the FIIK2 replicon region and the entire transfer locus, causing the loss of its ability to conjugate. To our knowledge, this is the first time that a pKpQIL-like plasmid, carrying blaKPC-3, highly diffused in Klebsiella pneumoniae strains, has been identified in a Salmonella strain in our country. The acquisition of blaKPC genes by Salmonella spp. is extremely rare, and is reported only sporadically. In zoonotic bacteria isolated from humans, the presence of a carbapenem resistance gene carried by mobile genetic elements, usually described in healthcare-associated infection bacteria, represents an important concern for public health.

P19-018-23 Social Media Mining for Food Safety Surveillance in Italy

P19-018-23 Social Media Mining for Food Safety Surveillance in Italy

Malaria surveillance system and Hospital Discharge Records: Assessing differences in Italy, 2011–2017 database analysis

BackgroundIn Italy, surveillance through mandatory notification of cases to the National Surveillance System (NSS) has shown evidence of underreporting over the years. To evaluate the overall quality of malaria dataset, Hospital Discharge Records (HDRs) were analyzed as a second data source. MethodsMalaria cases by NSS and by HRDs were compared and analyzed from 2011-through 2017. The impact of cases was estimated by annual rates per 100,000 residents. ResultsCases reported to NSS and to HDRs were 5,149 and 6,446, respectively. The annual rate recorded by NSS increased from 1.2 per 100,000 in 2011 to 1.4 per 100,000 in 2017, a similar trend was shown by HDRs, from 1.4 per 100,000 in 2011 to 1.6 per 100,000 in 2017. Every year, the number of NSS cases was lower than HDRs cases suggesting moderate underreporting of the mandatory notification. In both data sources adult males aged 25 to 44, and non-Italian travellers visiting friends and relatives were the most affected groups; Plasmodium falciparum was the prevalent agent identified, being the imported cases originated mainly from sub-Saharan Africa. As places of diagnosis and care, both data sources indicated hospitals located in Northern Italy in over 70% of cases. ConclusionsAlthough the comparison of malaria cases highlighted some underreporting by NSS, a fair agreement between the two institutional information systems was observed. The use of both data sources improves the performance of malaria surveillance in Italy, essentially for early warning systems in case of locally-acquired events and primary prevention in international travellers.

Chronic Wasting Disease Monitoring in Italy 2017-2019: Neuropathological Findings in Cervids.

Chronic wasting disease (CWD) is a prion disease that affects cervids; it is classified under transmissible spongiform encephalopathies (TSEs). CWD is particularly contagious, making its eradication in endemic areas very difficult and creating serious problems for cervid conservation and breeding. It has recently become an emerging public health risk to be managed by health authorities. Starting in 2017, active CWD surveillance in Italy has intensified with the monitoring of wild and farmed cervids. The present study summarizes findings from a histopathological survey of the brains from wild ruminants collected via CWD monitoring between 2017 and 2019. A total of 113 brains from 62 red deer (Cervus elaphus) and 51 roe deer (Capreolus capreolus) were submitted for analysis at the National Reference Center for Animal Encephalopathies (CEA) to determine major patterns of neuropathological lesions and correlated pathogens. Brain lesions were detected in 20 animals, 10 brain samples were unsuitable for examination, and 83 presented no lesions. Neuropathological examination revealed non-suppurative encephalitis or meningoencephalitis in most cases (15/20). This brain study revealed evidence for the absence of CWD in Italy and provided a reference spectrum of neuropathological lesions for differential diagnosis in cervids.

SARS-CoV-2 surveillance in Italy through phylogenomic inferences based on Hamming distances derived from pan-SNPs, -MNPs and -InDels

