Epidemic dissemination ofSalmonella enterica spp.enterica serovar Bovismorbificans in southern Italy in the years 1989–1991

Epidemic strains ofSalmonella enterica subsp.enterica serovar Bovismorbificans isolated in southern Italy during the years 1989–1991 were submitted to a molecular epidemiological study in comparison with isolates identified in the years 1980–1988 in the same geographic area. Genomic DNA fragments obtained by digestion withBglI orEco RI hybridized withEscherichia coli rRNA to produce three distinct, but highly related patterns. Ribotype 1, which had never been identified before 1989, was found to characterize most of the strains identified between 1989 and 1991. Such a finding supports the hypothesis of emergence and spread of a new bacterial clone associated with the increased number of human infections reported in the same years in southern Italy.     

Genetic diversity of clinical Salmonella enterica serovar Typhimurium in a university hospital of south Tunisia, 2000–2013

Typhimurium is one of the main Salmonella serovar responsible for non-typhoidal gastro-enteritis in Tunisia. Here, we aimed to assess the genetic diversity of 88 clinical Salmonella Typhimurium strains recovered during 14 years from 2000 to 2013. Phage typing, CRISPR polymorphisms (CRISPOL), pulsed-field gel electrophoresis (PFGE), multi-locus variable-number tandem repeat analysis (MLVA) and Whole genome sequencing (WGS) were used to study the relatedness and spatio-temporal evolution of Salmonella Typhimurium populations (Typhimurium (n = 81), monophasic (n = 3) and nonmotile (n = 4) variants).Seven-locus MLST from whole genome assemblies showed that all isolates, except one, belonged to ST19. The isolates were divided into 10 definitive phage (DT) types, dominated by DT104-L (39.8%), DT41 (14.8%), DT116 (11.4%) and DT120 (5.7%). Fifty-seven MLVA patterns (DI, 0.978) were obtained compared to 11 different CRISPOL types and 15 PFGE types (DI,0.845). For cgMLST analysis, 20 profiles were found. A total of 3056 SNPs were identified from the whole genome of the 88 Salmonella Typhimurium isolates. These SNPs resolved these isolates into 86 SNP haplotypes. The phylogeny result allocated most Salmonella Typhimurium isolates into four distinct clades and seven subclades. Genetic diversity between the four clades ranged in the order of 249 to 720 nucleotide changes. The prevalent phage type DT104L formed a major clade on the phylogenetic tree. Pairwise SNP differences between the strains of this clade ranged between 0 and 59.SNP-based WGS typing seems to be the most valuable molecular markers for studying the evolutionary relationships of homogeneous serovar Typhimurium isolates.     

Clinical–Environmental Surveillance of Legionellosis: An Experience in Southern Italy

In Italy, although the number of cases of legionellosis notified to the health authorities has significantly increased in recent years, the incidence is still believed to be underestimated. To verify the true frequency and identify the sources of infection, an active clinical–environmental surveillance program was instituted in three hospital facilities in Southern Italy. Between January 2001 and March 2005, a total of 1000 patients admitted to the three hospitals with a diagnosis of pneumonia were enrolled. The urinary antigen and anti-Legionella antibody titre were assayed in each subject, and direct searches for the microorganism were made in biological specimens. Legionellosis was found to be present in 5.9% of the patients. For each of the cases of legionellosis, microbiological surveys were made of the water supply in the public and/or private facilities involved. Overall, 197 water samples of hospital origin and 218 of community origin were analysed: Legionella spp was isolated in 44.2 and 36.7% of the cases, respectively. Comparison of our data with those of the routine surveillance system for the same area (only 7 cases during the period 1997–2000), showed that the frequency of legionellosis is grossly underestimated in Southern Italy. It is therefore necessary to set up more rigorous controls in both hospital and community facilities, so that timely preventive measures can be taken to avoid any further spread of the disease.     

Geographical clustering of lung cancer in the province of Lecce, Italy: 1992–2001

Background  

The triennial mortality rates for lung cancer in the two decades 1981–2001 in the province of Lecce, Italy, are significantly higher than those for the entire region of Apulia (to which the Province of Lecce belongs) and the national reference rates. Moreover, analyzing the rates in the three-year periods 1993–95, 1996–98 and 1999–01, there is a dramatic increase in mortality for both males and females, which still remains essentially unexplained: to understand the extent of this phenomenon, it is worth noting that the standardized mortality rate for males in 1999–01 is equal to 13.92 per 10000 person-years, compared to a value of 6.96 for Italy in the 2000–2002 period.     

