Unusual presence of the immune evasion gene cluster in livestock-associated MRSA of lineage CC398 causing peridural and psoas abscesses in a poultry farmer.

OBJECTIVE: To characterize a methicillin-resistant Staphylococcus aureus (MRSA) isolate responsible for an aggressive infection (peridural and psoas abscess secondary to haematogenous septic arthritis) in a poultry farmer. METHODS: Molecular characterization was performed, including spa- and multilocus sequence typing of the isolate, assessment of its resistance phenotype and detection of tetracycline resistance and of virulence and immune evasion cluster (IEC) genes were performed. RESULTS: The MRSA isolate was tetracycline- and fluorquinolone-resistant, and was ascribed to CC398, spa-t1451. The isolate harboured tet(M) (distinctive of livestock-associated (LA) MRSA-CC398 clade) and IEC-type B system (characteristic of the methicillin-susceptible human lineage, but typically absent in LA-MRSA-CC398 strains), and lacked toxin-coding genes lukF/lukS-PV, tsst-1, eta and etb. CONCLUSION: IEC re-acquisition by LA-MRSA-CC398-LA strains is an unusual finding, but could constitute an emerging public health problem. It would represent an evolutionary step towards LA-MRSA-CC398's adaptation to human hosts, and might enhance its invasiveness and ability to be transmitted to humans.

ß-Lactamases, transferable quinolone resistance determinants, and class 1 integron-mediated antimicrobial resistance in human clinical Salmonella enterica isolates of non-Typhimurium serotypes.

This work investigates the occurrence and features of class 1 integrons and the presence of transferable quinolone resistance determinants (TQRD) among 382 clinical Salmonella enterica isolates of non-Typhimurium serotypes as well as the ß-lactamases produced by amoxicillin-resistant isolates. These isolates were recovered in 2001 and from 2004 to 2009 from patients from the health region of Terres de l'Ebre (Catalonia, Spain) and comprised 41 different serotypes, mostly of serovar Enteritidis (n=272), being 16.5% multidrug-resistant (MDR). Among the 93 amoxicillin-resistant isolates, 84 produced TEM-1,4 produced an extended-spectrum ß-lactamase (CTX-M-9 in one S. Grumpensis and in one S. Virchow, CTX-M-15 in S. Kapemba, and SHV-12 in S. Enteritidis), one produced DHA-1 (S. Newport), and 4 did not present any of the investigated ß-lactamases. TQRD were found in 2 isolates (qnrA1 in CTX-M-9-producing S. Grumpensis and qnrB4 in DHA-1-producing S. Newport). Overall, 35 isolates (9.2% of all isolates and 54% of MDR isolates) belonging to 15 different serotypes carried class 1 integrons that were transferred by conjugation in 17 isolates. Eleven distinct cassette arrangements were identified, with dfrA1-aadA1, dfrA17-aadA5, and dfrA12-orfF-aadA2 being the most prevalent and widely distributed ones. Atypical sul3-associated integrons were detected in 5 isolates of serotypes Rissen and Enteritidis. Moreover, the presence of integrons in the serotypes Kapemba, Mikawasima, and [9,12:Iv:i:-], of the estX-psp (linked to sul3) and aadA13-sat cassette arrangements in S. enterica, of extended-spectrum ß-lactamases in S. Kapemba and S. Grumpensis, and of TQRD in S. Grumpensis is reported here for the first time.

Pneumococcal meningitis secondary to otitis media in two patients with COVID-19 omicron variant.

BACKGROUND: The SARS-CoV-2 omicron variant produces more symptoms in the upper respiratory tract than in the lower respiratory tract. This form of "common cold" can cause inflammation of the oropharynx and the Eustachian tube, leading to the multiplication of bacteria such as Streptococcus pneumoniae in the oropharynx. Eustachian tube dysfunction facilitates migration of these bacteria to the middle ear, causing inflammation and infection (otitis media), which in turn could lead to further complications such as acute mastoiditis and meningitis. CASE PRESENTATION: In January 2022, during the rapid spread of the omicron variant of the SARS-CoV-2 virus, two patients presented to the emergency room at our hospital complaining of headache and a low level of consciousness. A few days prior to admission, the patients had been diagnosed with COVID-19 based on clinical manifestations of a cold virus, without respiratory failure. Cranial computed tomography revealed signs of bilateral invasion of the middle ear in both cases. Lumbar puncture was compatible with acute bacterial meningitis, and S. pneumoniae was isolated in cerebrospinal fluid in both patients. RT-PCR tests for SARS-CoV-2 were repeated, confirming the presence of the omicron variant in one of the patients. We were unable to confirm the variant in the second patient due to the low viral load in the nasopharyngeal sample obtained at admission. However, the time of diagnosis (i.e., during the peak spread of the omicron variant), strongly suggest the presence of the omicron variant. Both patients were admitted to the intensive care unit and both showed rapid clinical improvement after initiation of antibiotic treatment. CONCLUSIONS: The omicron variant of the SARS-CoV-2 virus can promote the development of otitis media and secondary acute bacterial meningitis. S. pneumoniae is one of the main bacteria involved in this process.

