Molecular Epidemiological Characteristics Research Articles

Prevalence and molecular-genetic characteristics of hepatitis B virus in HIV-positive individuals at the Far Eastern Federal District

Current study was aimed at investigating prevalence of overt and occult hepatitis B infection in HIV-positive individuals as well as molecular-epidemiological characteristics of the circulating hepatitis B virus (HBV) strains in the Far Eastern Federal District (FEFD). A total number of 297 blood serum/plasma samples obtained from HIV-positive patients residing in the FEFD were enrolled in the study. The first control group included 351 blood serum/plasma samples of general population without indication on HIV and HBV-infection that underwent laboratory check up at the Centers for AIDS Prevention and Control. After evaluating the group of HIV-positive patients 20 HIV-HBV positive samples were selected for further detailed analysis. The second control group included 43 patients with chronic hepatitis B. All groups were age and gender-matched. The research included serological and molecular-genetic (real-time PCR, positive for HBV DNA samples underwent clonal sequencing of PCR-amplified HBV P/S gene) assessment of the biological material followed by a phylogenetic analysis of the HBV sequences. Our research revealed that HIV-positive patients are exposed to a higher risk of HBV infection compared to general population enrolled in the study, which is evident from the prevalence of anti-HBcAg antibodies in the groups examined. HIV-positive vs. first control group was positive for anti-HBcAg antibodies at higher rate (35.02%, CI 95: 29.5940.45% versus 22.22%, CI 95: 17.8726.57%, p = 0.0003). Abundance of ongoing HBV-infection markers was also higher in HIV-positive individuals compared to general population (6.73%, CI 95: 3.889.58% versus 0.85%, CI 95: 01.81%, p = 0.0001, respectively). Should be noted, that HBsAg-negative HBV infection in HIV-positive patient cohort comprised 1.01% (CI 95: 02.15%) whereas in general population this index was as low as 0.28% (CI 95: 00.84%). Virus hepatitis С and D were revealed at higher rate in HIV-positive individuals compared to patients with HIV-negative chronic HBV infection (p = 5.84 107 and p = 0.000001 respectively). HCV and HDV prevalence rates comprised 50.0% (CI 95: 27.4677.46%) and 40.0% (CI 95: 17.9762.03%) in HIV-positive patients. Similar indices in control group were 4.65% (CI 95: 010.94%) and 4.65% (CI 95: 010.94%), respectively. The phylogenetic analysis of the six isolated HBV sequences showed that the five samples belonged to genotype D, with dominant subtype D2 (verified in 4 cases). Further, HBV genotype С was detected only in one case. The obtained data indicate a necessity for further in-depth diagnostic examination of viral hepatitis in HIV-positive patients to lower a risk of developing life-threatening complications as well as preventing hepatitis spread in human population.

Molecular epidemiology survey and characterization of human influenza A viruses circulating among Palestinians in East Jerusalem and the West Bank in 2015.

Frequent typing and molecular characterization of influenza A (IAV) strains are crucial for the identification of circulating subtypes and for the selection of the subtypes’ lineages to be included in the annually prepared vaccine cocktail. We investigated IAV sampled from an underrepresented population from Palestine. 200 nasopharyngeal aspirates (NPA) were collected between February and May of 2015 from Palestinians in East Jerusalem and the West Bank suffering from mild to severe symptoms of upper respiratory infections. NPA were screened for the presence of IAV using RT-PCR. Epidemiological data, hemagglutinin (HA) and neuraminidase (NA) gene sequences were analyzed in IAV positive samples. 50 samples tested positive for IAV; 48% of which were identified as A(H1N1)pdm09 and 52% as A(H3N2), respectively. Infection with A(H1N1)pdm09 occurred mainly in April, while A(H3N2) infections were mainly detected in March. Most IAV infections in 6-year-olds and below were attributed to subtype A(H3N2), while A(H1N1)pdm09 was responsible for most infections in adults above 18-year-olds. Analyses of HA and NA amino acid sequences revealed numerous substitutions. Thereafter, and based on the HA analysis, the Palestinian A(H1N1)pdm09 isolates fell into clade 6B, while the A(H3N2) isolates fell into clades 3C.2 and 3C.3, respectively. This study is significant in providing the first insight into the epidemiology and genetic properties of IAV circulating in Palestine. In contrast to international reports for the same season, A(H3N2) was not the dominant subtype as in northern hemisphere, nor was A(H1N1)pdm09 as in WHO reports for the Middle East, however genetic properties of Palestinian A(H3N2) and A(H1N1)pdm09 were in line with global isolates.