Circulation in Italy of β-lactamase-producing strains within the major groups of bacterial pathogens

A multicenter study was undertaken in Italy to assess the circulation of -lactamase-producing organisms and their current incidence within the major groups of bacterial pathogens. Almost four thousand strains, all freshly isolated from clinical material, were examined at four centers serving different areas of Italy. Despite some significant center-to-center differences, this survey documented the occurrence of a large overall circulation of -lactamase-producing organisms among clinical bacterial isolates. In particular, ampicillin resistance was recorded in one third to one half of the isolates of some Enterobacteriaceae, including Escherichia coli, Proteus, and Citrobacter species, and 80–90% of these resistant strains proved to be B-lactamase producers. Both ampicillin resistance and -lactamase production were almost the rule in other Enterobacteriaceae, including Klebsiella, Enterobacter, and Serratia species. -lactamase was also produced by about 80% of glucose-non-fermenting gram-negative bacteria and Aeromonas hydrophila strains, by all of the isolates of Branhamella catarrhalis manifesting ampicillin resistance (i.e. more than half the total number of isolates), and by about two thirds of the ampicillin-resistantffaemophilus strains (which accounted for 20–25% of all Haemophilus isolates examined). In contrast, no B-lactamase producers were observed among Neisseria gonorrhoeae isolates.     

Botulism surveillance in Italy: 1992–1996

Though a relatively rare disease, botulism can be a serious problem of public health, particularly when connected with the consumption of industrial canned food; moreover, in the last years the shortage of botulism antitoxin has caused some concern in the Public Health Authorities. This work presents the results of a five-year surveillance of botulism in Italy, with the distribution of the cases by Regions (first level administrative units which, in Italy, have administrative and legislative competencies in the sanitary field) and by vehicle of transmission. All the relevant and confirmed botulism outbreaks that occurred in the period under consideration are described.     

Invasive Salmonella enterica Serotype Typhimurium Infections,Democratic Republic of the Congo, 2007–2011

Infection with Salmonella enterica serotype Typhimurium sequence type (ST) 313 is associated with high rates of drug resistance, bloodstream infections, and death. To determine whether ST313 is dominant in the Democratic Republic of the Congo, we studied 180 isolates collected during 2007–2011; 96% belonged to CRISPOL type CT28, which is associated with ST313.     

Three-Year (1999–2002) of Epidemiological and Virological Surveillance of Influenza in North-East Italy

The results of the epidemiological and virological surveillance of influenza performed during the 1999/2000, 2000/2001 and 2001/2002 seasons in the northeastern Italy were presented and the relationship between age-specific morbidity rates and circulating strains were discussed.The epidemiological findings pointed out a change in age distribution. During the 1999/2000 season, characterized by a circulation of viruses antigenically close to the vaccine strain, a similar incidence rate in the 0-14 and 15-64-year-old groups was observed, while during the 2001/ 2002 winter the virus infected mostly children. During 2001/2002 season, B type viruses predominated with at least three distinguishable molecular variants. In particular, B/Victoria/2/87-like viruses re-emerged after more than a decade, and the antibodies elicited by the vaccine strain and by the strains circulating in previous seasons were poor or not protecting. The accumulation of susceptible subjects in young age group during the 1990s, due to the lack of circulation of B/Victoria/2/87-like viruses, was responsible for the unusual morbidity in the 0-14 year group. No circulation of B/Victoria/2/87-like viruses was observed in > 64-year-old group during 2001/2002 epidemic, probably due to a long-lasting immunity against viruses belonging to this lineage.     

Multiply Resistant (MR) Salmonella enterica Serotype Typhimurium DT 12 and DT 120: A Case of MR DT 104 in Disguise?

Multiresistant Salmonella enterica serotype Typhimurium definitive phage type (DT) 12 and DT 120 are more closely related to DT 104 than to non-multiresistant strains of their respective phage types. Multiresistant DT 12 and DT 120 appear to have arisen due to changes in phage susceptibility of DT 104 rather than horizontal transfer of resistance genes.     

