Nasopharyngeal carriage of Haemophilus influenzae among adults with co-morbidities.

After the widespread use of Haemophilus influenzae type b (Hib) vaccine, H. influenzae invasive disease is now commonly due to non-encapsulated (NTHi), affecting mostly the youngest and the elderly. The objective of this study was to investigate H. influenzae nasopharyngeal carriage rate in adults with co-morbidities and possible associated risk factors. METHODS: Patients aged >50 years with co-morbidities attending medical centres were examined. A nasopharyngeal swab was analysed for H. influenzae presence by cultural and molecular methods (RT-PCR). Univariable and multivariable analysis of risk factors for H. influenzae carriage were performed. Serotype of isolates was determined by PCR capsular genotyping. Minimum inhibitory concentration (MIC) was determined by MIC gradient test and ß-lactamase production was detected by the nitrocephin test. Genotyping was performed by Multilocus sequence typing (MLST). Phylogenetic relationships among carriage and invasive NTHi strains were assessed. RESULTS: Among 248 enrolled patients (median age: 73 years), the carriage rate was 5.6% and 10.5% by cultural method or RT-PCR, respectively. Colonization with H. influenzae was significantly associated with the presence of acute respiratory symptoms (adjusted OR = 12.16, 95% CI: 3.05-48.58, p < 0.001). All colonizing isolates were NTHi. Three isolates (3/14, 21.4%) were resistant to ampicillin and beta-lactamase positive. MLST revealed a high degree of genetic diversity, with 11 different STs from 14 isolates. Eight out of the 11 (72.7%) STs were shared among carriage and invasive isolates. CONCLUSIONS: Adults ≥50 years old with co-morbidities are occasionally colonized by H. influenzae, even if the presence of co-morbidities is not a risk factor for colonization. The presence of acute respiratory symptoms is the only factor associated with H. influenzae colonization. Colonizing H. influenzae are all NTHi. Colonizing H. influenzae often belong to the same STs of invasive disease isolates.

First evidence of blaNDM-1 and blaOXA-23 carbapenemase genes in human body lice infesting a second-hand T-shirt in a street market in Italy.

BACKGROUND: The spread of carbapenems resistance is a public health concern. The main group of carbapenemases encoding the ß-lactamases activity (bla genes) is the Metallo-ß-lactamases (MBLs). METHODS: The presence of carbapenemase blaOXA-23-like, blaOXA-40-like, blaOXA-51-like, blaOXA-58-like, and blaNDM-1 genes was screened by real time PCR in 26 Pediculus humanus insects identified from second-hand clothes in a local market in Central Italy. Bacteria diversity was also characterized through shotgun metagenomic amplification for a deep sequencing of the host-associated bacterial microbiomes. RESULTS: The blaOXA-23 and blaNDM-1 carbapenemases genes were found and metagenomic analysis showed a great presence of Acinetobacter species. CONCLUSIONS: These results suggest a new potential transmission path for carbapenemase gene spread through bacteria ingested by insects infesting humans.

Multiplex Real-Time Reverse-Transcription Polymerase Chain Reaction Assays for Diagnostic Testing of Severe Acute Respiratory Syndrome Coronavirus 2 and Seasonal Influenza Viruses: A Challenge of the Phase 3 Pandemic Setting.

BACKGROUND: Pandemic coronavirus disease 2019 (COVID-19) disease represents a challenge for healthcare structures. The molecular confirmation of samples from infected individuals is crucial and therefore guides public health decision making. Clusters and possibly increased diffuse transmission could occur in the context of the next influenza season. For this reason, a diagnostic test able to discriminate severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from influenza viruses is urgently needed. METHODS: A multiplex real-time reverse-transcription polymerase chain reaction (PCR) assay was assessed using 1 laboratory protocol with different real-time PCR instruments. Overall, 1000 clinical samples (600 from samples SARS-CoV-2-infected patients, 200 samples from influenza-infected patients, and 200 negative samples) were analyzed. RESULTS: The assay developed was able to detect and discriminate each virus target and to intercept coinfections. The limit of quantification of each assay ranged between 5 and 10 genomic copy numbers, with a cutoff value of 37.7 and 37.8 for influenza and SARS-CoV-2 viruses, respectively. Only 2 influenza coinfections were detected in COVID-19 samples. CONCLUSIONS: This study suggests that multiplex assay is a rapid, valid, and accurate method for the detection of SARS-CoV-2 and influenza viruses in clinical samples. The test may be an important diagnostic tool for both diagnostic and surveillance purposes during the seasonal influenza activity period.