BackgroundFaced with the ongoing global pandemic of coronavirus disease, the ‘National Reference Centre for Whole Genome Sequencing of microbial pathogens: database and bioinformatic analysis’ (GENPAT) formally established at the ‘Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise’ (IZSAM) in Teramo (Italy) is in charge of the SARS-CoV-2 surveillance at the genomic scale. In a context of SARS-CoV-2 surveillance requiring correct and fast assessment of epidemiological clusters from substantial amount of samples, the present study proposes an analytical workflow for identifying accurately the PANGO lineages of SARS-CoV-2 samples and building of discriminant minimum spanning trees (MST) bypassing the usual time consuming phylogenomic inferences based on multiple sequence alignment (MSA) and substitution model.ResultsGENPAT constituted two collections of SARS-CoV-2 samples. The first collection consisted of SARS-CoV-2 positive swabs collected by IZSAM from the Abruzzo region (Italy), then sequenced by next generation sequencing (NGS) and analyzed in GENPAT (n = 1592), while the second collection included samples from several Italian provinces and retrieved from the reference Global Initiative on Sharing All Influenza Data (GISAID) (n = 17,201). The main results of the present work showed that (i) GENPAT and GISAID detected the same PANGO lineages, (ii) the PANGO lineages B.1.177 (i.e. historical in Italy) and B.1.1.7 (i.e. ‘UK variant’) are major concerns today in several Italian provinces, and the new MST-based method (iii) clusters most of the PANGO lineages together, (iv) with a higher dicriminatory power than PANGO lineages, (v) and faster that the usual phylogenomic methods based on MSA and substitution model.ConclusionsThe genome sequencing efforts of Italian provinces, combined with a structured national system of NGS data management, provided support for surveillance SARS-CoV-2 in Italy. We propose to build phylogenomic trees of SARS-CoV-2 variants through an accurate, discriminant and fast MST-based method avoiding the typical time consuming steps related to MSA and substitution model-based phylogenomic inference.

Emergence and Spread of SARS-CoV-2 Lineages B.1.1.7 and P.1 in Italy.

Italy’s second wave of SARS-CoV-2 has hit hard, with more than three million cases and over 100,000 deaths, representing an almost ten-fold increase in the numbers reported by August 2020. Herein, we present an analysis of 6515 SARS-CoV-2 sequences sampled in Italy between 29 January 2020 and 1 March 2021 and show how different lineages emerged multiple times independently despite lockdown restrictions. Virus lineage B.1.177 became the dominant variant in November 2020, when cases peaked at 40,000 a day, but since January 2021 this is being replaced by the B.1.1.7 ‘variant of concern’. In addition, we report a sudden increase in another documented variant of concern—lineage P.1—from December 2020 onwards, most likely caused by a single introduction into Italy. We again highlight how international importations drive the emergence of new lineages and that genome sequencing should remain a top priority for ongoing surveillance in Italy.

MoRoNet a network to strengthen the quality of measles and rubella surveillance in Italy

Abstract Background Measles is a vaccine-preventable infectious disease and it remains one of the leading causes of infant mortality globally. The World Health Organization (WHO) has adopted the goal of eliminating measles and rubella. Detection and control of communicable diseases would not be possible without accurate laboratory results regarding when and where a particular disease circulates. Methods WHO/Europe therefore works with all Member States to steadily improve the quality of the laboratory data in order to determine the Region's progress towards measles and rubella elimination. For this purpose coordinates the European Measles and Rubella Laboratory Network (MR LabNet). National labs in this network undergoes regular external quality assessment through an annual accreditation programme. Results In Italy, a Sub-national Reference Laboratories Network for measles and rubella (MoRoNET) has been developed since March 2017 and currently includes 15 laboratories. MoRoNet was developed following the indications of the MR LabNet. It is accreditate, coordinated and supervised by the National Reference Laboratory. Conclusions Strengthening the role of national laboratories in overseeing the performance of subnational laboratories has become a critical need in order to properly monitor the Region's measles and rubella elimination efforts. MoRoNet permits to Italy to develop a country-specific work plan for establishing national networks and oversight mechanism, including preliminary monitoring and evaluation indicators compliant with MR LabNet standards. This is very significant not only to optimize the participation in national and regional processes to verify disease elimination, but also to strengthen the quality of vaccine-preventable disease surveillance. MoRoNet Group: A Amendola; F Baldanti; MR Capobianchi; M Chironna; MG Cusi; P D'Agaro; P Lanzafame; T Lazzarotto; K Marinelli; A Orsi; E Pagani; G Palù; F Pittaluga, A Sacchi; F Tramuto. Key messages MoRoNet has permitted to Italy to develop a country-specific work plan for establishing national networks and oversight mechanism, compliant with WHO MR LabNet standards. MoRoNet network has permitted to optimize the participation in processes to verify disease elimination, but also to strengthen the quality of vaccine-preventable disease surveillance.

Food Hygiene Surveillance in Italy: Is Food Ice a Public Health Risk?