Molecular epidemiology and antibiotic resistance of Burkholderia pseudomallei isolates from Hainan, China: A STROBE compliant observational study.

Burkholderia pseudomallei is the causative agent of meliodosis, and the cases in China are gradually increasing. The present retrospective study aimed to surveil the molecular epidemiological characteristics and antibiotic resistance of B pseudomallei isolates. B pseudomallei strains were isolated and verified from meliodosis patients with relevant epidemiological information from 2004 to 2016 in Hainan, China. Pulsed-field gel electrophoresis based on Spe I digestion was carried out, and antimicrobial resistance of B pseudomallei strains was observed against 9 frequently-used antimicrobials. A total of 164 B pseudomallei isolates were successfully divided into 60 pulsed-field gel electrophoresis (PFGE) patterns, including 33 clusters and 27 single types, at an 85% similarity level. The isolates also exhibited a high level of ceftazidime resistance rate (12.8%, 21/164). B pseudomallei strains were mainly heterogenous with no predominant type, but there were some clonal populations, dominate clusters prevalent and the resistance rates of cephems antimicrobial increased significantly between 2004 and 2016 along with the number of melioidosis cases collected in Hainan (cefoperazone-sulbactam [SCF], rs = 0.96, P = .04; ceftazidime [CAZ], rs = 0.98, P = .01). In conclusion, this study will help to enhance our understanding of molecular characteristics and antibiotic resistance of B pseudomallei.

Next-generation sequencing improves molecular epidemiological characterization of thalassemia in Chenzhou Region, P.R. China.

ObjectivesThalassemia is a highly prevalent monogenic inherited disease in southern China. It is important to collect epidemiological data comprehensively for proper prevention and treatment.MethodsIn this study, blood samples collected from 15 807 residents of Chenzhou were primarily screened by hematological tests. A total of 3973 samples of suspected thalassemia carriers were further characterized by combined next‐generation sequencing (NGS) and Gap‐PCR.ResultsIn total, 1704 subjects were diagnosed as thalassemia carriers with a total prevalence rate of 10.78%, including 943 α‐thalassemia carriers, 708 β‐thalassemia carriers, and 53 composite α and β‐thalassemia carriers. The prevalence rates of α‐thalassemia, β‐thalassemia, and composite α and β‐thalassemia were 5.97%, 4.48%, and 0.34%, respectively. Meanwhile, we characterized 19 α‐thalassemia variations and 21 β‐thalassemia variations in thalassemia carriers. Approximately 2.88% of thalassemia carriers would be missed by traditional genetic analysis. In addition, four novel thalassemia mutations and one novel abnormal hemoglobin mutation were identified.ConclusionsOur data suggest a high prevalence of thalassemia and a diverse spectrum of thalassemia‐associated variations in Chenzhou. Also, combined NGS and Gap‐PCR is an effective thalassemia screening method. Our findings might be helpful for prevention and treatment of thalassemia in this region.