Epidemiological characteristics of COVID-19 cases and estimates of the reproductive numbers 1 month into the epidemic, Italy, 28 January to 31 March 2020.

BackgroundOn 20 February 2020, a locally acquired coronavirus disease (COVID-19) case was detected in Lombardy, Italy. This was the first signal of ongoing transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the country. The number of cases in Italy increased rapidly and the country became the first in Europe to experience a SARS-CoV-2 outbreak.AimOur aim was to describe the epidemiology and transmission dynamics of the first COVID-19 cases in Italy amid ongoing control measures.MethodsWe analysed all RT-PCR-confirmed COVID-19 cases reported to the national integrated surveillance system until 31 March 2020. We provide a descriptive epidemiological summary and estimate the basic and net reproductive numbers by region.ResultsOf the 98,716 cases of COVID-19 analysed, 9,512 were healthcare workers. Of the 10,943 reported COVID-19-associated deaths (crude case fatality ratio: 11.1%) 49.5% occurred in cases older than 80 years. Male sex and age were independent risk factors for COVID-19 death. Estimates of R0 varied between 2.50 (95% confidence interval (CI): 2.18-2.83) in Tuscany and 3.00 (95% CI: 2.68-3.33) in Lazio. The net reproduction number Rt in northern regions started decreasing immediately after the first detection.ConclusionThe COVID-19 outbreak in Italy showed a clustering onset similar to the one in Wuhan, China. R0 at 2.96 in Lombardy combined with delayed detection explains the high case load and rapid geographical spread. Overall, Rt in Italian regions showed early signs of decrease, with large diversity in incidence, supporting the importance of combined non-pharmacological control measures.

Laboratory management for SARS-CoV-2 detection: a user-friendly combination of the heat treatment approach and rt-Real-time PCR testing.

The RNA purification is the gold standard for the detection of SARS-CoV-2 in swab samples, but it is dependent on the availability of chemical reagents. In this study, we evaluated the heat treatment method without RNA extraction as a reliable option to nucleic acid purification.

Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe.

Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient's sequence clustered with sequences from Germany while the tourist's sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients' sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.

[Integrated Surveillance in Italy: outputs and related activities]. / La sorveglianza integrata COVID-19 in Italia: output e attività correlate.

OBJECTIVES: 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. METHODS: 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. RESULTS: 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. CONCLUSIONS: 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.

Plasmodium vivax exflagellated microgametes in human peripheral blood: a potential diagnostic dilemma.

Both malaria and relapsing fever Borrelia are infectious diseases characterized by fever, headache, myalgia, hepatosplenomegaly and tendency to relapse. Exflagellation of microgametocyte in malarial parasites is seen only in the definitive host, i.e., mosquitoes. Here we report an unusual case of a 23-year-old man who presented Plasmodium vivax infection with multiple exflagellated microgametes in the peripheral blood smear.

Primary Whipple disease of the Central Nervous System presenting with rhombencephalitis.

Primary Whipple disease of the Central Nervous System is a rare entity whose outcome might be fatal if not promptly diagnosed and treated. Few cases are reported in the literature with heterogeneous clinical and radiological presentations which often make the diagnosis extremely challenging. We report a case of primary Whipple disease of the Central Nervous System presenting with rhombencephalitis in a female patient in immunosuppressive treatment for rheumatoid arthritis. We describe the management of our patient and discuss the features of this rare clinical entity.

Pneumococcal carriage among adults aged 50 years and older with co-morbidities attending medical practices in Rome, Italy.