Food ice is used as an ingredient or as a coolant in drinks and in the storage of food, especially fishery products. Studies show that ice can be polluted both by chemical substances and by bacteria and fungi. In particular, the presence of fungi in these food matrices has acquired an important role in Public Health, as it can represent a risk factor for fungal complications in immunocompromised subjects. In the present study we evaluated the hygiene–sanitary quality of food ice from public and collective catering establishments in a large area of Southern Italy, investigating the mandatory parameters (Escherichia coli, coliform and Enterococci) and some accessory parameters (Staphylococcus aureus, Pseudomonas aeruginosa and fungi) provided for Italian Legislative Decree 31/01. Although 54.5% of samples were compliant, the results highlight a vast contamination of food ice by bacteria and fungi. In particular, 95.8% of samples were contaminated by fungi, stressing no difference between compliant and non-compliant samples. Their presence is generally attributable to the poor sanitation conditions in the production and/or administration phase and to the incorrect sanitization and ordinary maintenance procedures. It seems appropriate to suggest the need to carry out a specific risk assessment with respect to the self-control plans.

Integrated Surveillance in Italy: outputs and related activities

to describe the integrated surveillance system of COVID-19 in Italy, to illustrate the outputs used to return epidemiological information on the spread of the epidemic to the competent public health bodies and to the Italian population, and to describe how the surveillance data contributes to the ongoing weekly regional monitoring and risk assessment system. the COVID-19 integrated surveillance system is the result of a close and continuous collaboration between the Italian National Institute of Health (ISS), the Italian Ministry of Health, and the regional and local health authorities. Through a web platform, it collects individual data of laboratory confirmed cases of SARS-CoV-2 infection and gathers information on their residence, laboratory diagnosis, hospitalisation, clinical status, risk factors, and outcome. Results, for different levels of aggregation and risk categories, are published daily and weekly on the ISS website, and made available to national and regional public health authorities; these results contribute one of the information sources of the regional monitoring and risk assessment system. the COVID-19 integrated surveillance system monitors the space-time distribution of cases and their characteristics. Indicators used in the weekly regional monitoring and risk assessment system include process indicators on completeness and results indicators on weekly trends of newly diagnosed cases per Region. the outputs of the integrated surveillance system for COVID-19 provide timely information to health authorities and to the general population on the evolution of the epidemic in Italy. They also contribute to the continuous re-assessment of risk related to transmission and impact of the epidemic thus contributing to the management of COVID-19 in Italy.

Analysis of GII.P7 and GII.6 noroviruses circulating in Italy during 2011–2016 reveals a replacement of lineages and complex recombination history

Noroviruses are important human enteric pathogens and monitoring their genetic diversity is important for epidemiological surveillance, vaccine development, and understanding of RNA viruses evolution. Epidemiological investigations have revealed that genogroup II, genotype 6 noroviruses (GII.6) are common agents of gastroenteritis. Upon sequencing of the ORF2 (encoding the viral capsid), GII.6 viruses have been distinguished into three variants. Sentinel hospital-based surveillance in Italy revealed that GII.6 noroviruses were the second most common capsid genotype in 2015, mostly in association with a GII.P7 ORF1 (encoding the viral polymerase). Upon molecular characterization of the ORF1 and ORF2, the GII.P7_GII.6 epidemic viruses circulating in 2014–2015 (variant GII.6b) were different from those that circulated sporadically in 2011–2013 (variant GII.6a). Analysis of the ORF1 (GII.P7) and ORF2 (GII.6) sequences available in the databases unveiled marked genetic diversity and peculiarities in the phylogenetic segregation patterns, suggesting multiple recombination events. Phylogenetic analyses suggest that recent GII.P7_GII.6b viruses were circulating as early as 2008, and formed a genetically homogenous group that emerged globally.

Significant impact of pneumococcal conjugate vaccination on pediatric parapneumonic effusion: Italy 2006–2018