Staphylococcus aureus carriage in older populations in community residential care homes: Prevalence and molecular characterization of MRSA isolates

IntroductionThe epidemiology of S. aureus depends on conditions in specific populations. Few studies of S. aureus colonization in the older population have been performed in Spain. The aim of this study was to determine the prevalence of methicillin-resistant S. aureus (MRSA) colonization and its molecular epidemiological characteristics in an institutionalized population in community residential care homes in Cadiz, Spain. MethodsA cross-sectional epidemiological study was conducted in three residential care homes for older people. Axilla and nostril samples were tested. Identification of S. aureus and antimicrobial susceptibility testing were by MALDI-TOF and MicroScan panels. MRSA strains were subjected to SCCmec typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). The presence of Panton–Valentine leukocidin (PVL) genes was determined by PCR in all S. aureus strains. ResultsA total of 293 residents were included. Fifty-one residents (17.4%) were colonized with methicillin-sensitive S. aureus (MSSA) and 11 (3.8%) with MRSA. Resistance to at least two aminoglycosides was observed in 25.4% of MSSA and 90.9% and of MRSA isolates, and resistance to levofloxacin in 80.3% of MSSA and 100% of MRSA isolates. SCCmecIV was detected in all isolates and all except one (ST-125) were ST-8. None of the S. aureus isolates were positive for PVL. ConclusionsA low rate of S. aureus carriage was detected and the prevalence of MRSA was very low. ST8-MRSA-IVc was the dominant clone, and only one strain belonged to ST125-MRSA-IVc. We found MRSA transmission within the residential care homes and a very high rate of quinolone resistance in MSSA and MRSA.

Emergence of Haemophilus influenzae with low susceptibility to quinolones and persistence in tosufloxacin treatment.

The use of non-β-lactam agents has increased in Japan due to the prevalence of β-lactam-resistant pathogens. This study aimed to clarify the recent trend of antimicrobial susceptibility and molecular epidemiological features in Haemophilus influenzae. Fifty-seven Haemophilus influenzae isolated from a Japanese teaching hospital in 2017 were characterised, and the data were compared with those of a previous study. The MICs were determined using the broth dilution method. Genetic backgrounds were compared by multilocus sequence typing. The bactericidal activity of tosufloxacin at, or near, the therapeutic Cmax was determined in vitro, with susceptible isolates and quinolone low-susceptible isolates by time-kill assay. The results of the susceptibility tests showed that >90% of isolates were susceptible to cephalosporins and carbapenems, whereas ampicillin-susceptible and clarithromycin-susceptible isolates decreased. Regarding quinolones, low-susceptible isolates were noted in 2017, although all isolates were judged as susceptible. All low-susceptible isolates had an amino acid substitution in GyrA, and two isolates had an additional substitution in ParC. These isolates had different genetic backgrounds. Furthermore, the time-kill kinetic assay using the Cmax of tosufloxacin indicated that the low-susceptible isolates could persist for at least 8hours. This study revealed that Haemophilus influenzae has demonstrated multidrug low-susceptibility in recent years. The low-susceptible isolates had genetic diversity, meaning that resistance occurred independently.

Molecular Epidemiology of Echovirus 18 Circulating in Mainland China from 2015 to 2016.

Echovirus 18 (E18), a serotype of Enterovirus B (EV-B) species, is an important pathogen in aseptic meningitis. E18 had rarely been detected in mainland China, but became the predominant pathogen associated with viral encephalitis (VE) and meningitis in Hebei province for the first time in 2015. To investigate the molecular epidemiology and genetic characteristics of E18 in mainland China, sixteen E18 strains from patient throat swabs with hand, foot, and mouth disease (HFMD) in six provinces in China collected between 2015 and 2016, and four E18 strains isolated from 18 patient cerebrospinal fluid specimens with VE in Hebei Province in 2015 were obtained and sequenced. Combined with the sequences from the GenBank database, we performed an extensive genetic analysis. Phylogenetic analysis of VP1 gene sequences revealed that all E18 strains from mainland China after 2015 belonged to subgenotype C2. There were no obvious specific differences in phylogenetic and variation analyses of E18 genome sequences between HFMD and VE/meningitis strains. Potential multiple recombination may have occurred in the 5'-untranslated region and in the P2 and P3 nonstructural protein-encoding regions of E18 strains from China. The current E18 strains were potential multiple-recombinant viruses. Overall, these findings supported that E18 caused HFMD, VE, and meningitis, although there were no significant associations between clinical features and viral genomic characteristics.