Mechanisms of Linezolid Resistance Among Clinical Staphylococcus spp. in Spain: Spread of Methicillin- and Linezolid-Resistant S. epidermidis ST2.

This study aimed at determining the mechanisms of linezolid resistance and the molecular characteristics of clinical Staphylococcus aureus (n = 2) and coagulase-negative staphylococci (n = 15) isolates obtained from four Spanish hospitals. The detection of linezolid resistance mechanisms (mutations and acquisition of resistance genes) was performed by PCR/sequencing. The antimicrobial resistance and virulence profile was determined, and the isolates were typed by different molecular techniques. Moreover, the genetic environment of the cfr gene was determined by whole-genome sequencing. The cfr gene was detected in one methicillin-resistant S. aureus (MRSA) that also displayed the amino acid change Val118Ala in the ribosomal protein L4. The second S. aureus isolate was methicillin susceptible and showed different alterations in the ribosomal protein L4. All remaining linezolid-resistant Staphylococcus epidermidis (n = 14) and Staphylococcus hominis isolates (n = 1) showed the mutation G2576T (n = 14) or C2534T (n = 1) in the 23S rRNA. Moreover, different amino acid changes were detected in the ribosomal proteins L3 and L4 in S. epidermidis isolates. All S. epidermidis isolates belonged to the multilocus sequence type ST2. Linezolid-resistant staphylococci (LRS) showed a multiresistance phenotype, including methicillin resistance that was detected in all isolates but one, and was mediated by the mecA gene. The cfr gene in the MRSA isolate was located together with the fexA gene on a conjugative 38,864 bp plasmid. Linezolid- and methicillin-resistant S. epidermidis ST2 showing mutations in the 23S rRNA and in the ribosomal proteins L3 and L4 are spread among Spanish hospitals, whereas LRS carrying acquired linezolid resistance genes are rarely detected.

Extended-Spectrum ß-Lactamase- and Carbapenemase-Producing Enterobacterales Intestinal Carriage Among Outpatients: Microbiological and Epidemiological Differences Between Private Dwelling Residents and Nursing Home Residents.

The aim of this work was to assess the prevalence of carbapenemase-producing and extended-spectrum ß-lactamase-producing Enterobacterales (ESBLPE) intestinal carriage among private dwelling residents (PDR) and nursing home residents (NHR) from the catchment area of Hospital Verge de la Cinta (Tortosa. North-Eastern Spain), and to depict clinicoepidemiological features of colonized individuals. Prevalence of ESBLPE carriage amid 762 PDR (0-94 years) who had feces collected for routine culture was 7.3% and 31% among 71 NHR (68-98 years) screened upon hospital admission. The mean age of colonized and noncolonized subjects was 30 and 32.8 years in PDR (p = 0.58) and 85 and 87 years in NHR (p = 0.32). The predominant ESBLPE was CTX-M-15-producing Escherichia coli (42.8% in PDR and 68.2% in NHR [25% and 86.7% belonging to O25b-ST131 clone; p < 0.0001]), followed by CTX-M-9-group- and SHV-producing E. coli and by CTX-M-15-producing Klebsiella pneumoniae. Overall, 72.7% of ESBLPE were multidrug resistant and 46.2% carried transferable quinolone determinants. Institutionalization in a nursing home was a risk factor for ESBLPE and extended-spectrum ß-lactamase (ESBL)-producing O25b-ST131 E. coli carriage in individuals over 67 years (odds ratio 7.7 and 14.1). Previous antibiotic use and skin ulcers were significantly associated with ESBLPE carriage in NHR. Age <25 years in PDR and amoxicillin/clavulanate exposure in NHR protected against ESBL-producing O25b-ST131 E. coli colonization. Only two PDR, with known risk factors, bore OXA-48-producing isolates. These results highlight the role of nonhospitalized intestinal carriers, particularly NHR, as ESBLPE reservoirs and the preponderance of CTX-M-15, mainly linked to O25b-ST131 clone, as well as the emergence of carbapenemase-producing Enterobacterales carriers.