Encephalitis Surveillance through the Emerging Infections Program, 1997–2010

Encephalitis is a devastating illness that commonly causes neurologic disability and has a case fatality rate >5% in the United States. An etiologic agent is identified in <50% of cases, making diagnosis challenging. The Centers for Disease Control and Prevention Emerging Infections Program (EIP) Encephalitis Project established syndromic surveillance for encephalitis in New York, California, and Tennessee, with the primary goal of increased identification of causative agents and secondary goals of improvements in treatment and outcome. The project represents the largest cohort of patients with encephalitis studied to date and has influenced case definition and diagnostic evaluation of this condition. Results of this project have provided insight into well-established causal pathogens and identified newer causes of infectious and autoimmune encephalitis. The recognition of a possible relationship between enterovirus D68 and acute flaccid paralysis with myelitis underscores the need for ongoing vigilance for emerging causes of neurologic disease.     

Salmonella enterica Serotype Enteritidis in French Polynesia,South Pacific, 2008–2013

Outbreaks of Salmonella enterica serotype Enteritidis infectionsassociated with eggs occurred in French Polynesia during 2008–2013. Molecularanalysis of isolates by using clustered regularly interspaced short palindromicrepeat polymorphisms and multilocus variable-number tandem-repeat analysis wasperformed. This subtyping made defining the epidemic strain, finding the source, anddecontaminating affected poultry flocks possible.     

Representativeness of Tuberculosis Genotyping Surveillance in the United States, 2009–2010

Genotyping of Mycobacterium tuberculosis isolates contributes to tuberculosis (TB) control through detection of possible outbreaks. However, 20% of U.S. cases do not have an isolate for testing, and 10% of cases with isolates do not have a genotype reported. TB outbreaks in populations with incomplete genotyping data might be missed by genotyping-based outbreak detection. Therefore, we assessed the representativeness of TB genotyping data by comparing characteristics of cases reported during January 1, 2009–December 31, 2010, that had a genotype result with those cases that did not. Of 22,476 cases, 14,922 (66%) had a genotype result. Cases without genotype results were more likely to be patients <19 years of age, with unknown HIV status, of female sex, U.S.-born, and with no recent history of homelessness or substance abuse. Although cases with a genotype result are largely representative of all reported U.S. TB cases, outbreak detection methods that rely solely on genotyping data may underestimate TB transmission among certain groups.Since 2004, the Centers for Disease Control and Prevention (CDC) has offered routine genetic characterization (i.e., genotyping) of all U.S. tuberculosis (TB) cases with Mycobacterium tuberculosis (M. tuberculosis) isolates.¹ Genotyping is a laboratory method used to determine the relatedness of isolates; although not a perfect measure of transmission,² this tool contributes to TB control in multiple ways. Genotyping data contribute to TB control, including the detection of genotype clusters that might represent remote or recent transmission (including outbreaks).^3–6 TB genotyping data are also important for defining the scope of outbreaks,⁷ monitoring outbreaks over time,⁸ distinguishing relapse from reinfection,⁹ detecting or confirming false-positive culture results,^10,11 confirming known epidemiologic links, and finding unknown links between cases.^3,4,12 The utility of genotyping is limited in populations for which few cases are genotyped, because potential transmission relationships between cases might be missed. TB genotyping is most effective when data are representative of the entire population of TB cases.^13–15Applying TB genotyping data to TB control requires that an isolate be submitted for genotyping and that the genotyping result be linked to the patient''s demographic and clinical information. While some states have independent systems for generating and linking genotyping data, most states rely on the national CDC-funded system. In this system, an isolate is submitted for genotyping to the CDC-funded national genotyping laboratory, and genotyping results are linked to the patient''s demographic and clinical data, which are reported to the National Tuberculosis Surveillance System (NTSS).¹⁶ This linkage is facilitated by a CDC-developed and -funded national Web-based genotyping database, which includes both NTSS and genotyping data.First, specimens are collected from a suspected TB patient. Specimens are generally sent to a jurisdictional public health laboratory for culturing and processing and, when a specimen yields a culture that is positive for M. tuberculosis, an isolate is sent to the national genotyping laboratory. In some cases, a viable culture might not be available to be submitted for genotyping. In other cases, a viable culture might be available but not submitted to the genotyping laboratory. These latter cases represent a missed opportunity for genotyping. Although it is not possible to determine whether or not a viable culture was available for submission from nationally reported data, we can use the presence of drug susceptibility testing (DST) results, testing that requires a viable culture, to identify cases for which a viable culture was likely available to be submitted for genotyping.Once the isolate is genotyped, the result is entered into the national Web-based genotyping database. In parallel with this process, the patient''s demographic and clinical data are submitted to jurisdictional public health authorities for reporting to NTSS; these data are then uploaded into the national Web-based genotyping database. The state TB program is responsible for the critical step of linking the surveillance report to the genotyping result, using a state-assigned identification number. Failure to link the genotyping and surveillance records will result in the case appearing to have not been genotyped. Because surveillance and genotyping data are linked by the state, it is not possible at CDC to distinguish between cases that have not been genotyped and cases that have been genotyped but not linked.National TB genotyping coverage is defined as the proportion of TB cases with a culture yielding M. tuberculosis (referred to as “culture-positive cases”) that are linked to a genotype result in the national Web-based genotyping database. In 2010, national genotyping coverage was 88%. However, approximately 20% of TB cases in the United States are not culture positive and, therefore, do not have an isolate available for genotyping.¹⁷ A case could be missing a genotype result for three general reasons: it did not have an M. tuberculosis isolate, it had an isolate that was not genotyped, or the genotyping result was not linked to NTSS data in the national Web-based genotyping database. Our aim was to characterize cases that did not have a genotype result for any of these reasons to identify populations in which outbreaks might be missed by genotype-based outbreak detection methods, and to identify opportunities to increase genotyping.     