Novel variant strains of infectious bursal disease virus isolated in China

Infectious bursal disease (IBD) is one of the most important immunosuppressive diseases that seriously threaten poultry farming and food safety worldwide. The variant strain of infectious bursal disease virus (IBDV) has been greatly neglected for more than 30 years. Recently, the subclinical infection of suspected IBD, causing considerable economic losses, occurred in the main chicken-farming regions of China. Through RT-PCR, sequencing, and phylogenic analyses, novel variant IBDVs were first identified in six provinces of eastern China. Immunological detection further confirmed the antigenic variation of the Chinese variant IBDVs. The Chinese IBDV variants were obviously different from the American IBDV variants, with less than a 97.7% (VP1) or 98.7% (VP2) amino acid sequence identity. Animal experiments further confirmed the serious threat of the variant IBDVs to chickens, demonstrating irreversible damage to the central immune organ, obvious immunosuppression, and growth retardation. This study not only identified the pandemic nature of the novel variant IBDVs for the first time but also discovered the distinct molecular epidemiological characteristics of these viruses, which will contribute more to the control of the disease.

Molecular surveillance of antimicrobial resistance and transmission pattern of Mycobacterium leprae in Chinese leprosy patients

ABSTRACT Reports on antimicrobial resistance (AMR) of Mycobacterium leprae, relationship with bacteriological index (BI), and transmission in China are limited. We investigated the emergence of AMR mutations, the relationship between BI and AMR in complete, moderate and lack of BI decline cases, and molecular epidemiological features of AMR cases by enrolling 290 leprosy cases from four endemic provinces. Seven (2.41%), one (0.34%), five (1.72%), one (0.34%), and one (0.34%) strains had single mutations in folP1, rpoC, gyrA, gyrB, and 23S rRNA, respectively. Double mutations in folP1 and gyrA, rpoB and gyrA, and gyrA and 23S rRNA were observed in one (0.34%) strain each. Mutated strains occurred in three out of 81 (95% CI−0.005-0.079, p = 0.083) cases with complete BI decline, in seven out of 103 (95% CI 0.018-0.117, p = 0.008) cases with moderate BI decline, and in four out of 34 (95% CI 0.003-0.231, p = 0.044) cases with lack of BI decline. Most of these mutated strains were geographically separated and diverged genotypically. AMR mutations may not be the main cause of the lack of BI decline. The low transmission of AMR strains at the county level indicates an ongoing transmission at close contact levels.

Molecular epidemiological characteristics of Brucella spp. isolated from human and animal brucellosis

Brucellosis is the most common zoonotic disease in the Mediterranean region where Turkey is located. Therefore, particularly in this region, it is crucial to follow molecular surveillance methods for the control and eradication of this disease agent, which threatens both human and animal life. We have conducted a molecular-based surveillance study for detecting the origin of the possible reservoir in human brucellosis and transmission of Brucella spp. between humans and ruminants. For the detection of clonal relationships, we isolated Brucella spp. from human and ruminants diagnosed with brucellosis and evaluated them by PFGE and MLVA methods. We found 10 subclusters in PFGE and 22 subclusters in MLVA-16. Human and ruminant isolates were found to co-exist in MLVA-16-m1 and PFGE-a8, a9, a10 subcluster by both methods. In conclusion, the results revealed that these subcluster isolates that co-exist some ruminant and human isolates can be more effective in infecting humans.

Emergence and molecular characterization of multidrug-resistant Klebsiella pneumoniae isolates harboring bla CTX-M-15 extended-spectrum β-lactamases causing ventilator-associated pneumonia in China.