Mechanisms of Linezolid Resistance Among Enterococci of Clinical Origin in Spain-Detection of optrA- and cfr(D)-Carrying E. faecalis.

The mechanisms of linezolid resistance among 13 E. faecalis and 6 E. faecium isolates, recovered from six Spanish hospitals during 2017-2018, were investigated. The presence of acquired linezolid resistance genes and mutations in 23S rDNA and in genes encoding for ribosomal proteins was analyzed by PCR and amplicon sequencing. Moreover, the susceptibility to 18 antimicrobial agents was investigated, and the respective molecular background was elucidated by PCR-amplicon sequencing and whole genome sequencing. The transferability of the linezolid resistance genes was evaluated by filter-mating experiments. The optrA gene was detected in all 13 E. faecalis isolates; and one optrA-positive isolate also carried the recently described cfr(D) gene. Moreover, one E. faecalis isolate displayed the nucleotide mutation G2576T in the 23S rDNA. This mutation was also present in all six E. faecium isolates. All linezolid-resistant enterococci showed a multiresistance phenotype and harbored several antimicrobial resistance genes, as well as many virulence determinants. The fexA gene was located upstream of the optrA gene in 12 of the E. faecalis isolates. Moreover, an erm(A)-like gene was located downstream of optrA in two isolates recovered from the same hospital. The optrA gene was transferable in all but one E. faecalis isolates, in all cases along with the fexA gene. The cfr(D) gene was not transferable. The presence of optrA and mutations in the 23S rDNA are the main mechanisms of linezolid resistance among E. faecalis and E. faecium, respectively. We report the first description of the cfr(D) gene in E. faecalis. The presence of the optrA and cfr(D) genes in Spanish hospitals is a public health concern.

Group B streptococcal bacteriuria during pregnancy as a risk factor for maternal intrapartum colonization: a prospective cohort study.

PURPOSE: Current evidence is inconclusive regarding the intrapartum administration of chemoprophylaxis, merely based on the presence of group B streptococcal (GBS) bacteriuria of any colony count, in the prevention of early-onset neonatal GBS infection. The aim of this study was to assess whether GBS bacteriuria is a risk factor for intrapartum colonization (IPC) regardless of urinary concentration or the results of late third-trimester rectovaginal screening cultures (RVSCs). METHODOLOGY: Six hundred and eight pregnant women, with urine specimens cultured between May 2011 and May 2013, were enrolled in this prospective cohort study. RVSCs were available for 582 women and intrapartum rectovaginal cultures for 246. RESULTS: The prevalence of GBS bacteriuria and positive RVSCs was 10.8 and 16.5 %, respectively. The frequency of IPC was 15.9 % (39/246). Sensitivity, specificity, positive and negative predictive values of urine culture and of RVSC in predicting GBS IPC were 41, 94.7, 59.3 and 89.5 %, and 76.9, 95.4, 76.9 and 95.4 %, respectively. GBS bacteriuria was significantly associated with IPC, overall [relative risk (RR) 5.6] and in women with negative RVSC (RR 8.5), with bacteriuria <104 c.f.u. ml-1 (RR 5.9) or when both circumstances coexisted (RR 8.9). The urinary colony count was <104 c.f.u. ml-1 in 13 of the 16 women with GBS bacteriuria and IPC. CONCLUSION: GBS bacteriuria is a risk factor for IPC, irrespective of urinary GBS concentration or of colonization status at late gestation. Therefore, microbiology laboratories should search, and report, GBS of any colony count in urine from pregnant women, and not only in the presence of ≥104 c.f.u. ml-1 as the 2010 CDC guidelines recommend.

Molecular epidemiology and resistance mechanisms involved in reduced susceptibility to amoxicillin/clavulanic acid in Klebsiella pneumoniae isolates from a chronic care centre.