Etiology and serotyping of parapneumonic effusion (PPE) and the impact of vaccination was evaluated over a 12-year period, before and after the PCV13 introduction (2011) for Italian children From 0 to 16 years of age.Five hundred and two children were evaluated; 226 blood and 356 pleural fluid samples were obtained and tested using Realtime-PCR and culture. In the pre-PCV13 era S. pneumoniae was the most frequent pathogen identified (64/90; 71.1%) with a large predominance of serotypes 1 (42.4%), 3 (23.7%), 7F (5.1%) and 19A (11.9%).The impact of vaccination, calculated on children 0–8 years of age, demonstrated a significant reduction of PPE: with an incidence rate of 2.82 (95%CL 2.32–3.41) in the pre-PCV13 era and an age-standardized rate (ASR) of 0.66 (95% CL 0.37–1.99) in the post-PCV13 era, p < 0.0001. No increase in non-PCV13 serotypes was recorded. S. pneumoniae remained the most frequent pathogen identified in the post-PCV13 era in unvaccinated children with an unchanged serotype distribution: respectively 26/66 (39.4%), 25/66 (37.9%), 5/66 (7.6%), and 4/66 (6.1%) for 1, 3, 7F and 19A. On the other hand 7F and 19A disappeared in vaccinated children and serotype 1 and 3 decreased by 91.8% and 31.5%, respectively. Realtime PCR was significantly more sensitive than culture both in pleural fluid (79.7% vs 12.5%) and in blood (17.8% vs 7.4%).In conclusion, our findings indicate that routine immunization with PCV13 has significantly reduced the burden of childhood PPE in vaccinated children, without increasing PPE due to other bacteria and without serotype shift. Moreover, the impact of PCV13 may be underestimated due to the increase in pneumococcal surveillance in Italy. Data has also shown that Real-time PCR is an essential tool to better define the etiology of PPE and to monitor vaccination plans. Longer studies will be necessary to evaluate the role of herd protection in PPE prevention.

A new approach to outbreak management for bovine Cystic Echinococcosis cases in hypo-endemic areas.

Cystic Echinococcosis (CE) surveillance in Italy is based on detection of its larval stage (hydatic cysts) at the slaughterhouse. In northern Italy, a hypo-endemic area, local health authorities investigate each individual farm with positive animals to treat their dogs with cestocidal drugs, but this system is time-consuming and poorly effective for bovine farms. The study applied a new approach based on targeted epidemiological surveys in areas with aggregation of bovine CE cases, and compared the outcome with that of two control areas with farms individually investigated. The presence of territorial cluster of bovine farms with CE cases was investigated for 3 consecutive years (2013-2014-2015) in a high-risk area of Veneto Region (north-eastern Italy), using a spatial scan statistic. Epidemiological investigations, consisting of a questionnaire survey and canine faecal samples collection, were conducted in cluster and control areas. All faecal samples were analyzed for taeniids eggs and positive samples were sequenced and identified. In total, 99 farms were surveyed and 208 faecal samples were retrieved from dogs. Sixty-two farms (42 bovine and 20 sheep) were investigated in cluster areas and 37 farms (33 bovine and 4 sheep) in control areas. Based on the results of the cestode egg isolation procedure, 14 animals (6.7%) were positive to taeniid eggs. For molecular analysis, two dogs resulted positive to Echinococcus granulosus, and seven to Taenia hydatigena. Twelve positive dogs were found in targeted survey areas and ten of these dogs were shepherd dogs, belonging to transhumant sheep flocks known to pass in cluster areas. The new approach demonstrated to successfully identify the probable source of infection of CE positive bovines. Most of positive dogs belonged to transhumant flocks, underlining the importance to include shepherd dogs in the surveillance system for CE.

A new approach to outbreak management for bovine cystic echinococcosis cases in hypo-endemic areas

Cystic Echinococcosis (CE) surveillance in Italy is based on detection of its larval stage (hydatic cysts) at the slaughterhouse. In northern Italy, a hypo-endemic area, local health authorities investigate each individual farm with positive animals to treat their dogs with cestocidal drugs, but this system is time-consuming and poorly effective for bovine farms. The study applied a new approach based on targeted epidemiological surveys in areas with aggregation of bovine CE cases, and compared the outcome with that of two control areas with farms individually investigated. The presence of territorial cluster of bovine farms with CE cases was investigated for 3 consecutive years (2013-2014-2015) in a high-risk area of Veneto Region (north-eastern Italy), using a spatial scan statistic. Epidemiological investigations, consisting of a questionnaire survey and canine faecal samples collection, were conducted in cluster and control areas. All faecal samples were analyzed for taeniids eggs and positive samples were sequenced and identified. In total, 99 farms were surveyed and 208 faecal samples were retrieved from dogs. Sixty-two farms (42 bovine and 20 sheep) were investigated in cluster areas and 37 farms (33 bovine and 4 sheep) in control areas. Based on the results of the cestode egg isolation procedure, 14 animals (6.7%) were positive to taeniid eggs. For molecular analysis, two dogs resulted positive to Echinococcus granulosus, and seven to Taenia hydatigena. Twelve positive dogs were found in targeted survey areas and ten of these dogs were shepherd dogs, belonging to transhumant sheep flocks known to pass in cluster areas. The new approach demonstrated to successfully identify the probable source of infection of CE positive bovines. Most of positive dogs belonged to transhumant flocks, underlining the importance to include shepherd dogs in the surveillance system for CE.