Prevalence of antimicrobial resistant Streptococcus pneumoniae serotype 11A isolates in Korea,during 2004–2013, due to the increase of multidrug-resistant clone,CC166

Since the introduction of the pneumococcal conjugate vaccine (PCV7) in Korea in 2003, the proportion of non-vaccine serotypes has increased. Among non-vaccine serotypes, serotype 11A is highly prevalent in Korea. We investigated the prevalence and characteristics of Streptococcus pneumoniae serotype 11A isolates in a Korean tertiary-care hospital, during 2004–2013. A total of 1579 non-duplicate clinical S. pneumoniae isolates, collected from 2004 to 2013, were included in this study. Serotype was determined by the capsular Quellung method, and in vitro susceptibility testing was performed by broth microdilution method. Multilocus sequence typing was performed to determine the genotypes of the S. pneumoniae isolates. We identified 90 serotype 11A isolates (5.7%). During this period, the proportion of serotype 11A has increased from 3.2% up to 13.2% (in 2012). Among the serotype 11A isolates, two main clonal complexes (CCs), CC166 and CC99, were identified. The increase of serotype 11A was mainly due to the increase of CC166 isolates, which have high antimicrobial resistance rates. In addition, we identified that 14 isolates, belonging to ST8279, ST9875, and ST3598 of CC166, were non-susceptible to all antimicrobial agents tested in this study. We identified the increase of S. pneumoniae serotype 11A in Korea, which mainly due to the expansion of a resistant clonal group, CC166.     

Molecular analysis and genotyping of pathogenicity locus in Clostridioides difficile strains isolated from patients in Tehran hospitals during the years 2007–2010

Background & AimsClostridioides difficile (C. difficile) has been identified as the leading cause of antibiotic associated diarrhea (AAD). Co-carriage of an intact pathogenicity locus (PaLoc) with binary toxin genes in C. difficile strains seems to be linked with severe disease outcomes in the infected patients. Epidemiology of C. difficile infection (CDI) in hospital setting and knowledge about their genetic context help us to decrease the morbidity, mortality, and costs associated with Clostridioides difficile infection. In the present study was aimed to characterize genetic diversity of PaLoc among different C. difficile strains isolated from hospitalized patients and carriage of cytolethal distending toxin gene (cdt) in different hospitals.MethodC. difficile strains were isolated from stool samples of inpatients referred to a reference laboratory from different hospitals and also outpatients with diarrhea, during 2008–2011. DNA was extracted from pure culture of the bacterium and PCR was performed for tcdA, tcdB, tcdE, tcdC, tcdD, and cdu2 genes. Carriage of two binary toxin genes cdtA, cdtB was also determined in these strains. To find clonal strains, similarity of genotypes and integrity of PaLoc among the isolates was compared in each hospital.ResultsThe intact PaLoc was found most frequently among the isolates in the outpatients (19/51, 37.2%, Group I), while incomplete PaLoc found mostly in patients who were hospitalized in the infectious diseases and internal diagnosis wards. tcdA and tcdB genes were detected in different combinations among the studied strains. These strains showed tcdA⁺B⁺, tcdA⁺B⁻, and tcdA⁻B⁺ genotypes in a frequency of 76.4% (39/51), 7.8% (4/51), and 17.6% (9/51), respectively. Analysis of gene composition of the PaLoc showed 19 distinct genotypes among the 51 strains. Accordingly, 38 strains were classified mainly into 6 regular groups, while the remaining strains showed heterogeneous patterns. tcdC⁻/tcdD⁻ constituted the most common genotypic group among the strains with partial PaLoc (7/51, 13.7%). A hypertoxigenic genotype, tcdC⁻/tcdA⁺/tcdB⁺, was detected in 2 strains (2/51, 3.9%). The intact genotype was also detected in a C. difficile isolate from outpatients. Cdt encoding genes toxins was observed in low numbers of the strains (7/52, 13.5%). All of cdtA⁺B⁺ strains were belonged to PaLoc group 1 (intact genotype). Statistical analyses showed no correlation between particular genotypes and special wards of the hospitals (p value>0.05).ConclusionCollectively, our results showed diversity of C. difficile strains in most wards of the studied hospitals. Diversity of PaLoc genotypes in the strains that isolated from the same wards proposed endogenous routes of the infection, as common cause of CDI in these patients.     