The aim of this work was to investigate the molecular epidemiology and mechanisms responsible for reduced susceptibility to amoxicillin/clavulanic acid (AMC) amongst cefazolin-susceptible Klebsiella pneumoniae isolates from patients admitted to a chronic care institution. In total, 51 (29.8%) of 171 K. pneumoniae isolates recovered between 2006 and 2008 were non-susceptible to AMC, of which 45 were susceptible to cefazolin. Nucleotide sequencing analysis revealed that 19 produced IRT-11 and the remaining 26 were OXA-1-producers. All of the OXA-1-producing isolates harboured the aac(6')-Ib-cr-bla(OXA-1) cassette array, which in 23 isolates was located together with catB3 and arr3 within a class 1 integron and associated with qnrS2 (in 3 cases the integron lacked the qacEΔ1 and sul1 or sul3 genes). Genotyping analysis performed by enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) identified three different patterns amongst IRT-11-producing isolates (E1 to E3), with E1 being the most prevalent (63.2%), whilst the OXA-1-producing isolates were assigned to patterns E3 and E3a (isolates carrying typical class 1 integrons), E4 (isolates carrying defective integrons) and E5 (isolates without integrons). Genes encoding IRT-11 and OXA-1 were transferred by conjugation, and aac(6')-Ib-cr and qnrS2 were systematically co-transferred with bla(OXA-1). These results demonstrate that the high prevalence of decreased susceptibility to AMC amongst K. pneumoniae isolates from a chronic care hospital was mainly due to the simultaneous spread of two different clones, one of which comprised isolates producing IRT-11 and the other one comprised isolates that had acquired either the bla(OXA-1) gene located in a class 1 integron and linked to qnrS2 or the bla(IRT-11) gene.

[Effectiveness of systematic investigation for Group B Streptococcus in urine samples to identify colonized pregnant women]. / Impacto de la investigación sistemática de estreptococo del grupo B en orina en la identificación de gestantes colonizadas.

OBJECTIVE: To evaluate the effectiveness of systematic investigation for Group B Streptococcus (GBS) in urine samples to detect colonization in pregnant women. METHODS: This study included 1036 pregnant women whose urine samples were cultured in our laboratory during 2006. Any colony consistent with GBS was identified in urine or in rectovaginal samples submitted for screening of GBS colonization. RESULTS: GBS was recovered in urine samples from 111 of the 1036 women (10.7%), and in 77 of them bacterial count was <10(4) colony forming units/mL. Screening for GBS in rectovaginal samples was performed in 841 of the 925 pregnant women who did not have GBS bacteriuria (10.1% positive results) and in 61 of the 111 with GBS bacteriuria (60.7% positive results; no significant differences were found when results were stratified by colony count). Estimated rectovaginal colonization was 15.4%, and colonization exclusively detected in urine was 4.2%. Only 30% of pregnant women with GBS bacteriuria, but negative antenatal screening cultures who were admitted to our hospital for delivery received intrapartum antibiotic prophylaxis. CONCLUSIONS: Systematic investigation of the presence of GBS in urine samples from pregnant women improves the detection of carriers who are candidates for receiving intrapartum prophylaxis to prevent perinatal GBS infection, when compared with rectovaginal screening culture in the last trimester of gestation alone.

[Class 1 integrons among Salmonella enterica isolates producing different types of beta-lactamases from the health region of Tortosa (Spain)]. / Integrones de clase 1 en aislados de Salmonella enterica productores de diferentes tipos de betalactamasas recogidos en la región sanitaria de Tortosa.

OBJECTIVE: To assess the frequency of class 1 integrons among isolates of Salmonella enterica producing different types of beta-lactamases from the health region of Tortosa, and to attempt to establish the resistance genes located within their variable regions. METHODS: The presence of class 1 integrons and of aadA1, aadA2, dfrA1, tem-1, oxa-1 and pse-1 resistance genes within their variable regions was investigated by PCR in 100 ampicillin-resistant isolates of S. enterica (30 S. enteritidis, 56 S. Typhimurium and 14 from other serotypes) consecutively recovered in our laboratory between 2000 and 2001. Beta-lactamases were characterized by isoelectric focusing and PCR. RESULTS: a) 6/57 TEM-1 producing isolates carried integrons: 1 S. ser Panama, 2 S. ser Enteritidis and 1 S. ser Typhimurium (1600 pb/aadA1-dfrA1); 1 S. ser Panama (1600 pb/aadA2-dfrA1); 1 S. ser Grumpensis (1500 pb 1 1700 pb; aadA2 and ??) b) All OXA-1 producing isolates (20 S. ser Typhimurium) bore an integron of 2000 pb/aadA1-oxa-1; c) All PSE-1 producing isolates (22 S. ser Typhimurium, most of them 104 phage type, and 1 S. enterica immobile [4,12:-:-]) harbored 2 integrons (1000 pb/aadA1 and 1,00 pb/pse-1). CONCLUSION: The presence of class 1 integrons carrying oxa-1 or pse-1 resistance genes in all the OXA-1-producing and PSE-1-producing isolates investigated could have contributed to their spread and explain the increase in frequency of multiresistant S. ser Typhimurium isolates harboring these enzymes seen in the health region of Tortosa. In addition, we report the first isolate of S. ser enterica serotype Grumpensis harboring integrons.