Neisseria meningitidis Antimicrobial Resistance in Italy, 2006 to 2016.

The aim of this study was to evaluate the antimicrobial susceptibilities of 866 Neisseria meningitidis invasive strains during 11 years of surveillance in Italy. Two and six strains were resistant to ciprofloxacin and rifampin, respectively. Forty-five percent were penicillin intermediate, associated with hypervirulent serogroup C clonal complex 11. All of the strains were susceptible to cephalosporins.

Poliovirus and Other Enteroviruses from Environmental Surveillance in Italy, 2009-2015.

Within the initiatives for poliomyelitis eradication by WHO, Italy activated an environmental surveillance (ES) in 2005. ES complements clinical Acute Flaccid Paralysis (AFP) surveillance for possible polio cases, detects poliovirus circulation in environmental sewage, and is used to monitor transmission in communities. In addition to polioviruses, the analyses comprised: (i) the monitoring of the presence of non-polio enteroviruses in sewage samples and (ii) the temporal and geographical distribution of the detected viruses. From 2009 to 2015, 2880 sewage samples were collected from eight cities participating in the surveillance. Overall, 1479 samples resulted positive for enteroviruses. No wild-type polioviruses were found, although four Sabin-like polioviruses were detected. The low degree of mutation found in the genomes of these four isolates suggests that these viruses have had a limited circulation in the population. All non-polio enteroviruses belonged to species B and the most frequent serotype was CV-B5, followed by CV-B4, E-11, E-6, E-7, CV-B3, and CV-B2. Variations in the frequency of different serotypes were also observed in different seasons and/or Italian areas. Environmental surveillance in Italy, as part of the 'WHO global polio eradication program', is a powerful tool to augment the polio surveillance and to investigate the silent circulation or the re-emergence of enteroviruses in the population.

Regional HIV Surveillance in Italy: a starting point for the future national system

the Italian National HIV Surveillance, instituted by the Ministerial Decree of March 31st, 2008, is based on 21 regional surveillance systems and adopts an essential data collection form with a definite data flow. The unification of HIV and AIDS surveillance systems and the implementation of an identical data collection form are priorities of the Italian National HIV/AIDS Action Plan 2017 (PNAIDS). to describe the 21 regional HIV surveillance systems and to verify the feasibility of their unification. in March 2017, a questionnaire containing 13 questions was sent to all the regional representatives of the 21 surveillance systems. The main questions were about timeliness, data flow, and quality of the system. The quality was measured through a subjective evaluation expressed by the regional referent through scores from 1 (minimum) to 10 (maximum) regarding four indicators (regional coverage, timeliness, correctness, and completeness of the data). more than half of the regional systems use a computerized data collection method. Some of these regions have not completely adapted to the data collection form contained in the Decree and other regions declare a undernotification of the system. The majority of the regions record a slight notification delay by the reporting centres. Some regions report gaps in the completeness of the data received by the reporting centres. the main strengths of the HIV surveillance system are computerization of the systems and slightly reporting delay. Regarding the quality of the regional systems and its data, the study reports a good self-evaluation. This study also showed useful indications to improve the national HIV surveillance system, such as the unification of HIV surveillance with the AIDS surveillance and the implementation of a unique national system, as suggested by guidelines of the PNAIDS 2017.

Group A Rotavirus Associated with Encephalitis in Red Fox

Abstract In 2011, a group A rotavirus was isolated from the brain of a fox with encephalitis and neurologic signs, detected by rabies surveillance in Italy. Intracerebral inoculation of fox brain homogenates into mice was fatal. Genome sequencing revealed a heterologous rotavirus of avian origin, which could provide a model for investigating rotavirus neurovirulence.

Group A Rotavirus Associated with Encephalitis in Red Fox.

In 2011, a group A rotavirus was isolated from the brain of a fox with encephalitis and neurologic signs, detected by rabies surveillance in Italy. Intracerebral inoculation of fox brain homogenates into mice was fatal. Genome sequencing revealed a heterologous rotavirus of avian origin, which could provide a model for investigating rotavirus neurovirulence.