BackgroundVentilator-associated pneumonia (VAP) is a common nosocomial infection associated with high morbidity due to multidrug-resistant (MDR) pathogens. The purpose of this study was to determine the occurrence of extended-spectrum β-lactamase (ESBL) genes, especially blaCTX-M-15, in Klebsiella pneumoniae (K. pneumoniae)-associated VAP and to investigate the antimicrobial resistance patterns and molecular epidemiological characteristics of K. pneumoniae strains.Materials and methodsFrom January 2013 to December 2015, we retrospectively collected 89 VAP-causing K. pneumoniae isolates from tertiary-care hospitals in China, among which ESBL-producing strains were assessed for antimicrobial susceptibility. Several antibiotic resistance genes of clinical relevance in K. pneumonia isolates producing ESBL were investigated. Polymerase chain reaction (PCR) and DNA sequencing were employed to characterize the genetic contexts of blaCTX-M-15. Conjugative plasmids carrying blaCTX-M-15 were obtained by mating and further subjected to replicon typing. The genetic relatedness of isolates was assessed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing.ResultsAll of the 30 ESBL-producing isolates identified displayed MDR phenotype, with blaSHV, blaCTX-M, blaOXA, and blaTEM detected in 21, 21, 1, and 20 isolates, respectively. blaCTX-M-15 was the most prevalent ESBL gene (19/30, 63.33%), and ISEcp1 was detected 48 bp upstream of 15 blaCTX-M-15 genes. Based on S1-PFGE analyses, 25 isolates exhibited different plasmid profiles, ranging from ~70 to 320 kb. The blaCTX-M-15 with blaTEM and qnr genes and the ISEcp1 element from eight isolates were co-transferrable to recipients via conjugation, with IncFIB, IncFIC, and IncFII being the most prevalent replicons. Twenty different PFGE patterns and 11 sequence types were identified, with ST304 being dominant.ConclusionThis work reports the emergence of blaCTX-M-15 in K. pneumoniae-induced VAP in China. We showed that IncFIB, IncFIC, and/or IncFII plasmids carrying blaCTX-M-15 with blaTEM, qnr resistance genes, and the ISEcp1 element mediate the local prevalence in K. pneumoniae-associated VAP.

1489. Trends in Antimicrobial Resistance in N. gonorrhoeae Isolated in Korea During 2015–2017

BackgroundThe trends of antimicrobial resistance (AMR) and the molecular epidemiology of gonococcal strains were analyzed in Korean during 2015 to 2017.MethodsThe susceptibility tests of 187 N. gonorrhoeae isolates were investigated. The minimum inhibitory concentration (MIC) of N. gonorrhoeae isolates were determined by the agar dilution method. Penicillinase-producing N. gonorrhoeae (PPNG) and plasmid-mediated tetracycline-resistant N. gonorrhoeae (TRNG) were evaluated. Isolates were tested for mutations in penA and also genotyped using N. gonorrhoeae multi-antigen sequence typing (NG-MAST) to determine the molecular epidemiological characteristics of the isolates.ResultsThe rates of resistance to ceftriaxone (CRO) increased from 6.5% in 2015 to 13.4% in 2017. Azithromycin resistance was documented only in 1.1%, but 53.5% of isolates showed intermediate susceptibility. All isolates were susceptible to spectinomycin. However, none of isolates was susceptible to ciprofloxacin and penicillin (PEN) and 4.3% of isolates were susceptible to tetracycline. The PPNG and TRNG increased from 25.7% and 39.4% in 2015 to 47.8% and 81.5% in 2017, respectively. 74.7% of the extended-spectrum cephalosporins (ESCs)-resistant isolates contained the mosaic PBP2 X allele, which has been previously associated with ESC resistance including treatment failures. penA mosaic alleles X were found in 83.8% of all isolates that harbored decreased susceptibility to cefixime. Among the 16 N. gonorrhoeae isolates with decreased susceptibility to CRO, penA mosaic X allele was identified in the 11 isolates. The 189 N. gonorrhoeae isolates were assigned to 112 different NG-MASTs; seven sequence types (STs) were novel. The most common ST was 10,668 (16.1%), followed by ST15024 (7.1%). Two ST1407 strains have been isolated in 2015. Although ST1407 was known to display decreased susceptibility to ESCs or full resistance, they were susceptible for CRO (MIC = 0.06 μg/mL) and cefixime (MIC = 0.12 μg/mL).ConclusionThe recent emergence of ESC-resistant N. gonorrhoeae strains which was often associated with mutations in the penA gene is a major concern and enhanced AMR surveillance is necessary to prevent transmission of these strains.Disclosures All authors: No reported disclosures.

Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF80_0107) Among Men Who Have Sex with Men in China.

Since the emergence of CRF55_01B among men who have sex with men (MSM) group in China, more and more circulating recombinant forms (CRFs) and unique recombinant forms have been identified in the population in China. Here we characterize a novel CRF (CRF80_0107) consisted of CRF01_AE and CRF07_BC segments from three epidemiologically unlinked MSM. Two near full-length genome (NFLG) sequences were amplified and sequenced in two halves with RNA extracted from the plasma of two MSM in Beijing. Another gag-pol sequence was obtained from Los Alamos HIV Sequence Database with accession number KX198573, which was isolated from a man who has sex with men in Hebei province. Phylogenetic analysis based on NFLG sequences revealed that CRF80_0107 formed a monophyletic cluster with high bootstrap value of 100%. Recombination analysis demonstrated that the genome of CRF80_0107 was separated into eight segments by seven breakpoints. The subregion trees constructed by neighbor-joining method confirmed that those segments were originated from CRF01_AE and CRF07_BC strains circulating among MSM group in China. The emergence of CRF80_0107 indicates the frequent generation of novel recombinant forms and the increasing complication of HIV-1 epidemic among MSM group in China. This highlighted the importance of monitoring HIV-1 molecular epidemiological characteristics and the urgency for reducing HIV-1 epidemic among MSM in China.

Epidemiological study of carbapenem-resistant Klebsiella pneumoniae

BackgroundThis research is aimed to study the resistance and molecular epidemiological characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP).Methodology38 isolated CRKP strains were collected from clinical specimens.ResultsThe resistance rates were more than 70.0%. Ampicillin had the highest rates among them (100.0%). 34 strains (89.5%) among the 38 CRKP strains carried blaKPC-2 gene, and 3 strains (7.9%) carried blaIMP-4 gene. 36 strains (94.7%) among the 38 CRKP strains carried blaSHV gene, 29 strains (76.3%) carried blaTEM gene, and 26 strains (68.4%) carried blaCT-M gene. 7 strains (18.4%) among the 38 CRKP strains carried blaDHA-1 gene. 15 strains (39.5%) in 38 CRKP strains lost two fenestra proteins, ompK35 and ompK36, and the rest 23 strains carried ompK36 genes. 38 CRKP strains were divided into five kinds of ST types, with ST11 type as the most (86.8%, 33/38). The rest of the ST types included 2 strains of ST23 (5.3%, 2/38), one strain of ST15, ST1373 and ST1415 (2.6%, 1/38).ConclusionsCRKP resistance is severe, and the mechanism of drug resistance has become increasingly complex. Various ST types and resistance genes are related to CRKP. The clinical prevention and control work is imminent.

Analysis of Glucose-6-Phosphate Dehydrogenase Genetic Polymorphism in the Hakka Population in Southern China.

BackgroundIn southern China, glucose-6-phosphate dehydrogenase (G6PD) deficiency is a significant health problem. The aim of this study was to investigate the molecular epidemiological characteristic of the G6PD gene among Chinese Hakka in southern Guangdong province.Material/MethodsWe screened 611 unrelated subjects for G6PD genetic polymorphism analyzed by a gene chip analysis for common Chinese G6PD mutations. G-6-PD enzyme activity was determined by use of the G-6-PD quantitative detection kit.ResultsSeven mutation sites were detected from subjects in our study. G6PD Canton (c.1376 G→T)(33.06%), G6PD Kaiping (c.1388 G→A)(30.67%), and polymorphism (c.1311 C→T)(25.89%) account for 89.62% of mutations, followed by G6PD Gaohe (c.95 A→G)(5.97%), G6PD Chinese-5 (c.1024 C→T)(3.58%), G6PD Maewo (c.1360 C→T)(0.39%), and G6PD Viangchan (c.871G→A)(0.39%).ConclusionsWe studied the genetic polymorphisms and frequencies of G6PD gene in the Hakka population of Meizhou. Our results coincide with the results among the Chinese Jiangxi Hakka population. It was consistent with previous research reports on Chinese people. There were differences in the results of reports from some other Asian populations. Our results could be useful for future prevention and control of G6PD deficiency aimed at the Chinese Hakka population.