Genetic diversity and molecular evolution of human adenovirus serotype 41 strains circulating in Beijing,China, during 2010–2019

Human adenovirus serotype 41 (HAdV-F41) is an important pathogen that causes diarrhea in children. However, the data on its molecular genetic characteristics and evolutionary history are still neither comprehensive nor sufficient. Four capsid protein genes from 58 HAdV-F41-positive specimens taken from diarrheal children in Beijing during 2010–2019 were amplified and analyzed. Variant amino acids in the hexon gene (18 sites) and short fiber gene (4 sites) clustered these strains into two clades and four subclades. The deletion of 15 amino acids found in the gene seemed to have little effect on the genomic strain cluster same as to penton gene. The HAdV-F41 strains had high diversity, as assessed from the intraspecific recombination of hexon, short fiber and long fiber. The molecular evolutionary rate of HAdV-F41's concatenated genes was 4.07 × 10⁻⁵ substitutions/site/year, and it diverged from the most recent common ancestor in 1720. Apart from in the penton gene, positive selection codons were predicted in the other three genes, which may play a synergistic role in the evolution of HAdV-F41. These results provide new insights for understanding the characteristics of infectivity and developing vectors and vaccine vehicles for HAdV-F41.     

Rapid Emergence and Clonal Dissemination of CTX-M-15–Producing Salmonella enterica Serotype Virchow,South Korea

The prevalence of cefotaxime-resistant Salmonella enterica serotype Virchow has dramatically increased in South Korea since the first isolation in 2011. Of 68 isolates collected over 10 years, 28 cefotaxime-resistant isolates harbored the bla_CTX-M-15 extended-spectrum β-lactamase gene and were closely related genetically, demonstrating the clonal dissemination of CTX-M-15–producing Salmonella Virchow in South Korea.     

Surveillance results of nosocomial infections of the ICU in Kenézy Hospital, based on two years data

INTRODUCTION: According to data in the literature, the number of nosocomial infections in the ICU is far higher than in non-ICU patients. As a result of improving lifesaving technologies, the risk of nosocomial infections increases in ICUs. Utilization of epidemiological methods is recommended for the detection and follow up of nosocomial infections. Aims: Prospective surveillance to assess the epidemiology of nosocomial infections in an ICU. METHODS: Kenézy Hospital is a country hospital with 1637 beds and a 16-bed central ICU. During the investigated period (01. 04. 2004-31. 03. 2006) 1490 patients, with a total 8058 ICU days, were hospitalised in the mixed medical-surgical ICU. The commonest primary diagnosis were respiratory failure, multiple trauma and head injury. Surveillance was performed by a trained infection control nurse and was supervised by an infection control physician and infectious disease physician. CDC definitions were used to define nosocomial infections. RESULTS: A total of 194 nosocomial infections in 134 patients were detected during the study period. The overall incidence and incidence density of nosocomial infections were 13.0 per 100 patients and 24.0 per 1000 patient-days. Respiratory tract infections (44.3%) were the most frequent nosocomial infection, followed by urinary tract (21.1%) and bloodstream infections (20.1%). CONCLUSIONS: Nosocomial surveillance is useful in detecting nosocomial infections in ICU. A multidisciplinary approach and partnership between the physicians and infection control nurses is needed. Patient-to-nurse ratio is an independent risk factor for nosocomial infections in intensive care, this must be kept in mind when planning rationalization of the number of nursing staff.