BACKGROUND: Data on Streptococcus pneumoniae carriage in adults with co-morbidities are limited. In this study we estimated the pneumococcal carriage among adults with co-morbidities and evaluated socio-demographic and clinical risk factors. The potential coverage of the current pneumococcal vaccines recommended for adults (PCV13 and PPV23) was also investigated. METHODS: A cross-sectional study on S. pneumoniae carriage among unvaccinated adults ≥50 years with co-morbidities, presenting with or without acute respiratory symptoms at general practitioners in Rome, Italy, between October 2015 and July 2016 was conducted. Pneumococcal carriage was investigated by both cultural and molecular methods. Socio-demographic variables and co-morbidities were evaluated by logistic models as possible risk factors for pneumococcal carriage. RESULTS: Out of 248 patients (median age: 73 yrs; IQR: 65-79), 12 (4.8%) and 83 (33.5%) individuals were found colonized using cultural or molecular methods, respectively. Potential risk factors for pneumococcal colonization as ascertained by molecular methods were: low level of education (adjusted OR = 3.71, 95% CI: 1.62-9.40), winter months (December-March vs other months, adjusted OR = 2.56, 95% CI: 1.29-5.14), and presence of chronic lung diseases (adjusted OR = 2.18, 95% CI: 1.15-4.16). The combination of serotype-specific multiplex RT-PCR and conventional PCR allowed to identify 22 serotypes/group of serotypes, of which the most common were: 24F/24A/24B, 12F/12A/12B/44/46, 6A/6B, 14, 15B/15C, and 22F/22A. Prevalence of pneumococcal carriage due to PCV13 serotypes and non-PCV13 serotypes was 23.6% and 67.3%, respectively. Prevalence of colonization due to PPV23 serotypes was estimated to be 54.6%. CONCLUSIONS: A high prevalence of S. pneumoniae carriage was observed among adults with co-morbidities, especially among individuals affected by chronic lung diseases. These results support vaccine strategies based on the sequential administration of PCV13 and PPV23 to control potentially invasive pneumococcal strains in adults, especially in subjects with co-morbidities.

Detection of tick-borne pathogens in ticks collected in the suburban area of Monte Romano, Lazio Region, Central Italy.

BACKGROUND: A study on tick species characterization and tick borne pathogens detection was performed by a survey conducted during 2012 and 2013 in the Viterbo province (Lazio Region, Central Italy). Seven sites were selected for the study investigation, including two farms and a military zone. METHODS: A total of 255 ticks, Rhipicephalus (Boophilus) annulatus (n = 215), Rhipicephalus bursa (n = 28), and Hyalomma marginatum (n = 12) were screened individually by molecular methods for the tick borne bacterial agents: Borrelia burgdorferi sensu lato group, Bartonella spp., Coxiella burnetii, Ehrlichia spp., Francisella spp., and Rickettsia spp. RESULTS AND CONCLUSION: Overall, 182 ticks (71%) were infected with at least one pathogen; among these co-infections were found in 94 ticks. Tick borne pathogens identified were C. burnetii, B. burgdorferi s.l., Bartonella spp., Rickettsia spp., Francisella spp., and Ehrlichia spp. In R. bursa and H. marginatum, the presence of B. burgdorferi s.l. was positively correlated with that of C. burnetii, Rickettsia spp., and Bartonella spp. and their coinfection probabilities were 29.8%, 22.7% and 11.7%, respectively; the probability of coinfection for Francisella spp. and Rickettsia spp. and for Francisella spp. and Bartonella spp. was 14.9% and 17.9%, respectively. In R. (Boophilus) annulatus, the probability of coinfection between C. burnetii and B. burgdorferi s.l. was 11.3%, while those between C. burnetii and Bartonella spp. and between B. burgdorferi s.l. and Bartonella spp. were 0.8%. Further studies are needed in order to assess the risk associated with these unusual tick-borne pathogens in Central Italy.

Report of the human body louse (Pediculus humanus) from clothes sold in a market in central Italy.

BACKGROUND: Pediculus humanus, the human body louse, is widespread where overcrowding and lack of hygiene are present, in areas of the world affected by poverty, war, famine and presence of refugees. It has recently been considered re-emerging among homeless populations in developed countries. In Italy, it was last reported in 1945. Pediculus humanus is a vector of highly relevant human pathogens. METHODS: In October 2018, a woman found small insects on a T-shirt bought second-hand in a local street market in a village 35 km south of Rome (central Italy). Insects were identified both morphologically and by molecular analysis. Moreover, they were analyzed molecularly for the presence of Rickettsia prowazekii, Borrelia recurrentis, Bartonella quintana, Coxiella burnetii and Yersinia pestis. RESULTS: Morphological and molecular analyses of the insects identified them as 26 lice (12 females, 10 males and 4 nymphs) of the species P. humanus. Many nits were found on the T-shirt seams. DNA of the investigated pathogens was not detected in any of the lice. CONCLUSIONS: The exceptionality of the described case lies both in the report of P. humanus from a country where it had not been reported since 1945, and in its finding from second-hand clothes for sale in a market, constituting a potential source of infection for people buying this type of goods. The question arises, how did adults and nits of P. humanus infest clothes for sale on a market stall in a country where it had not been reported for decades. Given that the body louse requires frequent blood meals to survive and develop, its arrival on clothes imported from abroad is highly improbable. Hence, it must be presumed that people infected with the human body louse are present in Italy. This report points out a serious regulatory problem regarding the management of second-hand clothes prior to sale and, more generally, of controls in street markets.