Resistance phenotype and clinical molecular epidemiology of carbapenem-resistant <em>Klebsiella pneumoniae</em> among pediatric patients in Shanghai

BackgroundCarbapenem-resistant Klebsiella pneumoniae (CRKP) has caused wide global disseminations and serious clinical outcomes in pediatric patients, and the purpose of this study was to analyze drug resistance, molecular epidemiology, and clinical characteristics of CRKP from children in Shanghai, China.MethodsA retrospective study was conducted from January 2016 to December 2017, and a total of 170 CRKP isolates were collected. Antimicrobial susceptibility was determined by the broth microdilution method. MAST D73C and polymerase chain reaction were used for the analysis of carbapenemase types. Multilocus sequence typing of K. pneumoniae was performed for genetic relationship. Clinical data were also reviewed.ResultsOf the 170 CRKP isolates, blaOXA-232 was mainly detected with a proportion of 42.35%, followed by blaNDM-1 (20.59%), blaKPC-2 (17.65%), blaNDM-5 (16.47%), and blaIMP-4 (1.18%). The predominant gene was blaOXA-232 in 2016 (54.46%; 55/101) and blaNDM-1 in 2017 (31.88%; 22/69). All these 170 CRKP isolates showed high resistance to cephalosporins and carbapenems (>95%), except for tigecycline and colistin. Sixteen distinct sequence types were observed with ST15 being mostly identified (41.76%). Most CRKP harboring OXA-232 type carbapenemase belonged to ST15, while NDM-1 type belonged to ST37 and KPC-2 type belonged to ST11. Furthermore, other β-lactamase genes including blaTEM, blaCTX-M, and DHA-1 were also found in this study. Clinical data reviewed that more than half of the patients produced clinical infections (112/170), mainly lower respiratory tract (58/112) and bloodstream (21/112) infections. A majority of these children had received therapy of antibiotics before CRKP isolation, especially for carbapenems (76/170) and β-lactam/β-lactamase inhibitor combinations (91/170).ConclusionsOur data revealed the increasing incidence of OXA-232-producing K. pneumoniae from pediatric patients in Shanghai, and infection control measures should be conducted to limit the spread of CRKP strains.

Molecular epidemiology of Klebsiella pneumoniae blaKPC gene in Lishui from 2010 to 2016

Objective To investigate the distribution of blaKPC gene in Lishui and to analyze the molecular epidemiological characteristics of Klebsiella pneumoniae (K.pneumoniae) blaKPC gene. Methods From 2010 to 2016, all of the non-repetitive K. pneumoniae carbapenemase (KPC)-producing isolates in Lishui Municipal Central Hospital were collected. They were identified with VITEK 2 Compact system and typed by multilocus sequence typing (MLST). Plasmids were classified based on the DNA sequences of replication initiators. Transposons were detected by PCR. Locations of blaKPC gene were verified through complete sequencing of the plasmids by next-generation sequencing (NGS). Results A total of 125 strains were collected. K. pneumoniae strains accounted for 88.8% (111) and among them, 103 were ST11 type. IncF plasmids were detected in 48.6% of K. pneumoniae strains and most of them carried mutant Tn1721/Tn4401 chimera (48/54 isolates). Untypable plasmids were discovered in 50.5% of isolated strains and most of them were positive for the wild-type chimera (54/56 isolates). IncF-positive strains isolated during the period of 2011 and 2013 accounted for 94.4%, followed by a dramatic decrease. However, 76.8% of the strains harboring untypable plasmids were isolated from 2014 to 2016 and the number increased year by year. Conclusion K. pneumoniae of ST11 type was the main cause of blaKPC gene dissemination in Lishui area. Strains carrying the IncF plasmids integrated with the mutant Tn1721/Tn4401 chimera and the untypable plasmids with the wild-type chimera were prevalent before and after 2014, respectively. Key words: Klebsiella pneumoniae; blaKPC gene; Molecular epidemiology; Plasmid; Transposon

Correlation between restriction endonuclease analysis and PCR ribotyping for the identification of Clostridioides (Clostridium) difficile clinical strains

Restriction endonuclease analysis (REA) and PCR ribotyping are two typing systems that have been frequently utilized for molecular epidemiologic characterization of Clostridioides (Clostridium) difficile. To correlate typing data obtained from each method, we performed both REA and PCR ribotyping on a large and diverse set of historical and contemporary C. difficile infection clinical isolates. Eighty isolates were selected from each reference laboratory in the United States (Microbiology Reference Laboratory, Hines VA Medical Center) and United Kingdom (Clostridium difficile Network for England and Northern Ireland laboratory, University of Leeds). The 160 isolates were assigned to 82 unique ribotypes and 51 unique REA groups (116 unique REA types). In general, concordance between typing methods was good. Dendrogram analysis of PCR ribotype band patterns demonstrated close genetic relationships among strain types with discordant REA and ribotype assignments. While REA typing was more discriminatory, several REA types in this study were further discriminated by PCR ribotyping, indicating that discriminatory value of these typing methods may be strain dependent. These data will assist with molecular epidemiologic surveillance of strains identified by these two commonly used C. difficile typing systems.

Epidemic and drug-resistance patterns of Salmonella choleraesuis in the world

To study clinical infection and molecular epidemiological characteristics of Salmonella. Choleraesuis (S. Choleraesuis) and its drug resistance pattern were analyzed retrospectively based on big data of public health and laboratory surveillance and related literature both at home and abroad. The S. Choleraesuis is confirmed belong to a swine-adapted pathogen which can cause zoonosis among immunocompromised persons due to its highly invasive capacity. Livestock cultivation is probably the means by which S. Choleraesuis acquires drug resistance. Outbreaks or sporadic infections have been found in Thailand, Taiwan and the mainland of China over the past decades. In developed countries, the incidence and resistance rates are at very low levels, but people are susceptible to the disease and it is difficult to isolate S. Choleraesuis from stool samples, which are in consistent with the situation in Asia. It is essential for agricultural sector to take infection source control measures for the control of human and swine infections with S. Choleraesuis and drug resistance spread, and it is necessary to strengthen the capability building of laboratories at all levels to detect S. Choleraesuis. Experience on foodborne outbreaks investigation in developed countries is worth learning.

Staphylococcus aureus carriage in older populations in community residential care homes: Prevalence and molecular characterization of MRSA isolates

IntroductionThe epidemiology of S. aureus depends on conditions in specific populations. Few studies of S. aureus colonization in the older population have been performed in Spain. The aim of this study was to determine the prevalence of methicillin-resistant S. aureus (MRSA) colonization and its molecular epidemiological characteristics in an institutionalized population in community residential care homes in Cadiz, Spain. MethodsA cross-sectional epidemiological study was conducted in three residential care homes for older people. Axilla and nostril samples were tested. Identification of S. aureus and antimicrobial susceptibility testing were by MALDI-TOF and MicroScan panels. MRSA strains were subjected to SCCmec typing, multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). The presence of Panton–Valentine leukocidin (PVL) genes was determined by PCR in all S. aureus strains. ResultsA total of 293 residents were included. Fifty-one residents (17.4%) were colonized with methicillin-sensitive S. aureus (MSSA) and 11 (3.8%) with MRSA. Resistance to at least two aminoglycosides was observed in 25.4% of MSSA and 90.9% and of MRSA isolates, and resistance to levofloxacin in 80.3% of MSSA and 100% of MRSA isolates. SCCmecIV was detected in all isolates and all except one (ST-125) were ST-8. None of the S. aureus isolates were positive for PVL. ConclusionsA low rate of S. aureus carriage was detected and the prevalence of MRSA was very low. ST8-MRSA-IVc was the dominant clone, and only one strain belonged to ST125-MRSA-IVc. We found MRSA transmission within the residential care homes and a very high rate of quinolone resistance in MSSA and MRSA.