Meningitis with cranial polyneuritis and cavernous sinus thrombosis by Borrelia crocidurae: First autochthonous case in Europe.

Borrelia crocidurae is endemic in West Africa, where it represents the leading cause of tick-borne relapsing fever (TBRF). TBRF typically presents with high fever and systemic symptoms, followed by recurrent episodes. Neurological complications may occur during febrile relapses. B. crocidurae is considered the most neurotropic agent of TBRF and is associated to severe neurological manifestations i.e. meningitis and encephalitis. To date, European cases of B. crocidurae infection have been reported in travelers returning from endemic areas. We report the first autochthonous case in Europe of B. crocidurae infection, presenting as meningitis with cranial polyneuritis and cavernous sinus thrombosis that were not preceded by classic febrile recurrences.

Mediterranean spotted fever rickettsiosis in Italy, 2001-2015: Spatio-temporal distribution based on hospitalization records.

The Mediterranean spotted fever (MSF) rickettsiosis is the predominant rickettsial disease among the spotted fever group (SFG) rickettsiae in the Mediterranean countries and North Africa. Its causative agent is Rickettsia conorii, although, SFG rickettsiosis - cases due to Rickettsia monacensis, Rickettsia massiliae and Rickettsia aeschlimannii were also described. A retrospective study based on hospital discharge records with a diagnosis of SFG rickettsiosis was carried out to describe the spatial pattern, the trend of the disease, and the epidemiological characteristics of persons hospitalized in the period 2001-2015. Standardized hospitalization ratios were calculated at municipal level using the European population. Smoothed maps were produced using a localised smoothing Poisson model. The mean annual standardized hospitalization rate was 1.36/100,000 person years (95%CI: 1.34; 1.39). Rates showed strong summer seasonality and tended to decrease over time. During the study period, 28.89% of municipalities had smoothed standardized hospitalization ratios greater than 1 and 14.01% above 20. Higher standardized hospitalization ratios were found in areas along the Tyrrhenian coast, especially in the south of Calabria and in the islands of Sardinia and Sicily, where the disease is of public health relevance.

HPV and Chlamydia trachomatis coinfection in women with Pap smear abnormality: baseline data of the HPV Pathogen ISS study.

Chlamydia trachomatis (Ct) and human papillomavirus (HPV) are the most common sexually transmitted pathogens. Whereas it is well known that infection with oncogenic HPV genotypes increases the risk of cervical cancer (CC), the implication of Ct in the pathogenesis of CC is still controversial. Hence, to investigate the possible implication of Ct infection alone, or with concomitant HPV infection, in the severity of cervical lesions, we conducted a study in 164 Caucasian HIV-negative women with abnormal Pap. Genomic HPV and Ct DNA were detected in 97 (59%) and 16 (10%) women respectively, and 15 (9%) of women were infected by both. Of the HPV positive samples, 89 (79%) were HR-HPV types or probable HR types and HPV16 was the most represented genotype. Interestingly, it was observed that co-infection was more frequent than HPV infection alone in women with high grade lesions.

Draft Genome Sequence of Streptococcus suis Strain SsRC-1, a Human Isolate from a Fatal Case of Toxic Shock Syndrome.

Streptococcus suis is an economically important pathogen in the pig industry and is also an emerging zoonotic agent responsible for severe infections in humans. Here, we report the genome sequence of S. suis strain SsRC-1. Specifically, this strain was a serotype 2 and was isolated from a human fatal case of toxic shock syndrome (TSS) in Italy.

Tache Noire in a Patient with Acute Q Fever.

OBJECTIVE: To describe a rare case of acute Q fever with tache noire. CLINICAL PRESENTATION AND INTERVENTION: A 51-year-old man experienced acute Q fever showing tache noire, generally considered a pathognomonic sign of Mediterranean spotted fever (MSF) and MSF-like illness, but not a clinical feature of Q fever. The patient was treated with doxycycline 100 mg every 12 h. CONCLUSION: In the Mediterranean area, tache noire should be considered pathognomonic of MSF but it should not rule out Q fever. Clinical diagnosis should be supported by accurate laboratory diagnostic tests to guide proper management.